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Wangetal. BMC Biology (2024) 22:185
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BMC Biology
Phylogenomics analysis ofScutellaria
(Lamiaceae) oftheworld
Yinghui Wang1,2,3 , Chao Xu1,2, Xing Guo4, Yan Wang1,2,3, Yanyi Chen1,2,3, Jie Shen5, Chunnian He6, Yan Yu7 and
Qiang Wang1,2,3*
Abstract
Background Scutellaria, a sub-cosmopolitan genus, stands as one of the Lamiaceae family’s largest genera, encom-
passing approximately 500 species found in both temperate and tropical montane regions. Recognized for its
significant medicinal properties, this genus has garnered attention as a research focus, showcasing anti-cancer,
anti-inflammatory, antioxidant, and hepatoprotective qualities. Additionally, it finds application in agriculture and hor-
ticulture. Comprehending Scutellaria’s taxonomy is pivotal for its effective utilization and conservation. However,
the current taxonomic frameworks, primarily based on morphological characteristics, are inadequate. Despite several
phylogenetic studies, the species relationships and delimitations remain ambiguous, leaving the genus without a sta-
ble and reliable classification system.
Results This study analyzed 234 complete chloroplast genomes, comprising 220 new and 14 previously published
sequences across 206 species, subspecies, and varieties worldwide. Phylogenetic analysis was conducted using six
data matrices through Maximum Likelihood and Bayesian Inference, resulting in a robustly supported phylogenetic
framework for Scutellaria. We propose three subgenera, recommending the elevation of Section Anaspis to subge-
neric rank and the merging of Sections Lupulinaria and Apeltanthus. The circumscription of Subgenus Apeltanthus
and Section Perilomia needs to be reconsidered. Comparative analysis of chloroplast genomes highlighted the IR/
SC boundary feature as a significant taxonomic indicator. We identified a total of 758 SSRs, 558 longer repetitive
sequences, and ten highly variable regions, including trnK–rps16, trnC–petN, petN–psbM, accD–psaI, petA–psbJ, rpl32–
trnL, ccsA–ndhD, rps15–ycf1, ndhF, and ycf1. These findings serve as valuable references for future research on species
identification, phylogeny, and population genetics.
Conclusions The phylogeny of Scutellaria, based on the most comprehensive sample collection to date and com-
plete chloroplast genome analysis, has significantly enhanced our understanding of its infrageneric relationships. The
extensive examination of chloroplast genome characteristics establishes a solid foundation for the future develop-
ment and utilization of Scutellaria, an important medicinal plant globally.
Keywords Lamiaceae, Scutellaria, Phylogeny, Complete chloroplast genome
*Correspondence:
Qiang Wang
wangqiang@ibcas.ac.cn
Full list of author information is available at the end of the article
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Page 2 of 19
Wangetal. BMC Biology (2024) 22:185
Background
e sub-cosmopolitan genus Scutellaria, one of the
Lamiaceae family’s largest genera, comprises approxi-
mately 500 species, as reported by the Plants of the
World Online (POWO) [1]. ese species are predomi-
nantly distributed in tropical montane and temperate
regions. e Irano-Turanian regions, especially Central
Asia and the Iranian plateau, represent the genus’s maxi-
mum diversity center. Additionally, the eastern Medi-
terranean and the Andes serve as significant centers for
its speciation [2, 3]. Scutellaria can be distinctly identi-
fied at the generic level by its calyx, which features two
undivided lips and an appendage that folds into an erect,
sail-like structure on the upper lip, known as the scutel-
lum, giving rise to the genus’s name. Alternatively, this
structure may present as an appendage intumescence
rather than a scutellum [2, 4]. Another notable charac-
teristic is the corolla’s upper lip, which is usually galeate
except for some South American species placed in Sect.
Perilomia (Kunth) Epling [2]. is genus is renowned for
its medicinal properties, with many species being rich in
flavonoids, such as S. baicalensis Georgi [5], S. indica L.
[6, 7], and S. barbata D.Don [8]. ese species have been
utilized in medicinal practices across various countries,
particularly in China for over 2000years. As vital sources
of raw materials for Chinese medicinal formulations,
they are extensively employed in treating conditions such
as hepatitis, jaundice, tumors, leukemia, hyperlipidemia,
arteriosclerosis, diarrhea, and inflammatory diseases [9,
10]. e medicinal significance of this genus remains a
focal point of research, with modern pharmacology con-
firming its anticancer, anti-inflammatory, antioxidant,
and hepatoprotective properties [8, 11–16]. Addition-
ally, neoclerodane diterpenoids isolated from Scutellaria
species exhibit significant antifeedant activity, offering a
robust defense against herbivory by lepidopterous larvae,
benefiting agricultural production [17–20]. Furthermore,
numerous Scutellaria species hold economic value in the
horticultural industry, attributed to their rich colors and
broad adaptability, ranging from wetlands to rocky ter-
rains and from coastlines to alpine regions (Fig.1) [2].
Despite its significant economic value attracted the
attention of many botanists and evolutionary biologists,
the taxonomy of Scutellaria has remained poorly under-
stood. Hamilton [21] first divided Scutellaria into three
sections: Sect. Lupulinaria A. Ham., Sect. Galericularia
A. Ham., and Sect. Stachymacris A. Ham. Following
Hamilton, Bentham [22–24] merged Sect. Galericularia
and Sect. Stachymacris into Sect. Vulgare Benth., and
established Sect. Heteranthes Benth. Briquet [25] divided
the genus into Subgenus Scutellariopsis Briq. and Subg.
Euscutellaria Briq. including Bentham’s three sections.
Fig. 1 The representative species of Scutellaria. A S. amoena, B S. baicalensis, C S. hainanensis, D S. discolor, E S. lushuiensis, F S. kingiana, G S.
likiangensis, H S. hypericifolia, I S. rehderiana, J S. tenax, K S. strigillosa, L S. sieversii
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Page 3 of 19
Wangetal. BMC Biology (2024) 22:185
Different taxonomies emphasize different morpho-
logical characters. Later, regional treatments mainly
followed Briquet’s classification system but various tax-
onomies appeared because the global variation was not
taken into account [26–30]. e latest global taxonomy
was proposed by Paton [2] based on more comprehen-
sive morphological characters and samples. e num-
ber of species in Scutellaria is closer to 360 being lower
than the 500 reported in POWO as Paton employed a
broader species concept and believed that the species
concept employed in the Flora URSS and Flora Reipub-
licae Popularis Sinicae was too narrow [2]. e genus
was divided into Subg. Scutellaria and Subg. Apeltanthus
(Nevski ex Juz.) Juz. emend. A.J.Paton. e former subge-
nus was further divided into five sections: Sects. Scutel-
laria, Salazaria (Torrey) A.J.Paton., Perilomia (Kunth)
Epling emend. A.J.Paton, Anaspis (Rech.f.) A.J.Paton,
and Salviifoliae (Boiss.) Edmondson. Subg. Apelthanthus
was further divided into Sect. Apeltanthus Nevski ex Juz.
and Sect. Lupulinaria A. Ham., and then Sect. Lupuli-
naria was subdivided into Subsect. Lupulinaria (A.
Ham.) A.J.Paton and Subsect. Cystaspis (Juz.) A.J.Paton
[2]. Meanwhile, Paton’s analysis revealed that both Sect.
Scutellaria and Sect. Lupulinaria Subsect. Lupulinaria
are paraphyletic. e former encompasses approximately
240 species, tentatively organized into 34 species-groups,
while the latter comprises about 120 species, categorized
into four informal species-groups. Subsequent research
on the classification and evolution of Scutellaria has pre-
dominantly relied on Paton’s classification system.
Several molecular phylogenetic studies have provided
insights into the taxonomy and phylogeny of Scutellaria.
e phylogenetic study including 45 samples (34 taxa
from China) by Zhao etal. [31] using ITS and ETS sug-
gested that two clades were supported and clade I includ-
ing S. galericulata L., S. diffusa Benth. and S. nuristanica
Rech.f. at the base. Subgenus Apeltanthus was sister to S.
likiangensis Diels allies and embedded into Subg. Scutel-
laria, so Subg. Scutellaria was considered to be paraphy-
letic. Although Subg. Apeltanthus clustered into a clade,
the monophyly of the subgenus could be questioned
because only five species of that taxon were investigated.
In the study of Safikhani etal. [32], samples focused on
Subg. Apeltanthus. Using ITS and trnL-F of 42 samples
(36 samples from Iran), the phylogeny of Scutellaria
presented by Safikhani etal. [32] showed that the mem-
bers of Subg. Apeltanthus (31 samples) formed a clade,
but Sect. Lupulinaria was non-monophyletic because S.
stocksii Boiss. (Sect. Apeltanthus) was nested within it.
Sect. Scutellaria was also non-monophyletic because S.
galericulata was a sister to a clade including species of
Sects. Anaspis and Scutellaria. However, the phyloge-
netic research based on 44 species of Scutellaria using
ITS and trnL-F by Seyedipour etal. [33] considered that
Subg. Apeltanthus was paraphyletic because S. repens
Buch.-Ham. ex D.Don (Sect. Scutellaria) was embedded
within it. Subg. Scutellaria was also supported to be par-
aphyletic due to Subg. Apeltanthus nested within it. Also,
Sect. Scutellaria and Sect. Lupulinaria were not mono-
phyletic. e latest phylogeny of Scutellaria including 76
taxa from the sections of Paton also showed that Subg.
Scutellaria was paraphyletic to Subg. Apeltanthus based
on three plastid markers (matK-trnK, rpl16, trnL-F), and
three clades were well-supported resolved [34]. S. pontica
K. Koch and a clade including S. baicalensis, S. amoena
C.H.Wright, S. rehderiana Diels, and S. kingiana Prain
form an unresolved polytomy with Subg. Apelthanthus,
and S. schweinfurthii Subsp. paucifolia (Baker) A.J.Paton
is sister to that polytomy. Further, Sect. Salviifoliae was
not monophyletic due to the different phylogenetic
position between S. diffusa and S. pontica. Sect. Lupuli-
naria was also not monophyletic because S. poecilantha
Nevski ex Juz. (Sect. Apeltanthus) was nested within it,
and the members of Subsect. Lupulinaria were scattered
into different subclades. e study also showed that S.
kingiana belonging to Sect. Anaspis was sister to an East
Asian lineage including S. amoena, S. rehderiana, and S.
baicalensis (Sect. Scutellaria). S. galericulata placed in
Sect. Scutellaria was sister to S. minor Huds. Recently,
research on phylogenetic relationships within Scutel-
laria using the complete chloroplast genome (cpDNA)
was also processed with a few species [35, 36]. e results
consistently showed that S. kingiana belonging to Sect.
Anaspis formed a clade with S. baicalensis and allies, and
then was sister to Subg. Apeltanthus, which was con-
sistent with the results by Salimov etal. [34] and Zhao
etal. [31]. ese studies have significantly enhanced our
understanding of the phylogeny of Scutellaria. However,
the phylogenetic relationships within the genus are still
not well understood, primarily due to a lack of samples
or molecular markers with insufficient phylogenetic loci.
ere is a critical need for a well-resolved phylogeny of
the genus based on comprehensive global sampling.
Although unclear infrageneric relationships of Scutel-
laria, a series of phylogenetic studies strongly supported
the monophyly of Scutellaria [37–41]. Despite some of
the infrageneric taxa have been given generic rank in
the past, such as Anaspis Rech.f., Perilomia Kunth, Sala-
zaria Torrey, Harlanlewisia Epling, eresa Clos, and
Cruzia Phil., the morphological and molecular phyloge-
netic studies revealed that these taxa belong to the genus
Scutellaria [2, 3, 27, 28]. Recent studies showed that six
genera were circumscribed in the subfamily Scutellari-
oideae, which is characterized by abundant calyx fibers
and pericarps with tuberculate or elongate outgrowths
[37, 38, 41–47]. Scutellaria is the largest genus, followed
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Page 4 of 19
Wangetal. BMC Biology (2024) 22:185
by Tinnea (including 19 species) which is endemic to
Africa [43]. e other four genera including Holmski-
oldia Retz. [44], Wenchengia C.Y. Wu & S. Chow [45],
Renschia Vatke[43, 46], and Heliacria Bo Li, C.L. Xiang,
T.S. Hoang & Nuraliev[47] are all monospecific, which
are distributed to the southern Himalayas, Hainan prov-
ince of China and Vietnam, northern Somalia and Viet-
nam respectively. In the present study, the three genera
(including Tinnea, Holmskioldia, and Wenchengia)
closely related to Scutellaria were sampled as outgroups
[37–41].
Since the first cpDNA of tobacco was reported by
Shinozaki et al. [48], an increasing number of cpDNA
sequences have been published. Until June 2023, over
3800 cpDNA sequences have been published in the
National Center for Biotechnology Information (NCBI)
organelle genome database. However, only 21 cpDNA
sequences have been published in Scutellaria, and the
number of species is too few to discuss the phylogenetic
relationships based on omics data for the whole genus.
It is reported that the published chloroplast genome of
Scutellaria is a typical quadripartite structure contain-
ing two identical copies of inverted repeats (IRa and
IRb, IRs) separated by a small single-copy region (SSC)
and a large single-copy region (LSC), with a length from
151 to 154kb, which is consistent with the characteris-
tics of most photosynthetic land plant plastid chromo-
somes with a size from 120 to 160kb [49–51]. e gene
content and order of cpDNA within this genus are highly
conserved comprising 112–114 distinct genes: 79–80
protein-coding genes, 29–30 transfer RNAs (tRNAs),
and four ribosomal RNAs (rRNAs), similar to most ter-
restrial plants [51, 52]. e properties of stable maternal
inheritance, highly conserved sequences, low mutation
and recombination rates, as well as small genome make
the cpDNA become an ideal model to study taxonomy
and evolution, and many scholars have used it to study
the evolutionary relationships of different taxa [52–57].
For Scutellaria, however, most studies based on a few
molecular markers mainly focus on species identification
and phylogeny of some taxonomic complexes in recent
two decades [58–60]. e construction of phylogenetic
trees was mainly based on ITS or chloroplast DNA frag-
ments [31–34]. Phylogenetic relationships on the genus
using the complete chloroplast genome were carried out
with a few species by Zhao etal. [36] and Shan etal. [35].
Extensive sampling and more genomic data in improv-
ing phylogenetic inference are helpful [61, 62]. In this
study, we acquired 234 cpDNA sequences encompassing
206 species, subspecies, and varieties of Scutellaria from
regions across Eurasia, Americas, Africa, and Oceania.
Additionally, four samples from three genera within the
Scutellarioideae—Tinnea aethiopicaKotschy ex Hook. f.,
Wenchengia alternifoliaC.Y. Wu & S. Chow, andHolm-
skioldia sanguinea Retz.—were included as outgroups.
Utilizing this extensive dataset, our objectives were to
(1) enhance the resolution of the phylogenetic frame-
work for Scutellaria; (2) describe and compare the struc-
ture and gene content of Scutellaria cpDNA sequences;
(3) identify candidate DNA markers within the cpDNA
sequences for efficient and accurate species identifica-
tion, with a focus on medicinal species and potential
adulterants, and to facilitate future phylogenetic and phy-
logeographic studies.
Results
Chloroplast genome characteristics ofScutellaria
In the present study, a total of 220 samples representing
196 species, subspecies, and varieties of Scutellaria were
sequenced successfully for the first time. Together with
sequences obtained online, the size of the 234 cpDNA
sequences ranged from 150,867 bp (S. incana Biehler)
to 154,253 bp (S. coerulea Moc. & Sessé ex Benth.),
exhibiting a variation of 3386bp (Fig.2). All chloroplast
genomes showed a typical quadripartite structure, con-
sisting of a pair of inverted repeats (IRa and IRb) regions
(24,850–25,633 bp) separated by a large single-copy
(LSC) region (83,245–86,276bp) and a small single-copy
(SSC) region (17,205–17,582bp). e total guanine-cyto-
sine (GC) content across all cpDNA sequences was rela-
tively consistent, ranging from 38.19% (S. arabica Jaub.
& Spach) to 38.54% (S. scutellarioides (Kunth) Harley),
with IR regions exhibiting significantly higher GC con-
tent (43.49–43.72%) compared to the LSC region (36.17–
36.65%) and the SSC region (31.89–32.95%) (Additional
file1: TableS1).
Typically, the Scutellaria chloroplast genomes con-
tained 112–115 coding genes, including 79–81 protein-
coding genes, 29–30 transfer RNA (tRNA), and four
ribosomal RNA (rRNA) genes, arranged in the same
sequence (Additional file 1: Table S1). Most protein-
coding genes were present in a single copy, except for
ndhB, rpl2, rpl23, rps7, ycf2, and ycf15, which had two
copies. All rRNA genes were duplicated, and a relatively
high proportion of tRNA genes (7/30) had two copies,
including trnA-UGC , trnI-CAU , trnI-GAU , trnL-CAA ,
trnN-GUU , trnR-ACG , and trnV-GAC . While most genes
lacked introns, nine protein-coding genes (ndhA, ndhB,
petB, petD, atpF, rpl16, rpl2, rps16, rpoC1) and six tRNA
genes (trnA-UGC , trnG-UCC , trnI-GAU , trnK-UUU , trnL-
UAA , trnV-UAC ) contained one intron. Furthermore,
the clpP, ycf3, and rps12 genes had two introns, mark-
ing the highest intron count among all genes. Nota-
bly, the rps12 gene underwent a trans-splicing event,
with the 5’-rps12 (including exon 1) located in the LSC
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Page 5 of 19
Wangetal. BMC Biology (2024) 22:185
region and the 3’-rps12 (containing exon 2, exon 3, and
an intron) generally situated in the IR region (Additional
file1: TableS2).
Phylogenetic analysis
Following alignment adjustments, the lengths of three
sequence matrices were determined: 78,001 bp for 81
protein-coding genes, 30 tRNA genes, and four rRNA
genes (PC), 59,245 bp for 134 non-coding regions
(NC), and 137,246bp for a concatenation matrix of 115
genes and 134 non-coding regions (PCN). Based on
the unpartitioned and partitioned strategies (PC, NC,
PCN, PC-p, NC-p, PCN-p) using Maximum Likelihood
(ML) and Bayesian Inference (BI), 12 phylogenetic trees
obtained a largely consistent topology and the relation-
ships within eight clades were well-resolved with strong
support (Fig.3, Additional file2: Figs. S1–S11). Clade 1
emerged as the earliest diverging group. Clades 2, 3, and 4
formed a monophyletic group and were identified as sis-
ter to another monophyletic branch that included Clades
5, 6, 7, and 8. Given comprehensive loci and higher reso-
lution, the phylogenetic tree based on PCN-p combined
Fig. 2 Complete chloroplast genome map of Scutellaria. Genes inside the circle are transcribed clockwise, while those outside the circle are
transcribed counterclockwise. The darker gray inner circle shows the GC content, while the lighter represents the AT content. Different colors
represent different types of genes. LSC, large single copy; SSC, small single copy; IRA, inverted repeat region A; IRB, inverted repeat region B
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Page 6 of 19
Wangetal. BMC Biology (2024) 22:185
ML and BI methods is presented in Fig. 3. e mono-
phyletic Scutellaria defined by Paton [2] was strongly
supported by all trees (BS = 100%, SH = 100%, PP = 1;
Fig.3, Additional file2: Figs. S1–S11). Tinnea as an Africa
endemic genus is closer related to Scutellaria with the
maximum support (BS = 100%, SH = 100%, PP = 1) in
Scutellarioideae. Members of the Subgenus Scutellaria,
as defined by Paton [2], were distributed across all clades
except Clade 4 belonging to Subg. Apeltanthus. e
phylogeny indicated that Subg. Apeltanthus was com-
pletely nested within Subg. Scutellaria, and suggested
that Subg. Scutellaria is not monophyletic and requires
significant reclassification. Furthermore, the largest sec-
tion Subg. Scutellaria Sect. Scutellaria was identified as
polyphyletic since its members were scattered across dif-
ferent clades, excluding Clade 4 (Fig.3).
Clade 1 (27 accessions) was identified as the earli-
est diverging group. Within this clade, Section Anaspis,
Fig. 3 The phylogenetic tree of Scutellaria combined Maximum likelihood and Bayesian inference using a partition matrix of 115 genes and 134
non-coding regions (PCN-p). The support values of bootstrap support (BS), SH-like approximate likelihood ratio (SH-aLRT), and posterior
probabilities (PP) were shown in turn near the nodes. Only the support rates of BS and SH-aLRT were shown when the topologies of ML and BI
trees were inconsistent. Values equal to 100% or 1 were replaced with asterisks. Clades 1–8 of Scutellaria were marked. Clade 8 was subdivided
into Clades 8a–8d. All species belonging to the classification system by Paton were marked with different colored rectangles for different sections.
Some unlabeled species have not been classified yet. The boundary genes of different parts in each cpDNA were mapped to the topology. The “-”
showed consistency with the length of the reference and the “↑” represented the distance between the boundary gene and the nearest boundary
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Page 7 of 19
Wangetal. BMC Biology (2024) 22:185
excluding S. kingiana, was sister to a lineage of S. meg-
alaspis Rech.f.–S. tournefortii Benth. from Sect. Scutel-
laria, receiving strong support (BS = 100%, SH = 100%,
PP = 1). Sect. Anaspis was not monophyletic because
S. kingiana (Sect. Anaspis) was located in Clade 3. S.
altissima L. was sister to S. tournefortii, both related to S.
brevibracteata Stapf allies with high support (BS = 99.2%,
SH = 100%, PP = 1). e lineage of S. megalaspis–S. pereg-
rina L. (Sect. Scutellaria) was resolved with moderately
supported (BS = 87%, SH = 96%, PP = 1).
Clades 2, 3, and 4 collectively formed a monophyletic
group, serving as a sister group to another monophyletic
group comprising Clades 5, 6, 7, and 8. Clade 2 (4 acces-
sions), belonging to Section Scutellaria, featured spe-
cies endemic to Africa, with well-resolved phylogenetic
relationships among S. schweinfurthii Briq., S. schwein-
furthii subsp. paucifolia, S. polyadena Briq., and S. vio-
lascens Gürke (BS = 100%, SH = 100%, PP = 1). In Clade
3 (17 accessions), two lineages were disjunct in distri-
bution between Eastern Mediterranean to Turkey (Sect.
Salviifoliae) and China (S. kingiana and relatives), but
the sister relationships between them were highly sup-
ported (BS = 99.8%, SH = 100%, PP = 1). e members
of Sect. Salviifoliae were strongly supported cluster-
ing into a monophyletic group (BS = 100%, SH = 100%,
PP = 1). S. kingiana (Sect. Anaspis) was placed as a sis-
ter to an eastern Asia lineage of S. baicalensis alliances
(Sect. Scutellaria), so the location of the species needs
to be reconsidered. Subgenus Apeltanthus mainly dis-
tributed in Central Asia was clustered into Clade 4 (56
accessions), which was resolved as monophyly. However,
Sects. Apeltanthus and Lupulinaria were polyphyletic
because S. guttata Nevski ex Juz. (Sect. Apeltanthus)
was sister to S. cordifrons Juz. (Sect. Lupulinaria) with
strong support (BS = 100%, SH = 100%, PP = 1), and S.
immaculata Nevski ex Juz. (Sect. Apeltanthus) as sister
to S. leptosiphon Nevski (Sect. Apeltanthus) were embed-
ded within Sect. Lupulinaria. ese members of Sect.
Apeltanthus appeared in different positions from S. stock-
sii (Sect. Apeltanthus) which is sister to the rest of Subg.
Apeltanthus with high support (BS = 100%, SH = 100%,
PP = 1).
Within Section Perilomia, S. scutellarioides and S. floc-
culosa Epling & Mathias formed a clade with S. eplingii
Legname and S. woodii J.M.Mercado unplaced by Paton
[2], then together these species were sister to Mexico
group of S. hintoniana Epling and S. coerulea of Sect.
Scutellaria in Clade 5 (15 accessions). Two main sub-
clades were branched in Clade 5. e one subclade
where Sect. Perilomia was located as sister to the other
subclade of S. seleriana Loes. and its relatives with the
maximum support (BS = 100%, SH = 100%, PP = 1). All
members in this clade are mainly distributed in neotropi-
cal regions. Single species S. violacea B.Heyne ex Benth.
was defined as Clade 6 and the sister relationships among
Clades 6, 7, and 8 were strongly supported (BS = 100%,
SH = 100%, PP = 1). S. violacea is mainly distributed in
the Indian Peninsula, Indochinese Peninsula to East
Asia. ere were two subclades in Clade 7 (11 acces-
sions) and the phylogenetic relationships between them
were strong support (BS = 100%, SH = 100%, PP = 1). e
members of this clade belonging to Sect. Scutellaria are
mainly distributed in USA, except for S. suffrutescens
S.Watson from Northeast Mexico. Clade 8 (103 acces-
sions) included the most species of Sect. Scutellaria and
was subdivided into Clades 8a, 8b, 8c, 8d. S. scandens
D.Don mainly distributed in East Asia was sister to S.
racemosa Pers. grown in the New World with high sup-
port in Clade 8a (BS = 98.6%, SH = 100%, PP = 1). e
members of Clade 8b are mainly distributed in East Asia
and North America, except for S. galericulata widely
found in the Northern Hemisphere, S. minor native to
West Europe, and S. hastifolia L. widely distributed in
Mid-West Europe. In Clade 8c, S. humilis R.Br. from Aus-
tralia was sister to a North American lineage of S. nana
A.Gray and its relatives with strong support (BS = 100%,
SH = 100%, PP = 1). e remaining members of Clade 8
were mostly from East Asia, particularly China. e line-
age of S. rubropunctata Hayata–S. meehanioides C.Y.Wu
was not fully resolved, appearing in a polytomy.
Although the phylogenetic trees largely agreed, the
positions of some species within Clades 4 and 8 varied
due to weakly supported relationships among several
species, resulting in some species being grouped in poly-
tomies (Fig.3, Additional file2: Figs. S1–S11). e posi-
tion of S. minor, S. hastifolia, and S. tuberifera C.Y.Wu &
C.Chen in Clade 8 differed in different analyses. S. minor
was sister to S. hastifolia using the partitioned NC matri-
ces with ML and BI methods (BS = 92.2%, SH = 73%,
PP = 0.9587), similar to the ML phylogeny of unparti-
tioned NC matrices with moderate support (BS = 85.5%,
SH = 73%). e ML phylogeny based on PCN, PCN-p,
and PC-p showed that S. minor was sister to S. shikoki-
ana Makino allies with low support. However, the phy-
logenetic tree based on BI suggested S. tuberifera was
sister to S. shikokiana with high support using PCN and
PCN-p. Additionally, S. immaculata and S. leptosiphon
formed a clade, being sister to a lineage of S. ossethica
Kharadze–S. fruticosa P.Willemet based on NC, NC-p,
PCN, and PCN-p matrices with ML or BI methods, while
phylogenies based on PC and PC-p showed the lineage of
S. immaculata and S. leptosiphon remained in a tritomy.
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Page 8 of 19
Wangetal. BMC Biology (2024) 22:185
Comparative analyses ofcpDNA sequences ofthegenus
Sequence variation analysis
Comparative chloroplast genomic analyses were con-
ducted on 18 representative species spanning various
branches. e genomic collinearity analysis revealed
that the cpDNA sequences of these 18 species were
highly conserved, with no gene inversion or rearrange-
ment events detected (Additional file3: Fig. S12). Multi-
ple sequence alignment maps (Additional file3: Fig. S13)
and nucleotide polymorphism analysis consistently found
that IR regions were relatively more conserved than LSC
and SSC regions. e pi values in IR regions were signifi-
cantly lower than 0.01, with a maximum value of 0.007,
while nearly 49.2% of pi values in LSC were higher than
0.01, with the highest value reaching 0.038 and 79.3%
pi values exceeding 0.01 in SSC with a maximum value
of 0.048 (Additional file1: TableS3). In addition, multi-
ple sequence alignment maps showed that the cpDNA
sequences were more highly divergent in the intergenic
spacers compared to coding regions. e nucleotide pol-
ymorphism analysis identified ten notably hyper-variable
regions, including trnK–rps16, trnC–petN, petN–psbM,
accD–psaI, petA–psbJ, ndhF, rpl32–trnL, ccsA–ndhD,
rps15–ycf1, and ycf1, with pi values exceeding 0.025.
Among these, only two loci were located in coding
regions (Fig.4).
IR/SC boundary feature
All 234 cpDNA sequences of Scutellaria contained the
same boundary genes that junction of LSC/IRb (JLB)
within rps19, junction of IRb/SSC (JSB) within ndhF or
trnN–ndhF, junction of SSC/IRa (JSA) within ycf1 or
ycf1–trnN, and junction of IRa/LSC (JLA) within trnH or
rpl2–trnH. For JSB, 233 cpDNA sequences (99.6%) were
located in ndhF, and discovered that this gene of S. peti-
olata Hemsl. ex Lace & Prain with only 885bp was signif-
icantly shorter than others, which resulted in a distance
of 1223bp from the JSB. In addition, ycf1 of S. serrata
Andrews and S. creticola Juz. were slightly shorter, not
crossing the JSA with a distance of 17 and 207bp from
the JSA, respectively. Only JLA was not within genes
except for the cpDNA sequences of S223, S. chungtien-
ensis C.Y.Wu, and S. amoena with trnH spanning IRa and
LSC regions.
e location of the boundaries varied in different taxa.
Rpl2 in IRs had a distance of 95bp from JLA or JLB in
Clade 8 with 86 cpDNA sequences (83.5%), which were
also present in Clades 2 and 6. However, the main bound-
ary distance was 100 bp in Clade 4 with 48 cpDNA
sequences (85.7%) (Fig.3). TrnN, the other gene located
in the IRs, was distant from JLA and JLB with 1101bp
in Clade 4 accounting for 89.3%, but only 12 cpDNA
sequences (11.7%) in Clade 8. e trnN was distant from
the boundaries with 1108bp in 60 cpDNA sequences of
Clade 8 (58.3%), followed by 1107 bp with 18 cpDNA
sequences (17.5%). Additionally, in the LSC, the distance
of 2bp between trnH and JLA in all cpDNA sequences of
Clades 2 and 6, was also present in 95 cpDNA sequences
(92.2%) of Clade 8. But 3 bp was the most common
boundary distance in Clade 4 with 45 cpDNA sequences
(80.3%). Another gene, rps19 spanned LSC and IRb
regions and the length located in LSC was 233 bp in
Clade 4 with 53 cpDNA sequences (94.6%), but it was
mainly 238bp in Clade 1 and Clade 8, having 19 cpDNA
Fig. 4 Sliding window analysis of cpDNA sequences from 18 representative species randomly selected covering all clades of Scutellaria. X-axis:
the length of the windows, Y-axis: nucleotide diversity within each window (window length: 600 bp, step size: 200 bp)
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Page 9 of 19
Wangetal. BMC Biology (2024) 22:185
sequences (70.4%) and 95 cpDNA sequences (92.2%),
respectively. Besides, ndhF also crossed two regions, SSC
and IRb, and almost all of ndhF had 45bp located in IRb
of Clade 4 (87.5%), but the length in other clades var-
ied greatly. Mapping the boundary feature of all cpDNA
sequences to the phylogenetic trees, a detailed schematic
diagram was drawn in Fig.3.
SSRs andrepetitive sequences
A total of 758 SSRs were identified, with 593 (78.2%)
located in the LSC region, significantly outnumber-
ing those in the SSC and IR regions, which contained
107 (14.1%) and 58 (7.7%) SSRs, respectively. Further-
more, 465 SSRs (61.3%) were found in intergenic spacers
(IGS), markedly exceeding the numbers in introns and
CDS, with 158 (20.8%) and 135 (17.8%) SSRs, respec-
tively (Additional file 1: Table S4). Six types of SSRs
were investigated including mononucleotide, dinucleo-
tide, trinucleotide, tetranucleotide, pentanucleotide, and
hexanucleotide. Mononucleotide repeats were the most
abundant with 456 SSRs (60.2%), followed by tetranucle-
otide having 124 SSRs (16.4%), and pentanucleotide was
the least with 5 SSRs only present in S. parvula Michx.,
S. galericulata, S. violacea, and S. petiolata but hexa-
nucleotide was absent in all species (Fig. 5, Additional
file1: TableS5). In terms of repeat types, the majority
motif of mononucleotide repeats was A/T with 390 SSRs,
accounting for 85.5%, and dinucleotide only had an AT/
TA motif (Additional file1: TableS6). ese repeat types
were present in all species. Additionally, repeat units
of GAA/TTC, ATA/TAT, and AATA/TATT were also
exited in all species. Conversely, AATG/CATT, AAGA/
TCTT, and TTCT/AGAA of tetranucleotide repeats were
unique motifs in S. scandens, S. barbata, and S. scutel-
larioides, respectively. And rare pentanucleotide repeats
including AAAAG/CTTTT, GAATA/TATTC, CTTAT/
ATAAG, AAATA/TATTT, and ATAAA/TTTAT were
exclusive to S. parvula, S. galericulata, S. petiolate, and S.
violacea, respectively (Additional file1: TableS7).
A total of 558 repetitive sequences were identified, cat-
egorized into four types: palindromic (P), forward (F),
reverse (R), and complement (C), among which the most
abundant repeat type of P with 297 repeats (53.2%), fol-
lowed by F with 244 repeats (43.7%) that were widely dis-
tributed in all species (Fig.5, Additional file1: TableS8).
However, R type was detected in S. scandens, S. incana, S.
oligodonta Juz., and S. stocksii and C type was only found
in S. petiolata (Additional file 1: Tables S8–S9). e
abundant repeats were located in LSC with 306 repeats
(54.8%), followed by IRs with 140 repeats, but the repeats
were the least in SSC (Additional file1: TableS9). ese
sequences ranged from 30 to 1096 bp, with repeats of
Fig. 5 The statistics of the simple sequence repeats (SSRs) and repetitive sequences of cpDNA sequences from 18 representative species
randomly selected covering all clades of Scutellaria. A The location distribution of 18 representative species in the topology. B Proportion of five
kinds of a total of SSRs. C The number of five types of SSRs in each species. mono-, mononucleotides; di-, dinucleotides; tri-, trinucleotides; tetra-,
tetranucleotides; penta-, pentanucleotides. D Proportion of four kinds of repeats. E The number of four types of repetitive sequences in each species
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Page 10 of 19
Wangetal. BMC Biology (2024) 22:185
30, 39, and 60bp present in all species (Additional file1:
TableS10).
Discussion
The phylogeny ofScutellaria
Our study represents the most comprehensive phylog-
enomic analysis of Scutellaria to date, employing the
largest sample size and a substantial number of cpDNA
sequences published for the first time. Compared to pre-
vious phylogenetic analyses, our research significantly
enhanced tree resolutions and established a robust
framework for understanding Scutellaria’s phylogeny uti-
lizing six sequence matrices (PC, NC, PCN, PC-p, NC-p,
PCN-p). Consistently, all phylogenetic trees affirmed
that Scutellaria, as defined by Paton [2], is monophyl-
etic, aligning with the findings of earlier studies [31–34,
37–41].
e monophyly of the Subgenus Scutellaria was not
supported, as all phylogenetic trees indicated that Subg.
Apeltanthus was nested within Subg. Scutellaria, with
members of Subg. Scutellaria dispersed across all clades
except for Clade 4 (Fig.3, Additional file2: Figs. S1–S11).
is finding aligns with recent molecular research [31, 34,
36]. On the basis of morphology, Scutellaria was divided
into Subg. Scutellaria and Subg. Apeltanthus by Paton
[2], the former with one-sided or rarely spiral inflores-
cence and flowers subtended by leaves or leaf-like bracts,
while 4-sided inflorescence with flowers subtended by
cucullate bracts in the latter subgenus. However, the
inflorescence of some species such as S. linearis Benth., S.
luteocaerulea Bornm. & Sint., and S. litwinowii Bornm. &
Sint. (Subg. Apeltanthus Sect. Lupulinaria) is one-sided,
but bracts are still cucullate and nutlets have similar mor-
phology to those of other species in Subg. Apeltanthus.
Seyedipour etal. [33] considered that Subg. Apeltanthus
was paraphyletic because S. repens (Subg. Scutellaria)
was sister to S. luteocaerulea and its relatives (Subg.
Apeltanthus Sect. Lupulinaria). e nutlet of S. repens is
gray-black and completely covers the surface with hairs,
also similar to the nutlets of Subg. Apeltanthus Sect.
Lupulinaria [2]. However, the inflorescence is secund and
the bracts are not cucullate. S. repens was placed into “S.
repens species-group” (sect. Scutellaria) circumscribed
by Paton based on axillary inflorescences subtended by
leaf-like bracts. However, nutlet morphology showed that
this species-group may not be a natural group [2, 63].
Nevertheless, the absence of S. repens in this and prior
studies, underscores the need for further research with
more comprehensive samples and loci information to
investigate the placement of S. repens.
Subgenus Apeltanthus, divided into Sections Apelt-
anthus and Lupulinaria by Paton, exhibits varying
calyx and nutlet characteristics across these sections
[2]. However, the monophyly of Sects. Apeltanthus and
Lupulinaria was not supported by this analysis because
S. guttata (Sect. Apeltanthus) was sister to S. cordifrons
(Sect. Lupulinaria) with the strong support. S. leptosi-
phon and S. immaculata (Sect. Apeltanthus) were also
nested into Sect. Lupulinaria, distant from the phyloge-
netic position of S. guttata and S. stocksii. e monophyly
of Sect. Lupulinaria was also questioned in previous
research based on ITS that S. stocksii of Sect. Apeltanthus
was nested into Sect. Lupulinaria Subsect. Lupulinaria
[32], which was consistent with the results of Seyedipour
etal. [33] and Salimov etal. [34]. Sects. Lupulinaria and
Apeltanthus should be merged as there is no evidence
from this or previous molecular phylogenetic studies to
maintain them as separate taxa [34]. e characteristics
of boundary genes in this clade were evident. e dis-
tance of 100bp between rpl2 and JLA or JLB presents in
48 species (85.7%) of Subg. Apeltanthus and the 233bp of
rps19 of 53 species (94.6%) located in LSC. Subg. Apelt-
anthus is distributed from the Caucasus eastward to the
Pamir Mountains and southward to the Iranian plateau,
though S. alpina L. occurs in western Europe. It is mainly
concentrated in the western Irano-Turanian region which
is the center of species diversity distribution [2, 34]. e
presence of numerous short internal branches in Clade 4
further indicates rapid radiation within the Irano-Tura-
nian region.
In the analyses of Salimov etal. [34], the Caucasian S.
pontica (Section Salviifoliae), an East Asian lineage com-
prising Sect. Scutellaria (S. baicalensis, S. amoena, and S.
rehderiana) and Sect. Anaspis (S. kingiana), along with
Subg. Apeltanthus formed a tritomy [34]. Furthermore,
Sect. Salviifoliae was not monophyletic, as S. diffusa’s
phylogenetic position differed from S. pontica. However,
in this study, the resolution among the aforementioned
groups has been improved, and the species of Sect. Salvi-
ifoliae formed a monophyletic clade with strong support.
Sect. Salviifoliae was strongly supported as a sister to
the East Asian lineage (S. baicalensis and its relatives),
together were sister to Subg. Apeltanthus with high
support (Fig. 3, Additional file 2: Figs. S1–S11), which
is consistent with Sect. Salviifoliae being morphologi-
cally intermediate between Sect. Scutellaria and Subg.
Apeltanthus, as reported by Bentham [23] and Paton [2].
Sect. Salviifoliae was distinguished from the East Asian
lineage by the apomorphy of hairs completely covering
the nutlet surface, and from Sect. Lupulinaria Subsect.
Lupulinaria due to the lack of the four-sided inflores-
cence, cucullate bracts, as well as strongly flattened pedi-
cels. e analysis of boundary genes also indicated that
the distance of 99bp between rpl2 and JLA or JLB, 3bp
between trnH and JLA, and the length of 233bp of rps19
in the LSC were both present in Sect. Salviifoliae and S.
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Page 11 of 19
Wangetal. BMC Biology (2024) 22:185
ossethica, S. raddeana Juz., S. orientalis L., and S. farsis-
tanica Rech.f. of Sect. Lupulinaria, inferencing that Sect.
Salviifoliae was possibly viewed as the closest ancestor of
Subg. Apeltanthus. e monophyletic clade containing
Clades 2–4 was strongly supported, which is consistent
with morphological characteristics in leaves with obtuse
teeth or entire on each margin growing in arid upland
or mountains, suggesting that Subg. Apeltanthus might
include the larger clade containing Clades 2–4. Moreo-
ver, members of Sect. Apeltanthus were nested within
Sect. Lupulinaria across various positions in Clade 4,
suggesting that these two sections should be merged.
S. kingiana, previously classified under Subgenus
Anaspis [28, 30] or Subgenus Scutellaria Section Anaspis
[2], in this study, is shown to be sister to the East Asian
lineage of the S. baicalensis alliance from Sect. Scutellaria
with strong support (Fig. 3, Additional file2: Figs. S1–
S11). e phylogenetic relationships within this lineage
are consistent with leaf morphology and habitat: species
adapt to relatively arid zones with stem leaves dentate-
serrate, crenate, to subentire or entire. S. kingiana and
the members of Sect. Anaspis were clustered into differ-
ent clades in this study, S. kingiana in Clade 3 and Sect.
Anaspis in Clade 1. us, S. kingiana may not belong to
Sect. Anaspis andSect. Anaspis was non-monophyletic.
All phylogenetic trees showed that Sect. Anaspis except
for S. kingiana was sister to a lineage of S. megalaspis–S.
tournefortii with strong support in Clade 1 (Fig.3, Addi-
tional file2: Figs. S1–S11). e lineage except for S. utri-
culata Labill. corresponding to “S. albida species-group”
(Sect. Scutellaria) defined by Paton is similar to Sect.
Anaspis (excluding S. kingiana) in nutlets type that gray-
black nutlets with hairs partially covering the surface, the
papillae with interior air space and lacking glands on the
internal surface [2]. Species of “S. albida species-group”
and S. utriculata probably should be transferred to Sect.
Anaspis.
Subgenus Scutellaria Section Scutellaria, compris-
ing approximately 240 species distributed across the Old
and New Worlds, was divided into 34 informal species-
groups by Paton [2]. Consistent with the morphologi-
cal basis classifying Sect. Scutellaria as paraphyletic,
this study also found that the monophyly of the section
was not supported, aligning with previous analyses [31,
33–36]. As the largest section within Subg. Scutellaria,
the sub-cosmopolitan Sect. Scutellaria was dispersed
across various clades, yet exhibited clear morphological
and geographic patterns within the section. e lineage
of S. megalaspis–S. tournefortii was identified as sister
to Sect. Anaspis excluding S. kingiana, based on similar
nutlet anatomy. African species S. schweinfurthii, S. poly-
adena, and S. violascens were clustered into Clade 2 with
strong support. S. baicalensis allies (Sect. Scutellaria),
primarily found in China, were determined to be sister to
Sect. Salviifoliae in Clade 3. Neotropical species of Sect.
Scutellaria in Clade 5 were identified as sister to Sect.
Perilomia with strong support. Xerophytic species from
America and Mexico, characterized by a woody rhizome,
formed a distinct clade in Clade 7. A lineage of Sect.
Scutellaria spanning from East Asia to North America
was grouped into Clade 8, excluding Australian species S.
humilis and West European species S. minor and S. hasti-
folia. e most comprehensive infrageneric classification
of Scutellaria by Paton only included 13 species from
China, despite China being a major center of diversity for
the genus with 102 species, notably with most Chinese
species being closely related to Sect. Scutellaria in Clade
8d. erefore, a more detailed division of Sect. Scutel-
laria, based on denser sampling, is necessary.
e inferred close relationship between Clades 7 and
8 corresponds to their widespread distribution in East
Asia and North America, suggesting a potential crossing
between these regions via the Beringian land bridge, sim-
ilar to the dispersion of the mint tribe Elsholtzieae (Lami-
aceae) [64]. e widespread species S. galericulata in the
Old and New World may be migrated by water and birds
because it was grown near the waterside [3]. S. minor
and S. hastifolia mainly distributed in West Europe were
strongly supported as a sister to East Asia and North
America species. Species migration in Europe and North
America is likely to occur via Greenland in the Late Cre-
taceous and Early Tertiary and the Late Paleocene and
Early Eocene, respectively [3, 65]. S. violacea, distributed
across the Indian Peninsula, the Indo-China Peninsula,
and East Himalaya, was positioned in Clade 6 as a sister
to Clades 7 and 8, probably affected by the impact of the
Indian Plate’s collision with Asia [3, 65].
Within the neotropical clade (Clade 5), relationships
are well-resolved. Scutellaria scutellarioides, the type
species of Sect. Perilomia, and S. flocculosa from Peru are
strongly supported as a sister to the neotropical species
of Sect. Scutellaria. is result aligns with the research by
Salimov etal. [34], which showed that S. scutellarioides
and S. volubilis Kunth (Sect. Perilomia) were a sister to
S. costaricana H.Wendl. and S. incarnata Vent. of Sect.
Scutellaria. e inferred relationships correspond well
with the floral morphology of a one-sided inflorescence,
red or scarlet flowers, and a corolla tube that bends dis-
tally. erefore, we recommend considering a wider
circumscription of Sect. Perilomia. Intriguingly, S. suf-
frutescens primarily distributed in Northeast Mexico was
sister to S. wrightii A. Gray, S. drummondii Benth., and S.
resinosa Torr., which occur in America, with strong sup-
port in Clade 7. e formation of a connection between
North and South America during the Eocene–Oligocene,
named Gaarlandia, corresponding to the present-day
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Page 12 of 19
Wangetal. BMC Biology (2024) 22:185
Caribbean islands [65], might have facilitated the disper-
sal of species in the New World.
Combining this study with other recent molecular phy-
logenetic studies, we suggest that updates to the taxon-
omy of the genus are urgently needed:
(1) ree main clades of Scutellaria were well-
resolved, consistent with the inference by Salimov
et al. [34] using chloroplast molecular fragments.
Clade 1 in this study, equivalent to Clade B in Sali-
mov’s study, Clades 2–4 corresponding to Clade A,
and Clades 5–8 equal to Clade C, are suggested to
represent three subgenera. However, differences in
phylogenetic relationships among them are evident.
In Salimov’s research [34], Clade A and Clade B
formed a clade, but the relationship between the two
clades was resolved with moderate support. In con-
trast, Clades 2–4 are strongly supported as sister to
Clades 5–8 in this study. us, Clade 1 in this study
is considered as the early-divergent branch of Scutel-
laria.
(2) Members of Section Apeltanthus were nested
within Sect. Lupulinaria in different positions with
high support in Clade 4, similar to the result by Sali-
mov etal. and others[32–34]. erefore, Sect. Apelt-
anthus and Sect. Lupulinaria should be merged. e
monophyletic clade containing Clades 2–4 was con-
sistent with morphological characteristics of leaves
with obtuse teeth or entirely on each margin grow-
ing in arid upland or mountains, suggesting that the
circumscription of Subg. Apeltanthus needs to be
revised. Furthermore, African species S. schwein-
furthii relatives (Sect. Scutellaria), Sect. Salviifoliae,
S. kingiana (Sect. Anaspis) and S. baicalensis alliance
(Sect. Scutellaria) should be transferred to Subg.
Apeltanthus instead of Subg. Scutellaria whose type
is S. galericulata within Clade 8. Subg. Scutellaria
would then include Clades 5–8.
(3)Section Anaspis, excluding S. kingiana, was sis-
ter to the lineage of S. tournefortii–S. megalaspis
in Clade 1, with similar nutlet anatomy, gray-black
nutlets with hairs partially covering the surface, and
papillae with interior air space but lacking glands on
the internal surface. us, we suggest elevating Sect.
Anaspis, except for S. kingiana, to subgeneric rank,
as the name Anaspis was once considered at subge-
neric rank in Flora URSS [28] and Flora Reipublicae
Popularis Sinicae [30]. e lineage of S. tournefortii–
S. megalaspis should be separated from Sect. Scutel-
laria and transferred to the new subgenus. Further
analysis is needed to confirm the phylogenetic posi-
tion of S. fedtschenkoi Bornm., the type species of the
section, due to the lack of DNA sequences.
(4) Based on the close phylogenetic relationships
and similarities in morphological characters and
geographical distribution between Sect. Perilomia
and the neotropical population of Sect. Scutellaria,
the circumscription of Sect. Perilomia should be
expanded to include more neotropical species.
(5) e position of S. kingiana is distinct from the
remaining members of Sect. Anaspis. However, S.
kingiana is strongly supported as a sister to the S.
baicalensis relatives with similar leaf morphology,
habitat, and geographical distribution. erefore, S.
kingiana should be transferred to the section where
the S. baicalensis alliance is located.
Unclear species identication
e identification of certain species complexes is prob-
lematic because the representatives of varieties of the
same species do not form a clade, as observed in the
Scutellaria scordiifolia Fisch. ex Schrank, S. pekinensis
Maxim., and S. indica complexes. is issue highlights
the need for extensive revision of a large number of spe-
cies and variants. Establishing clear species boundaries
is crucial for phylogenetic studies. In Flora of Pan-Hima-
laya [66], S. nuristanica was considered as a synonym of
S. petiolata because there were no obvious differences in
geographical disjunction and morphology of stem indu-
mentum between the two species. Consistent with the
present study, S. nuristanica was sister to S. petiolata
with strong support. In addition, despite S. altaicola
C.Y.Wu & H.W.Li being treated as a synonym for S. alta-
ica Fisch. ex Sweet based on morphology [1], our analysis
suggests it should remain an independent species due to
their non-clustering in a clade (Fig.3, Additional file2:
Figs. S1–S11). Species delimitation in Scutellaria often
poses challenges, necessitating further revision work.
Potential molecular markers forScutellaria
DNA barcoding, a tool for species identification and dis-
covery of novel or cryptic species, supports food safety
and identifies candidate exemplar taxa [67–71]. Since it
was first proposed in 2003 [72], it has been applied to
research on multiple taxa [70, 73, 74]. e technology has
also been used for species identification in Scutellaria.
S. baicalensis, the botanical origin of a well-known tra-
ditional Chinese medicine “Huang Qin”, which is facing
the rapid decline of natural resources due to high market
demand, overexploitation, habitat destruction, and eco-
system degradation, resulting in high price in the market.
is scarcity has led to a very common phenomenon of
fraudulent adulteration with inherent differences that
seriously affect the safety of medication [75, 76]. Some
molecular markers, such as chloroplast fragments rbcL,
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Page 13 of 19
Wangetal. BMC Biology (2024) 22:185
matK, psbA–trnH, rpl16, and rpl16–rpl14, and nuclear
ribosomal ITS, have been used to discriminate S. bai-
calensis and its adulterants [59, 60, 75, 77]. However,
these studies only focused on a few species. Chloroplast
fragments trnL intron, matK–trnK, trnL–trnF, and ITS
have been also applied to analyze intrageneric relation-
ships of Scutellaria [32, 34]. However, resolution within
related species was poor caused by insufficient phyloge-
netic signal of these markers with low diversity. In this
study, 10 highly variable markers of cpDNA sequences
with variation exceeding 0.025 were identified that can
serve as potential DNA barcodes for species identifica-
tion and phylogeny for Scutellaria, consistent with the
result based on 11 species of Scutellaria by Zhao et al.
[36]. Among them, candidate DNA barcodes includ-
ing trnH-psbA, trnK-rps16, petN-psbM, petA-psbJ, and
ycf1 were identified based on three species of the genus
by Jiang etal. [78]. While the reliability of these markers
requires further validation, they provide a basis for future
research in species identification, phylogeny, and popula-
tion genetics.
SSRs, valuable for constructing high-density genome
maps and establishing genetic and evolutionary rela-
tionships [79–82], are abundant in cpDNA sequences of
Scutellaria, predominantly consisting of poly-adenine
(A) and poly-thymine (T) repeats. SSRs tend to occur in
intergenic spacer regions, although they are also found
in coding regions where they can influence gene activ-
ity and protein expression. is study observed SSRs in
regions that encode essential components of the chloro-
plast transcription machinery and detected mono- and
tetranucleotide SSRs as the most abundant types within
Scutellaria. e new SSRs identified offer potential
molecular markers for medicinal species identification,
genetic diversity estimation, and phylogenetic analysis.
Conclusions
Our study represents the most comprehensive phylog-
enomic analysis of Scutellaria to date, based on com-
plete chloroplast genomes. It marks an improvement
over previous studies, which were limited by either insuf-
ficient sampling or the range of genetic loci examined.
Our results identified eight highly supported clades,
with Clade 1 emerging as the earliest divergent branch
and Clades 2–4 being sister to the monophyletic Clades
5–8. rough the integration of morphological and geo-
graphical distribution data, we proposed three subgen-
era and offered suggestions for updates to the genus’s
taxonomy. However, these proposals require validation
through more extensive sampling and the inclusion of
informative loci, including nuclear genes. e analysis of
chloroplast genome characteristics provides a foundation
for studying the genetic structure and diversity of this
resource-rich genus. Furthermore, comparative analyses
of the chloroplast genomes of 18 representative species
have identified potential molecular markers for taxon-
omy, genetic diversity, and species identification, particu-
larly useful for distinguishing adulterants. Nevertheless,
the rapid advancement of omics technologies and the
need for an extensive multidisciplinary approach encom-
passing molecular systematics, phylogenomics, morpho-
logical anatomy, and taxonomy underscore the future
directions for the phylogenetic study of Scutellaria.
Methods
Taxa sampling, DNA extraction, sequencing
Chloroplast genomes of 220 accessions, represent-
ing 196 species, subspecies, and varieties of Scutellaria
spanning Eurasia, Americas, Africa, and Oceania, were
newly sequenced. Additionally, we retrieved 14 cpDNA
sequences corresponding to ten species and varieties
from the NCBI GenBank database, including S. altaica
(GenBank accession number: MN128387) [36, 83], S.
indica var. coccinea S.Kim & S.Lee (MN047312) [84, 85],
S. orthocalyx Hand.-Mazz. (MN128383) [36, 86], S. mol-
lifolia C.Y. Wu & H.W. Li (MN128384) [36, 87], S. calcar-
ata C.Y. Wu & H.W. Li (MN128385) [36, 88], S. kingiana
(MN128389) [36, 89], S. insignis Nakai (NC028533 and
KT750009) [90, 91], S. rehderiana (MT982397 and
NC060314) [92, 93], S. tuberifera (MW376477 and
NC059812) [94, 95], and S. meehanioides (MW381011
and NC057189) [96, 97]. us, a total of 234 cpDNA
sequences were employed for phylogenetic and compara-
tive genomic analyses, encompassing all sections except
for Sect. Salazaria (Torrey) A.J.Paton. Additionally, four
cpDNA sequences from three genera within the Scutel-
larioideae—Holmskioldia sanguinea (MN128388) [36,
98], Tinnea aethiopica (MN128380) [36, 99], and two
sequences of Wenchengia alternifolia (MN128378 and
MN128379) [36, 100, 101]—were selected as outgroups.
Detailed information and voucher specimens for these
accessions were cataloged in Additional file1: TableS11.
High-quality total genomic DNA was extracted from
about 1.5g herbarium or silica gel-dried leaves using a
modified cetyltrimethylammonium bromide (CTAB)
protocol [102]. DNA quality was evaluated using horizon-
tal electrophoresis with 1.5% agarose gel. Libraries con-
struction was performed according to the manufacturer’s
manual (Illumina, San Diego, CA, USA) and sequenced
on the Illumina NovaSeq 6000 platform with 2 × 150 bp
paired-end reads by Tianjin Novogene Technology Co.,
ltd. Approximately 20GB of raw data was generated for
each sample. Fastp was used to trim the raw reads and
adapter to obtain high-quality clean data by removing
the connector sequences and the low-quality reads, and
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 14 of 19
Wangetal. BMC Biology (2024) 22:185
detailed information on sequencing data was placed in
Additional file1: TableS12 [103].
Chloroplast genome assembly andannotation
e complete chloroplast genomes were assembled with
NOVOWrap v1.20 [104] and GetOrangelle v1.7.2a [105]
and selected the best-quality genome for annotation. In
this study, we chose the cpDNA of Scutellaria barbata
(NC059814) as a reference when we used NOVOWrap
v1.20. Afterward, we selected the best genome accord-
ing to the schematic diagram of the collinearity analy-
sis of the assembly results. In addition, we also used
GetOrangelle v1.7.2a to assemble with default parame-
ters: -F embplant_pt -R 15 -k 21,45,65,85,105. en, PGA
was used to annotate with Amborella trichopoda Baill.
(NC005086) and S. baicalensis (NC027262) as references
[106]. To improve the accuracy of annotation results,
we have manually corrected the annotation results in
Geneious v2021.1.1 [107]. A circular map of the cpDNA
was visualized using Organellar Genome DRAW v1.3.1
(OGDRAW) [108].
Phylogenetic analyses
All of the protein-coding genes (CDS), tRNAs, rRNAs,
and non-coding regions were automatically extracted
based on annotation results by a custom Python script:
get_annotated_regions_from_gb.py (https:// github. com/
Kingg erm/ Perso nalUt iliti es/). Each locus was individually
aligned using MAFFT v7.471 with default settings except
–localpair and –maxiterate 1000 [109]. Removal of diver-
gent and ambiguous sequence alignments may improve
topology [110]. All sequences were adjusted manually
after being checked to improve positional homology fol-
lowing the rules of Löhne etal. [111] (Additional file1:
Table S13). We formed three sequence matrices after
adjusting the alignment: (1) PC including 81 protein-cod-
ing genes, 30 tRNA genes, and four rRNA genes, (2) NC
contained 134 non-coding regions, (3) PCN comprised
115 gene sequences and 134 non-coding regions. e
phylogenetic trees were analyzed using an unpartitioned
strategy on the three sequence matrices, respectively,
because chloroplast genomes are often considered as a
linked single locus [112, 113]. Empirical studies showed
that different regions may not be regarded as a single
locus due to experiencing divergent evolutionary forces
[114, 115]. us, a total of six matrices with or without
partitioning (PC, NC, PCN, PC-p, NC-p, PCN-p) were
implemented for phylogenetic analysis using ML and BI
methods, respectively.
For unpartitioned strategies, three unpartitioned
super-matrices were used for phylogeny using ML and BI.
e best-fit substitution model was identified based on
the Bayesian Information Criterion (BIC) criterion using
ModelFinder embedded in IQ-TREE, with GTR + F + R3
model for PC, TVM + F + R10 model for NC, and
GTR + F + R6 model for PCN, together with default set-
tings except for 1000 Ultrafast bootstrap replicates and
1000 bootstrap replicates of SH-like approximate likeli-
hood ratio test (SH-aLRT) to program ML analysis using
IQ-TREE v 1.6.12 [116]. BI analysis was conducted with
Mrbayes v 3.2.7a under the GTR + I + G model [117].
Four Markov Chain Monte Carlo chains with one cold
and three hot chains were implemented for 1,000,000
generations and sampled every 500 generations, and
the first 25% of all trees were discarded as ‘burn-in’ (the
defaultsettings of Mrbayes).
In terms of partitioned strategy, the appropriate parti-
tion schemes were obtained in the process of gene con-
catenation using a plug-in in PhyloSuite v1.2.2 [118].
Partitionfinder v2.1.1 was used to estimate the evolu-
tionary model of each partition [119]. For ML analysis,
the evolutionary model was obtained based on param-
eters branchlengths = linked, mo dels = all, model_selec-
tion = aicc, and search = rcluster. e phylogenetic trees
were inferred using IQ-TREE v 1.6.12 with 1000 Ultra-
fast bootstrap replicates and SH-aLRT, and the parament
-spp to provide the most appropriate partition scheme
and evolutionary model. In BI analysis, the evolutionary
model of each partition was determined based on options
branchlengths = unlinked, models = mrbayes, model_
selection = aicc, and search = greedy, and the phylogeny
was analyzed with Mrbayes v 3.2.7a. Four Markov Chain
Monte Carlo chains (one cold and three hot chains) were
run for 1,000,000 generations and sampled every 500
generations, and the first 25% of all trees were discarded
as ‘burn-in’ (the default settingsof Mrbayes). All phylo-
genetic relationships were visualized using FigTree v1.4.4
[120]. e Bayesian trees with posterior probability (PP)
and ML trees with bootstrap support (BS) and SH-aLRT
support (SH) were shown in all trees.
Comparative analyses ofcpDNA sequences inthegenus
CPJSdraw v1.0.0 and IRscope were used for boundary
visualization analysis of IR/SC for the whole cpDNA
sequences [121, 122].
In addition, we randomly selected 18 species covering
eight clades for comparative genomic analyses. We used
Mauve v2.4.0 for estimating the collinearity to analyze
whether there was a large segment sequence rearrange-
ment among cpDNA sequences [123]. For divergence
analysis, the online comparison tool mVISTA was applied
to compare and visualize the similarity with the shuffle-
LAGAN mode, and S. scutellarioides newly sequenced
in this study was used as a reference [124]. Additionally,
to assess the nucleotide variabilities, cpDNA sequences
of 18 representative species were aligned using MAFFT
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 15 of 19
Wangetal. BMC Biology (2024) 22:185
v7.471 with default settings except for –maxiterate 1000
and –localpair [109]. en, nucleotide diversity (pi)
values were calculated using DnaSP v6 with a window
length of 600bp and a step size of 200bp [125].
Simple sequence repeats (SSRs) or microsatellites were
identified by the online tool MISA v2.1 with a settled
minimum threshold of mono-, di-, tri-, tetra-, penta-, and
hexanucleotide repeats set to 10, 5, 4, 3, 3, and 3, respec-
tively, and set an option about the maximum length of
sequence between two SSRs to register as compound SSR
to 0 [126]. en, the results were annotated to obtain the
location of SSRs in the cpDNA sequences by the plat-
form JSHYCloud (http:// cloud. genep ioneer. com: 9929).
e repeat sequences including forward, reverse, pal-
indromic, and complementary formats were predicted
using the online software REPuter with a minimal size of
30bp and Hamming distance of 3 [127]. e results were
also annotated to determine the location in the cpDNA
sequences by the platform JSHYCloud (http:// cloud.
genep ioneer. com: 9929).
Abbreviations
POWO Plants of the World Online
cpDNA Complete chloroplast genome
IRs Two identical copies of inverted repeats
SSC A small single-copy region
LSC A large single-copy region
JSB Junction of IRb/SSC
JSA Junction of SSC/IRa
JLA Junction of IRa/LSC
JLB Junction of LSC/IRb
PC An unpartitioned matrix including 81 protein-coding genes, 30
tRNA genes, and four rRNA genes
PC-p A partitioned matrix including 81 protein-coding genes, 30 tRNA
genes, and four rRNA genes
NC An unpartitioned matrix of 134 non-coding regions
NC-p A partitioned matrix of 134 non-coding regions
PCN An unpartitioned matrix of 115 genes and 134 non-coding regions
PCN-p A partitioned matrix of 115 genes and 134 non-coding regions
Supplementary Information
The online version contains supplementary material available at https:// doi.
org/ 10. 1186/ s12915- 024- 01982-2.
Additional file 1: Table S1. Characteristics of 234 complete chloroplast
genome of Scutellaria. Table S2. List of genes of cpDNA of Scutellaria.
Table S3. Statistics of Pi values based on DnaSP. Table S4. The type and
position of SSRs from cpDNA sequences of 18 representative species of
Scutellaria. Table S5. Statistics about the number and proportion of differ-
ent types of SSRs from cpDNA sequences of 18 representative species of
Scutellaria. Table S6. The number and proportion of different repeat units
of SSRs from cpDNA sequences of 18 representative species of Scutellaria.
Table S7. Statistics on the presence or absence of repetitive units of SSRs
in each representative species. Table S8. The type, length, and position of
repetitive sequences from cpDNA sequences of 18 representative species
of Scutellaria. Table S9. Statistics of the number of repetitive sequences for
different types and regions from cpDNA sequences of 18 representative
species of Scutellaria. Table S10. Statistics about the number of repeat
sequences of different lengths in cpDNA sequences of 18 representative
species of Scutellaria. Table S11. The origin of materials and accession
numbers. Table S12. Sequencing data size and quality of the accessions.
Table S13. The positions were masked during alignment adjustment.
Additional file 2: Fig. S1. The phylogeny of Scutellaria based on
Maximum likelihood was inferred based on a tandem matrix of 115
genes (PC). The support values of bootstrap support (BS) and SH-like
approximate likelihood ratio (SH-aLRT) were shown in turn near the
notes. All species belonging to the classification system by Paton were
marked with different colored rectangles for different sections. Some
unlabeled species have not been classified yet. Clades 1–8 of Scutellaria
were marked. Clade 8 was subdivided into Clades 8a–8d. Values equal
to 100 % were replaced with asterisks. Fig. S2. The phylogeny of Scutel-
laria based on Bayesian inference was inferred based on a tandem
matrix of 115 genes (PC). The support values of posterior probabilities
(PP) were shown near the notes. All species belonging to the classifica-
tion system by Paton were marked with different colored rectangles
for different sections. Some unlabeled species have not been classified
yet. Clades 1–8 of Scutellaria were marked. Clade 8 was subdivided
into Clades 8a–8d. Values equal to 1 were replaced with asterisks. Fig.
S3. The phylogeny of Scutellaria based on Maximum likelihood was
inferred based on a partition matrix of 115 genes (PC-p). The support
values of bootstrap support (BS) and SH-like approximate likelihood
ratio (SH-aLRT) were shown in turn near the notes. All species belong-
ing to the classification system by Paton were marked with different
colored rectangles for different sections. Some unlabeled species have
not been classified yet. Clades 1–8 of Scutellaria were marked. Clade 8
was subdivided into Clades 8a–8d. Values equal to 100 % were replaced
with asterisks. Fig. S4. The phylogeny of Scutellaria based on Bayesian
inference was inferred based on a partition matrix of 115 genes (PC-p).
The support values of posterior probabilities (PP) were shown near the
notes. All species belonging to the classification system by Paton were
marked with different colored rectangles for different sections. Some
unlabeled species have not been classified yet. Clades 1–8 of Scutellaria
were marked. Clade 8 was subdivided into Clades 8a–8d. Values equal
to 1 were replaced with asterisks. Fig. S5. The phylogeny of Scutellaria
based on Maximum likelihood was inferred based on a tandem matrix
of 134 non-coding regions (NC). The support values of bootstrap
support (BS) and SH-like approximate likelihood ratio (SH-aLRT) were
shown in turn near the notes. All species belonging to the classifica-
tion system by Paton were marked with different colored rectangles
for different sections. Some unlabeled species have not been classified
yet. Clades 1–8 of Scutellaria were marked. Clade 8 was subdivided into
Clades 8a–8d. Values equal to 100 % were replaced with asterisks. Fig.
S6. The phylogeny of Scutellaria based on Bayesian inference was
inferred based on a tandem matrix of 134 non-coding regions (NC).
The support values of posterior probabilities (PP) were shown near the
notes. All species belonging to the classification system by Paton were
marked with different colored rectangles for different sections. Some
unlabeled species have not been classified yet. Clades 1–8 of Scutellaria
were marked. Clade 8 was subdivided into Clades 8a–8d. Values equal
to 1 were replaced with asterisks. Fig. S7. The phylogeny of Scutellaria
based on Maximum likelihood was inferred based on a partition matrix
of 134 non-coding regions (NC-p). The support values of bootstrap
support (BS) and SH-like approximate likelihood ratio (SH-aLRT) were
shown in turn near the notes. All species belonging to the classifica-
tion system by Paton were marked with different colored rectangles
for different sections. Some unlabeled species have not been classified
yet. Clades 1–8 of Scutellaria were marked. Clade 8 was subdivided into
Clades 8a–8d. Values equal to 100 % were replaced with asterisks. Fig.
S8. The phylogeny of Scutellaria based on Bayesian inference was
inferred based on a partition matrix of 134 non-coding regions (NC-p).
The support values of posterior probabilities (PP) were shown near the
notes. All species belonging to the classification system by Paton were
marked with different colored rectangles for different sections. Some
unlabeled species have not been classified yet. Clades 1–8 of Scutellaria
were marked. Clade 8 was subdivided into Clades 8a–8d. Values equal
to 1 were replaced with asterisks. Fig. S9. The phylogeny of Scutellaria
based on Maximum likelihood was inferred based on a tandem matrix
including 115 genes and 134 non-coding regions (PCN). The support
values of bootstrap support (BS) and SH-like approximate likelihood
ratio (SH-aLRT) were shown in turn near the notes. All species belong-
ing to the classification system by Paton were marked with different
colored rectangles for different sections. Some unlabeled species have
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 16 of 19
Wangetal. BMC Biology (2024) 22:185
not been classified yet. Clades 1–8 of Scutellaria were marked. Clade 8 was
subdivided into Clades 8a–8d. Values equal to 100 % were replaced with
asterisks. Fig. S10. The phylogeny of Scutellaria based on Bayesian infer-
ence was inferred based on a tandem matrix including 115 genes and 134
non-coding regions (PCN). The support values of posterior probabilities
(PP) were shown near the notes. All species belonging to the classification
system by Paton were marked with different colored rectangles for differ-
ent sections. Some unlabeled species have not been classified yet. Clades
1–8 of Scutellaria were marked. Clade 8 was subdivided into Clades 8a–8d.
Values equal to 1 were replaced with asterisks. Fig. S11. The phylogeny of
Scutellaria based on Bayesian inference was inferred based on a partition
matrix of 115 genes and 134 non-coding regions (PCN-p). The support
values of posterior probabilities (PP) were shown near the notes. All spe-
cies belonging to the classification system by Paton were marked with
different colored rectangles for different sections. Some unlabeled species
have not been classified yet. Clades 1–8 of Scutellaria were marked. Clade
8 was subdivided into Clades 8a–8d. Values equal to 1 were replaced with
asterisks.
Additional file 3: Fig. S12. Collinearity analysis of cpDNA sequences from
18 representative species randomly selected covering all clades of Scutel-
laria. The white rectangle box represents CDS, the red box represents
rRNA, and tRNAs are indicated by green boxes. The two pink elongated
rectangular boxes present in each genome are IR regions. Fig. S13.
Visualization for comparison of cpDNA sequences from 18 representative
species randomly selected covering all clades of the genus with S. scutel-
larioides as the reference using mVISTA. The X-axis depicts the sequence
length, and the Y-axis depicts the percentage identity of the reference.
Genome regions are color-coded as exon, UTR, mRNA, and conserved
noncoding sequences (CNS). Gray arrows at the top line show the direc-
tion and position of each gene. The vertical scale represents the percent-
age of sequence identity, ranging from 50% to 100%.
Acknowledgements
We are grateful to the Royal Botanic Gardens, Kew and BGI Research for the
great help, and to Dongming FANG and Fang WANG for suggestions on phylo-
genetic and comparative genome analyses.
Authors’ contributions
This study was conceived and designed by Y.H.W. and Q.W. DNA extraction
was performed by C.X. Analyses were performed by Y.H.W. and manual cor-
rection of chloroplast genome annotation was performed by Y.H.W., Y.W., and
Y.Y.C. The manuscript was written by Y.H.W. and Q.W. with contributions from
Y.W., Y.Y.C., X.G., J.S., C.N.H., and Y.Y. The authors read and approved the final
manuscript.
Funding
This work was supported by Science & Technology Fundamental Resources
Investigation Program (Grant No. 2022FY202200), Survey of Wildlife Resources
in Key Areas of Tibet (Grant Nos. ZL202203601 & ZL202303601), Youth
Innovation Promotion Association, Chinese Academy of Sciences (Grant No.
Y2022032), the K. C. Wong Education Foundation (Grant No. GJTD-2020–05),
and the National Natural Science Foundation of China (Grant Nos. 31870181,
32071666, 32271552) .
Availability of data and materials
All data generated in this study will be available on the NCBI. The GenBank
accession numbers were listed in Additional file 1: Table S11. The plant materi-
als collected for this study came from herbarium that voucher information
in Additional file 1: Table S11. The information about the download data of
a few species is included in the article. Sequence alignments underlying
analyses and phylogenetic trees could be available from figshare (https://doi.
org/10.6084/m9.figshare.26213495.v1) [128].
Declarations
Ethics approval and consent to participate
Not applicable.
Consent for publication
Not applicable.
Competing interests
The authors declare that they have no competing interests.
Author details
1 State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Bot-
any, Chinese Academy of Sciences, Beijing 100093, China. 2 China National
Botanical Garden, Beijing 100093, China. 3 College of Life Sciences, University
of Chinese Academy of Sciences, Beijing 100049, China. 4 State Key Laboratory
of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture,
BGI Research, Wuhan 430047, China. 5 School of Medical Laboratory, Shandong
Second Medical University, Weifang 261053, China. 6 Key Laboratory of Bioac-
tive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry
of Education, Institute of Medicinal Plant Development, Chinese Academy
of Medical Sciences, Peking Union Medical College, Beijing 100193, China.
7 Key Laborator y of Bio-Resources and Eco-Environment of Ministry of Educa-
tion, College of Sciences, Sichuan University, Chengdu 610065, China.
Received: 29 November 2023 Accepted: 15 August 2024
References
1. Govaerts R. World Checklist of Selected Plant Families Database in
ACCESS: 1–216203. The Board of Trustees of the Royal Botanic Gardens,
Kew. https:// powo. scien ce. kew. org/ taxon/ urn: lsid: ipni. org: names: 30003
498-2 (2003).
2. Paton A. A global taxonomic investigation of Scutellaria (Labiatae). Kew
Bull. 1990:399–450.
3. Paton A. The phytogeography of Scutellaria L. Notes Roy Bot Gard
Edinburgh. 1990;46(3):345–59.
4. Mercado JM, Paton AJ. Scutellaria L. (Lamiaceae) in Bolivia with observa-
tions on sect. Perilomia. Kew Bull. 2006;61:549–58.
5. Kudo Michiko, Kobayashi-Nakamura Kumiko, Tsuji-Naito K. Bifunctional
effects of O-methylated flavones from Scutellaria baicalensis Georgi
on melanocytes: Inhibition of melanin production and intracellular
melanosome transport. PLoS One. 2017;12(2):e0171513.
6. Miyaichi Y, Imoto Y, Tomimori T, Lin C-C. Studies on the constituents
of Scutellaria species. IX. On the flavonoid constituents of the root of
Scutellaria indica L. Chem Pharm Bull. 1987;35(9):3720–5.
7. Miyaichi Y, Kizu H, Tomimori T, Lin CC. Studies on the constituents of
Scutellaria species. XI. On the flavonoid constituents of the aerial parts
of Scutellaria indica L. Chem Pharm Bull. 1989;37(3):794–7.
8. Sato Y, Suzaki S, Nishikawa T, Kihara M, Shibata H, Higuti T. Phytochemi-
cal flavones isolated from Scutellaria barbata and antibacterial activity
against methicillin-resistant Staphylococcus aureus. J Ethnopharmacol.
2000;72(3):483–8.
9. Shen J, Li P, Liu S, Liu Q, Li Y, Sun Y, et al. Traditional uses, ten-
years research progress on phytochemistry and pharmacology,
and clinical studies of the genus Scutellaria. J Ethnopharmacol.
2021;2021(265):113198.
10. Wang Z, Qi F, Cui Y, Zhao L, Sun X, Tang W, et al. An update on Chinese
herbal medicines as adjuvant treatment of anticancer therapeutics.
Biosci Trends. 2018;12(3):220–39.
11. Dong Q, Chu F, Wu C, Huo Q, Gan H, Li X, et al. Scutellaria baicalensis
Georgi extract protects against alcoholinduced acute liver injury
in mice and affects the mechanism of ER stress. Mol Biol Evol.
2016;13:3052–62.
12. Yin X, Zhou J, Jie C, Xing D, Zhang Y. Anticancer activity and mechanism
of Scutellaria barbata extract on human lung cancer cell line A549. Life
Sci. 2004;75(18):2233–44.
13. Ye F, Xui L, Yi J, Zhang W, Zhang DY. Anticancer activity of Scutellaria
baicalensis and its potential mechanism. J Altern Complement Med.
2002;8(5):567–72.
14. Lohani M, Ahuja M, Buabeid MA, Dean S, Dennis S, Suppiramaniam
V, et al. Anti-oxidative and DNA protecting effects of flavonoids-rich
Scutellaria lateriflora. Nat Prod Commun. 2013;8(10):1415–8.
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 17 of 19
Wangetal. BMC Biology (2024) 22:185
15. Chen Q-Y, Wang C-Q, Yang Z-W, Tang Q, Tan H-R, Wang X, et al. Dif-
ferences in anti-inflammatory effects between two specifications of
Scutellariae Radix in LPS-induced macrophages in vitro. Chin J Nat Med.
2017;15(7):0515–24.
16. Shang X, He X, He X, Li M, Zhang R, Fan P, et al. The genus Scutellaria an
ethnopharmacological and phytochemical review. J Ethnopharmacol.
2010;128(2):279–313.
17. Kizu H, Sugita N, Tomimori T. Studies on Nepalese crude drugs. XXIV.
Diterpenoid constituents of the leaves of Scutellaria repens Buch.-Ham.
ex D. Don. Chem Pharm Bull. 1998;46(6):988–1000.
18. Bruno M, Piozzi F, Maggio AM, Simmonds MSJ. Antifeedant activity
of neoclerodane diterpenoids from two Sicilian species of Scutellaria.
Biochem Syst Ecol. 2002;30(8):793–9.
19. Bozova PI, Georgieva YP. Antifeedant Activity of Neo-clerodane Diterpe-
noids from Scutellaria altissima against Colorado Potato Beetle Larvae.
Nat Prod Commun. 2017;12(3):327–8.
20. Rodríguez B,Torre MCdl, Rodríguez B, Bruno M, Piozzi F, Savona G, et al.
Neo-clerodane insect antifeedants from Scutellaria galericulata. Phyto-
chemistry. 1993;33(2):309–15.
21. Hamilton A. Esquisse d’une monographie du genre Scutellaria ou
toque. Lyon: Louis Perrin; 1832.
22. Bentham G. Scutellaria. In: Candolle AP, editor. Paris: Prodromus Sys-
tematis Naturalis; 1848. p. 412–32.
23. Bentham G. Scutellaria, Salazaria and Perilomia. In: Bentham G, Hooker
JD, editors. Genera Plantarum. London: Lovell Reeve & Co; 1876. p.
1201–3.
24. Bentham G. Scutellaria and Perilomia. Labiatarum Genera and Species.
London: Ridgeway; 1834. p. 416–46.
25. Briquet J. Scutellaria, Salazaria and Perilomia. In: Engler A, Prantl KAE,
editors. Die Natiirlichen Pflanzenfamilien. 1896. p. 224–33.
26. Edmondson JR. Scutellaria. In: Davis PH, editor. Flora of Turkey. Edin-
burgh: University Press; 1982. p. 78–100.
27. Epling C. American species of Scutellaria. Univ Cal Publ Bot.
1942;20:1–146.
28. Juzepczuk SV. Scutellaria. In: Shishkin BK, Juzepczuk SV, editors. Flora
URSS. Moscow: Academiae Scientarum URSS; 1954. p. 71–225.
29. Rechinger KH. Scutellaria. In: Rechinger KH, editor. Flora Iranica. 1982. p.
48–84.
30. Wu CY, Li HW. Scutellaria. Beijing: Flora Reipublicae Popularis Sinicae;
1977. p. 124–248.
31. Zhao F, Liu E-D, Peng H, Xiang C-L. A new species of Scutellaria (Scutel-
larioideae, Lamiaceae) from Sichuan Province in southwest China. PeerJ.
2017;5:e3624.
32. Safikhani K, Jamzad Z, Saeidi H. Phylogenetic relationships in Iranian
Scutellaria (Lamiaceae) based on nuclear ribosomal ITS and chloroplast
trnL-F DNA data. Plant Syst Evol. 2018;304(9):1077–89.
33. Seyedipour S, Salmaki Y, Xiang C-L. Molecular phylogeny of Scutellaria
(Lamiaceae; Scutellarioideae) in Iranian highlands inferred from nrITS
and trnL-F sequences. Proc Biol Sci. 2020;7(2):169–81.
34. Salimov RA, Parolly G, Borsch T. Overall phylogenetic relationships
of Scutellaria (Lamiaceae) shed light on the origin of the predomi-
nantly Caucasian and Irano-Turanian S. orientalis group. Willdenowia.
2021;51(3):395–427.
35. Shan Y, Pei X, Yong S, Li J, Yu J. Analysis of the complete chloroplast
genomes of Scutellaria tsinyunensis and Scutellaria tuberifera (Lami-
aceae). Mitochondrial DNA B Resour. 2021;6(9):2672–80.
36. Zhao F, Li B, Drew BT, Chen Y-P, Wang Q, Yu W-B, et al. Leveraging
plastomes for comparative analysis and phylogenomic inference within
Scutellarioideae (Lamiaceae). PLoS ONE. 2020;15(5):e0232602.
37. Li B, Cantino PD, Olmstead RG, Bramley GLC, Xiang C-L, Ma Z-H, et al. A
large-scale chloroplast phylogeny of the Lamiaceae sheds new light on
its subfamilial classification. Sci Rep. 2016;6:34343.
38. Li B, Xu W, Tu T, Wang Z, Olmstead RG, Peng H, et al. Phylogenetic
position of Wenchengia (Lamiaceae): a taxonomically enigmatic and
critically endangered genus. Taxon. 2012;61(2):392–401.
39. Bendiksby M, Thorbek L, Scheen A-C, Lindqvist C, Ryding O. An updated
phylogeny and classification of Lamiaceae subfamily Lamioideae.
Taxon. 2011;60(2):471–84.
40. Chen Y-P, Drew BT, Li B, Soltis DE, Soltis PS, Xiang C-L. Resolving the phy-
logenetic position of Ombrocharis (Lamiaceae), with reference to the
molecular phylogeny of tribe Elsholtzieae. Taxon. 2016;65(1):123–36.
41. Chen Y-P, Li B, Olmstead RG, Cantino PD, Liu E-D, Xiang C-L. Phylo-
genetic placement of the enigmatic genus Holocheila (Lamiaceae)
inferred from plastid DNA sequences. Taxon. 2014;63(2):355–66.
42. Zhao F, Chen Y-P, Salmaki Y, Drew BT, Wilson TC, Scheen A-C, et al. An
updated tribal classification of Lamiaceae based on plastome phylog-
enomics. BMC Biol. 2021;19:2.
43. Vollesen K. A taxonomic revision of the genera Tinnea and Renschia
(Lamiaceae, Ajugoideae). Bot Tidsskr. 1975;70(1):1–63.
44. Atkins S. Holmskioldia sanguinea Labiatae, formerly Verbenaceae. Bot
Mag. 1996;13:79–81.
45. Paton A, Phillipson PB, Suddee S. Records of Wenchengia (Lamiaceae)
from Vietnam. Biodivers Data J. 2016;4:e9596.
46. Bullock A. The Genera Tinnea and Renschia. Kew Bull.
1931;1931(9):455–7.
47. Li Bo, Hoang Thanh Son, Nuraliev Maxim S, Tai Vu Anh, Kuznetsov
Andrey N, Kuznetsova Svetlana P, et al. Heliacria gen. nov. (Scutel-
larioideae, Lamiaceae) from Coastal Southern Vietnam. J Trop Subtrop
Botany. 2023;31(5):727–35.
48. Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsub-
ayashi T, et al. The complete nucleotide sequence of the tobacco
chloroplast genome: its gene organization and expression. EMBO J.
1986;5(9):2043–9.
49. Wang R-J, Cheng C-L, Chang C-C, Wu C-L, Su T-M, Chaw S-M. Dynamics
and evolution of the inverted repeat-large single copy junctions in the
chloroplast genomes of monocots. BMC Evol Biol. 2008;8:36.
50. Ruhlman TA, Jansen RK. The plastid genomes of flowering plants. Meth-
ods Mol Biol. 2014;1132:3–38.
51. Wicke S, Schneeweiss GM, dePamphilis CW, Muller KF, Quandt D. The
evolution of the plastid chromosome in land plants: gene content,
gene order, gene function. Plant Mol Biol. 2011;76:273–97.
52. Daniell H, Lin C-S, Yu M, Chang W-J. Chloroplast genomes: diversity,
evolution, and applications in genetic engineering. Genome Biol.
2016;17(1):134.
53. Wu Y, Liu F, Yang D-G, Li W, Zhou X-J, Pei X-Y, et al. Comparative Chloro-
plast Genomics of Gossypium Species: Insights Into Repeat Sequence
Variations and Phylogeny. Front Plant Sci. 2018;9:376.
54. Ahmed I. Chloroplast Genome Sequencing: Some Reflections. Next
Gener Seq Appl. 2015;2(2):119.
55. Wang N, Chen S, Xie L, Wang L, Feng Y, Lv T, et al. The complete chlo-
roplast genomes of three Hamamelidaceae species: Comparative and
phylogenetic analyses. Ecol Evol. 2022;12:e8637.
56. Song W, Chen Z, He L, Feng Q, Zhang H, Du G, et al. Comparative Chlo-
roplast Genome Analysis of Wax Gourd (Benincasa hispida) with Three
Benincaseae Species, Revealing Evolutionary Dynamic Patterns and
Phylogenetic Implications. Genes. 2022;13:461.
57. Lian C, Yang H, Lan J, Zhang X, Zhang F, Yang J, et al. Comparative
analysis of chloroplast genomes reveals phylogenetic relationships and
intraspecific variation in the medicinal plant Isodon rubescens. PLoS
ONE. 2022;17(4):e0266546.
58. Hosokawa K, Minami M, Kawahara K, Nakamura I, Shibata T. Discrimina-
tion among three species of medicinal Scutellaria plants using RAPD
markers. Planta Med. 2000;66:270–2.
59. Hosokawa K, Minami M, Nakamura I, Hishida A, Shibata T. The
sequences of the plastid gene rpl16 and the rpl16–rpl14 spacer region
allow discrimination among six species of Scutellaria. J Ethnopharma-
col. 2005;99:105–8.
60. Chen S-y, Zhao R, Xu L, Feng Q-j, Wang B, Kang T-g. DNA Barcoding
of Mongolian Medicinal Plant Scutellaria scordifolia. Zhong Yao Cai.
2016;39(7):1483–7.
61. Yao G, Zhang Y-Q, Barrett C, Xue B, Bellot S, Baker WJ, et al. A plastid
phylogenomic framework for the palm family (Arecaceae). BMC Biol.
2023;21(1):50.
62. Pick KS, Philippe H, Schreiber F, Erpenbeck D, Jackson DJ, Wrede P, et al.
Improved phylogenomic taxon sampling noticeably affects nonbilate-
rian relationships. Mol Biol Evol. 2010;27(9):1983–7.
63. Paton A, Suddee S, Bongcheewin B. Two new species of Scutellaria
(Lamiaceae) from Thailand and Burma. Kew Bull. 2016;71(1):3.
64. Li P, Qi Z-C, Liu L-X, Ohi-Toma T, Lee J, Hsieh T-H, et al. Molecular phylo-
genetics and biogeography of the mint tribe Elsholtzieae (Nepetoideae,
Lamiaceae), with an emphasis on its diversification in East Asia. Sci Rep.
2017;7(1):2057.
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 18 of 19
Wangetal. BMC Biology (2024) 22:185
65. Morley RJ. Interplate dispersal paths for megathermal angiosperms.
Perspect Plant Ecol Evol Syst. 2003;6(1–2):5–20.
66. Wang Q. Scutellaria. Flora of Pan-Himalaya. Beijing; 2019. p. 180–230.
67. Vassou SL, Kusuma G, Parani M. DNA barcoding for species iden-
tification from dried and powdered plant parts: A case study with
authentication of the raw drug market samples of Sida cordifolia. Gene.
2015;559(1):86–93.
68. Mishra P, Kumar A, Nagireddy A, Mani DN, Shukla AK, Tiwari R, et al. DNA
barcoding: an efficient tool to overcome authentication challenges in
the herbal market. Plant Biotechnol J. 2015;14:8–21.
69. Singh A, Rai VP, Singh M, Singh AK, Sinha B. Molecular diversity analysis
of Asparagus racemosus and its adulterants using random amplified
polymorphic DNA (RAPD). J Med Plant Res. 2013;7(16):1050–6.
70. Gao T-X, Ji D-P, Xiao Y-S, Xue T-Q, Yanagimoto T, Setoguma T. Descrip-
tion and DNA Barcoding of a New Sillago Species, Sillago sinica
(Perciformes: Sillaginidae), from Coastal Waters of China. Zool Stud.
2011;50(2):254–63.
71. Hosein FN, Austin N, Maharaj S, Johnson W, Rostant L, Ramdass AC,
et al. Utility of DNA barcoding to identify rare endemic vascular plant
species in Trinidad. Ecol Evol. 2017;7:7311–33.
72. Hebert PDN, Cywinska A, Ball SL, Dewaard JR. Biological identifica-
tions through DNA barcodes. Proc R Soc Lond B. 2003;270:313–21.
73. Saunders GW. Applying DNA barcoding to red macroalgae: a prelimi-
nary appraisal holds promise for future applications. Phil Trans R Soc
B. 2005;360:1879–88.
74. Sass C, Little DP, Stevenson DW, Specht CD. DNA Barcoding in the
Cycadales: Testing the Potential of Proposed Barcoding Markers for
Species Identification of Cycads. PLoS ONE. 2007;2(11):e1154.
75. Guo X, Wang X, Su W, Zhang G, Zhou R. DNA barcodes for discrimi-
nating the medicinal plant Scutellaria baicalensis (Lamiaceae) and its
adulterants. Biol Pharm Bull. 2011;34(8):1198–203.
76. Irvin L, Vaidya BN, Arun A, Joshee N. DNA Barcoding Studies in the
Medicinal Genus Scutellaria. 2016.
77. Xia Z, Feng C-y, Gao Z-m, Li H-m, Zhang H-r. Authentication of DNA
barcoding of Scutellaria baicalensis and its related species. Zhong
Cao Yao. 2014;45(1):107–12.
78. Jiang D, Zhao Z, Zhang T, Zhong W, Liu C, Yuan Q, et al. The Chloro-
plast Genome Sequence of Scutellaria baicalensis Provides Insight
into Intraspecific and Interspecific Chloroplast Genome Diversity in
Scutellaria. Genes. 2017;8(9):227.
79. Lambert P, Hagen LS, Arus P, Audergon JM. Genetic linkage maps
of two apricot cultivars ( Prunus armeniaca L.) compared with the
almond Texas x peach Earlygold reference map for Prunus. Theor
Appl Genet. 2004;108(6):1120–30.
80. Cai G, Yang Q, Yang Q, Zhao Z, Zhou Y. Identification of candidate
genes of QTLs for seed weight in Brassica napus through compara-
tive mapping among Arabidopsis and Brassica species. BMC Genet.
2012;13:105.
81. Matsuoka Y, Vigouroux Y, Goodman MM, Jesus SG, Buckler E, Doebley
J. A single domestication for maize shown by multilocus microsatel-
lite genotyping. PNAS. 2002;99(9):6080–4.
82. Neeraja CN, Maghirang-Rodriguez R, Pamplona A, Heuer S, Collard
BCY, Septiningsih EM, et al. A marker-assisted backcross approach for
developing submergence-tolerant rice cultivars. Theor Appl Genet.
2007;115(6):767–76.
83. Zhao F, Li B, Drew BT, Chen YP, Wang Q, Yu WB, et al. Scutellaria altaica
chloroplast, complete genome. GenBank https:// www. ncbi. nlm. nih.
gov/ nucco re/ MN128 387 (2020).
84. Lee Y, Kim S. Scutellaria indica var. coccinea chloroplast, complete
genome. GenBank https:// www. ncbi. nlm. nih. gov/ nucco re/ MN047
312.1/ (2020).
85. Lee Y, Kim S. The complete chloroplast genome of Scutellaria indica
var coccinea (Lamiaceae), an endemic taxon in Korea. Mitochondrial
DNA B Resour. 2019;4(2):2539–40.
86. Zhao F, Li B, Drew BT, Chen YP, Wang Q, Yu WB, et al. Scutellaria ortho-
calyx chloroplast, complete genome. GenBank https:// www. ncbi. nlm.
nih. gov/ nucco re/ MN128 383.1/ (2020).
87. Zhao F, Li B, Drew BT, Chen YP, Wang Q, Yu WB, et al. Scutellaria molli-
folia chloroplast, complete genome. GenBank https:// www. ncbi. nlm.
nih. gov/ nucco re/ MN128 384 (2020).
88. Zhao F, Li B, Drew BT, Chen YP, Wang Q, Yu WB, et al. Scutellaria
calcarata chloroplast, complete genome. GenBank https:// www. ncbi.
nlm. nih. gov/ nucco re/ MN128 385 (2020).
89. Zhao F, Li B, Drew BT, Chen YP, Wang Q, Yu WB, et al. Scutellaria kingi-
ana chloroplast, complete genome. GenBank https:// www. ncbi. nlm.
nih. gov/ nucco re/ MN128 389 (2020).
90. Son O, Park S. Scutellaria insignis chloroplast, complete genome.
GenBank https:// www. ncbi. nlm. nih. gov/ nucco re/ NC_ 028533 (2023).
91. Son O, Park S. Scutellaria insignis chloroplast, complete genome.
GenBank https:// www. ncbi. nlm. nih. gov/ nucco re/ KT750 009 (2015).
92. Cai Z. Scutellaria rehderiana chloroplast, complete sequence. Gen-
Bank https:// www. ncbi. nlm. nih. gov/ nucco re/ NC_ 060314 (2023).
93. Cai Z. Scutellaria rehderiana voucher SREHD20200816 chloroplast,
complete genome. GenBank https:// www. ncbi. nlm. nih. gov/ nucco re/
MT982 397 (2021).
94. Li J, Shan y, Pei X, Yong S, Yu J. Scutellaria tuberifera chloroplast,
complete genome. GenBank https:// www. ncbi. nlm. nih. gov/ nucco re/
MW376 477 (2021).
95. Li J, Shan y, Pei X, Yong S, Yu J. Scutellaria tuberifera chloroplast, com-
plete genome. GenBank https:// www. ncbi. nlm. nih. gov/ nucco re/ NC_
059812 (2023).
96. Zhang C. Scutellaria meehanioides chloroplast, complete genome.
GenBank https:// www. ncbi. nlm. nih. gov/ nucco re/ NC_ 057189 (2023).
97. Zhang C. Scutellaria meehanioides chloroplast, complete genome.
GenBank https:// www. ncbi. nlm. nih. gov/ nucco re/ MW381 011 (2021).
98. Zhao F, Li B, Drew BT, Chen YP, Wang Q, Yu WB, et al. Holmskioldia san-
guinea chloroplast, complete genome. GenBank https:// www. ncbi. nlm.
nih. gov/ nucco re/ MN128 388 (2020).
99. Zhao F, Li B, Drew BT, Chen YP, Wang Q, Yu WB, et al. Tinnea aethiopica
chloroplast, complete genome. GenBank https:// www. ncbi. nlm. nih.
gov/ nucco re/ MN128 380 (2020).
100. Zhao F, Li B, Drew BT, Chen YP, Wang Q, Yu WB, et al. Wenchengia alterni-
folia isolate VN chloroplast, complete genome. GenBank https:// www.
ncbi. nlm. nih. gov/ nucco re/ MN128 378 (2020).
101. Zhao F, Li B, Drew BT, Chen YP, Wang Q, Yu WB, et al. Wenchengia alterni-
folia isolate HN chloroplast, complete genome. GenBank https:// www.
ncbi. nlm. nih. gov/ nucco re/ MN128 379 (2020).
102. Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities
of fresh leaf tissue. Phytochem Bull. 1987;19:11–5.
103. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ pre-
processor. Bioinformatics. 2018;34(17):i884–90.
104. Wu P, Xu C, Chen H, Yang J, Zhang X, Zhou S. NOVOWrap: An auto-
mated solution for plastid genome assembly and structure standardiza-
tion. Mol Ecol Resour. 2021;21(6):2177–86.
105. Jin J-J, Yu W-B, Yang J-B, Song Y, dePamphilis CW, Yi T-S, et al. GetOr-
ganelle: a fast and versatile toolkit for accurate de novo assembly of
organelle genomes. Genome Biol. 2020;21(1):241.
106. Qu XJ, Moore MJ, Li DZ, Yi TS. PGA: a software package for rapid,
accurate, and flexible batch annotation of plastomes. Plant Methods.
2019;15(1):50.
107. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al.
Geneious Basic: an integrated and extendable desktop software plat-
form for the organization and analysis of sequence data. Bioinformatics.
2012;28(12):1647–9.
108. Stephan G, Pascal L, Ralph B. OrganellarGenomeDRAW (OGDRAW) ver-
sion 1.3.1: expanded toolkit for the graphical visualization of organellar
genomes. Nucleic Acids Res. 2019;47(W1):W59–64.
109. Katoh K, Standley DM. MAFFT multiple sequence alignment software
version 7: improvements in performance and usability. Mol Biol Evol.
2013;30(4):772–80.
110. Talavera G, Castresana J. Improvement of phylogenies after removing
divergent and ambiguously aligned blocks from protein sequence
alignments. Syst Biol. 2007;56(4):564–77.
111. Löhne C, Borsch T. Molecular evolution and phylogenetic utility of the
petD group II intron: a case study in basal angiosperms. Mol Biol Evol.
2005;22(2):317–32.
112. Green BR. Chloroplast genomes of photosynthetic eukaryotes. Plant J.
2011;66(1):34–44.
113. Zhang X, Sun Y, Landis JB, Lv Z, Shen J, Zhang H, et al. Plastome phy-
logenomic study of Gentianeae (Gentianaceae): widespread gene tree
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 19 of 19
Wangetal. BMC Biology (2024) 22:185
discordance and its association with evolutionary rate heterogeneity of
plastid genes. BMC Plant Biol. 2020;20:340.
114. Schwarz EN, Ruhlman TA, Weng M-L, Khiyami MA, Sabir JSM, Hajarah
NH, et al. Plastome-Wide Nucleotide Substitution Rates Reveal Acceler-
ated Rates in Papilionoideae and Correlations with Genome Features
Across Legume Subfamilies. J Mol Evol. 2017;84(4):187–203.
115. Gonalves DJP, Simpson BB, Ortiz EM, Shimizu GH, Jansen RK. Incongru-
ence between gene trees and species trees and phylogenetic signal
variation in plastid genes. Mol Phylogenet Evol. 2019;138:219–32.
116. Nguyen L-T, Schmidt HA, Haeseler Av, Minh BQ. IQ-TREE: A Fast and
Effective Stochastic Algorithm for Estimating Maximum-Likelihood
Phylogenies. Mol Biol Evol. 2014;32(1):268–74.
117. Ronquist F, Teslenko M, Mark PVD, Ayres DL, Darling A, Höhna S, et al.
MrBayes 3.2: efficient Bayesian phylogenetic inference and model
choice across a large model space. Syst Biol. 2012;61(3):539–42.
118. Zhang D, Gao F, Jakovlić I, Zou H, Zhang J, Li WX, et al. PhyloSuite: an
integrated and scalable desktop platform for streamlined molecular
sequence data management and evolutionary phylogenetics studies.
Mol Ecol Resour. 2020;20(1):348–55.
119. Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. PartitionFinder
2: New Methods for Selecting Partitioned Models of Evolution for
Molecular and Morphological Phylogenetic Analyses. Mol Biol Evol.
2017;34(3):772–3.
120. Rambaut A. Figtree v1.4.4. http:// tree. bio. ed. ac. uk/ softw are/ figtr ee/
(2018).
121. Li H, Guo Q, Xu L, Gao H, Liu L, Zhou X. CPJSdraw: analysis and visualiza-
tion of junction sites of chloroplast genomes. PeerJ. 2023;11:e15326.
122. Amiryousefi A, Hyvonen J, Poczai P. IRscope: an online program to
visualize the junction sites of chloroplast genomes. Bioinformatics.
2018;34(17):3030–1.
123. Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment
of conserved genomic sequence with rearrangements. Genome Res.
2004;14(7):1394–403.
124. Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, et al.
VISTA: visualizing global DNA sequence alignments of arbitrary length.
Bioinformatics. 2000;16(11):1046–7.
125. Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R. DnaSP, DNA poly-
morphism analyses by the coalescent and other methods. Bioinformat-
ics. 2003;19(18):2496–7.
126. Beier S, Thiel T, Munch T, Scholz U, Mascher M. MISA-web: a web server
for microsatellite prediction. Bioinformatics. 2017;33(16):2583–5.
127. Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J,
Giegerich R. REPuter: the manifold applications of repeat analysis on a
genomic scale. Nucleic Acids Res. 2001;29(22):4633–42.
128. Wang YH, Xu C, Guo X, Wang Y, Chen YY, Shen J, He CN, Yu Y, Wang Q.
Phylogenomics analysis of Scutellaria (Lamiaceae) of the world. figshare
https:// doi. org/ 10. 6084/ m9. figsh are. 26213 495. v1 (2024).
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