ArticlePDF Available

Phylogenetic incongruence in an Asiatic species complex of the genus Caryodaphnopsis (Lauraceae)

Authors:

Abstract and Figures

Background Caryodaphnopsis, a group of tropical trees (ca. 20 spp.) in the family Lauraceae, has an amphi-Pacific disjunct distribution: ten species are distributed in Southeast Asia, while eight species are restricted to tropical rainforests in South America. Previously, phylogenetic analyses using two nuclear markers resolved the relationships among the five species from Latin America. However, the phylogenetic relationships between the species in Asia remain poorly known. Results Here, we first determined the complete mitochondrial genome (mitogenome), plastome, and the nuclear ribosomal cistron (nrDNA) sequences of C. henryi with lengths of 1,168,029 bp, 154,938 bp, and 6495 bp, respectively. We found 2233 repeats and 368 potential SSRs in the mitogenome of C. henryi and 50 homologous DNA fragments between its mitogenome and plastome. Gene synteny analysis revealed a mass of rearrangements in the mitogenomes of Magnolia biondii, Hernandia nymphaeifolia, and C. henryi and only six conserved clustered genes among them. In order to reconstruct relationships for the ten Caryodaphnopsis species in Asia, we created three datasets: one for the mitogenome (coding genes and ten intergenic regions), another for the plastome (whole genome), and the other for the nuclear ribosomal cistron. All of the 22 Caryodaphnopsis individuals were divided into four, five, and six different clades in the phylogenies based on mitogenome, plastome, and nrDNA datasets, respectively. Conclusions The study showed phylogenetic conflicts within and between nuclear and organellar genome data of Caryodaphnopsis species. The sympatric Caryodaphnopsis species in Hekou and Malipo SW China may be related to the incomplete lineage sorting, chloroplast capture, and/or hybridization, which mixed the species as a complex in their evolutionary history.
This content is subject to copyright. Terms and conditions apply.
Yangetal. BMC Plant Biology (2024) 24:616
https://doi.org/10.1186/s12870-024-05050-3
RESEARCH Open Access
© The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which
permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the
original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or
other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line
to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory
regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this
licence, visit http:// creat iveco mmons. org/ licen ses/ by/4. 0/. The Creative Commons Public Domain Dedication waiver (http:// creat iveco
mmons. org/ publi cdoma in/ zero/1. 0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
BMC Plant Biology
Phylogenetic incongruence inanAsiatic
species complex ofthegenus Caryodaphnopsis
(Lauraceae)
Shiting Yang1, Jiepeng Huang1, Yaya Qu2, Di Zhang3, Yunhong Tan3, Shujun Wen4* and Yu Song1*
Abstract
Background Caryodaphnopsis, a group of tropical trees (ca. 20 spp.) in the family Lauraceae, has an amphi-Pacific
disjunct distribution: ten species are distributed in Southeast Asia, while eight species are restricted to tropical
rainforests in South America. Previously, phylogenetic analyses using two nuclear markers resolved the relationships
among the five species from Latin America. However, the phylogenetic relationships between the species in Asia
remain poorly known.
Results Here, we first determined the complete mitochondrial genome (mitogenome), plastome, and the nuclear
ribosomal cistron (nrDNA) sequences of C. henryi with lengths of 1,168,029 bp, 154,938 bp, and 6495 bp, respec-
tively. We found 2233 repeats and 368 potential SSRs in the mitogenome of C. henryi and 50 homologous DNA
fragments between its mitogenome and plastome. Gene synteny analysis revealed a mass of rearrangements
in the mitogenomes of Magnolia biondii, Hernandia nymphaeifolia, and C. henryi and only six conserved clustered
genes among them. In order to reconstruct relationships for the ten Caryodaphnopsis species in Asia, we created
three datasets: one for the mitogenome (coding genes and ten intergenic regions), another for the plastome (whole
genome), and the other for the nuclear ribosomal cistron. All of the 22 Caryodaphnopsis individuals were divided
into four, five, and six different clades in the phylogenies based on mitogenome, plastome, and nrDNA datasets,
respectively.
Conclusions The study showed phylogenetic conflicts within and between nuclear and organellar genome data of
Caryodaphnopsis species. The sympatric Caryodaphnopsis species in Hekou and Malipo SW China may be related
to the incomplete lineage sorting, chloroplast capture, and/or hybridization, which mixed the species as a complex
in their evolutionary history.
Keywords Phylogenetic incongruence, Species complex, Tropical tree, Mitochondrial genome, Plastome, nrDNA
*Correspondence:
Shujun Wen
wenshujun@gxib.cn
Yu Song
songyu@gxnu.edu.cn
Full list of author information is available at the end of the article
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 2 of 18
Yangetal. BMC Plant Biology (2024) 24:616
Background
Trees remain a fundamental component in forest eco-
system stability with around 73,000 species and almost
20% of global plant species diversity [1]. ere are an
estimated 9,000 undiscovered tree species, among which
roughly half to two-thirds of all is still waiting to be iden-
tified in tropical and subtropical forests [1]. ese broad-
leaved tree species often refer to rapid diversification and
frequent introgression and compound taxonomic confu-
sion. For instance, studies on Chinese oaks have revealed
negative linear relationships between diversification rates
and genetic variation, suggesting complex associations
between morphological divergence and species diversi-
fication [2]. Similarly, the Pedicularis siphonantha com-
plex in southwest China has shown rapid diversification,
frequent introgression, and cryptic species complexes,
highlighting the challenges of species delimitation based
on morphological characters [3]. e phenotypes and
genetic lineages of the tropical and subtropical tree spe-
cies have narrowed over time in similar environments
[4]. Species identification, delimitation, and description
usually depend on morphological characters, but these
traits often fail to distinguish the recently diverged spe-
cies in tropical and subtropical forests, leading to a long
and controversial debate such as species complex [4, 5].
Species complexes are a group of taxa consisting of
multiple species-level lineages that cannot be reliably
separated using ordinary knowledge [6]. Resolution is
often hindered by their cryptic nature, making it diffi-
cult to distinguish them using traditional methods like
external morphology [4, 6]. To study species complexes,
a variety of methodswere continuouslyimproved, which
mightinvolve analyzing differences in individual traits,
conducting reproductive isolation tests, and utilizing
DNA-based techniques like molecular phylogenetics [7].
ese approaches help researchers determine the bound-
aries between closely related organisms within a species
complex. By examining the genetic, morphological, and
ecological characteristics of these organisms, it is pos-
sible to identify cryptic species, hidden sibling species,
and other components of a species complex [8, 9]. Recent
researches have revealed that the species in difficult line-
ages such as bamboos, palms, oaks, rosids, and camellias
[1014], believed to be nominal species actually repre-
senting a group of closely related species, are sometimes
morphologically indistinguishable.
In plants, mitochondrion and chloroplast are two
DNA-containing organelles. Both have low rates of
nucleotide substitution, significant variation in genome
sizes, and abundant repetitive sequences [15]. Recom-
bination is crucial for DNA replication in all organisms
[16]. Mitochondrial homologous recombination essen-
tially refers to reversible, frequent exchange of large
repeats, which, if not harmful to mitochondrial func-
tion, could be retained, leading to an overall increase in
mitogenome size [17]. Assembly of the mitogenomes is
challenging due to their large repetitive sequences and
multipartite structures. Second-togetherwiththird-gen-
eration sequencing methods help in assembling and dis-
covering these structures [18].
Recent advances in sequencing technologies have
greatly improved the acquisition of large amounts of
genomic data, making it ideal for phylogenetic analy-
sis. Plastomes, the complete DNA sequences of chlo-
roplast, are widely utilized in phylogenetic studies
inthe familyLauraceaedue to their ease of sequenc-
ing, assembly, and annotation [1921]. The inclusion
of the mitogenome in phylogenetic analysis has been
increasingly applied in the angiosperm [2224]. It is
the diversity of genomic data that has brought the dis-
cordance of organelle and nuclear signalling into focus
[25, 26]. Cytonuclear discordance refers to the incon-
gruence between the evolutionary histories of nuclear
and cytoplasmic genomes within a species or a group
of species. The discordance always refers tohybridi-
zation, incomplete lineage sorting, or horizontal gene
transfer [27]. Recent studies have indeed highlighted
the prevalence of cytonuclear discordance in various
plant species [2830].
e amphi-Pacific genus Caryodaphnopsis Airy Shaw
in the family Lauraceae includes about 20 tropical tree
species distributed in Southeast Asia and South Amer-
ica [3135]. e Caryodaphnopsis species in Asia dif-
fer from Alseodaphne and Nothaphoebe species by their
opposite leaves, unequal filaments, and unaltered fruit
pedicels, although the species in the three groups have
unequal tepals and large staminodes [31, 32]. In 1940,
the leaves of C. baviensis (Lecomte) Airy Shaw, C. henryi
Airy Shaw, and C. tonkinensis (Lecomte) Airy Shaw were
described as being similar to those of Cryptocarya laevi-
gata Blume, while their flowers and fruits looked much
like those of Dehaasia Blume species [31]. Recent stud-
ies have reported six new species of Caryodaphnopsis,
including C. laotia Airy Shaw [36], C. latifolia W.T. Wang
[37], C. metalliea Kosterm, C. poilanei Kosterm [32], C.
bilocellata van der Werff & Dao [38], andC. malipoensis
Bing Liu & Y. Yang [39]. On the other side of the Pacific
Ocean, there are eight accepted species, such as C. fos-
terivan der Werff [40], C. cogolloi van der Werff [41], C.
tomentosa van der Werff [42], and C. parviflora van der
Werff [43].
Caryodaphnopsis has no reliable fossil record, but two
molecular analyses have dated the separation between
species in Asia and America to the middle Eocene (44
or 48 million years ago) [44, 45]. Both geographical
groups were supported as monophyletic by previous
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 3 of 18
Yangetal. BMC Plant Biology (2024) 24:616
phylogenetic analyses. e first reported chloroplast
marker in Caryodaphnopsis was matK, which was used
for phylogenetic analysis within the Lauraceae and sug-
gested that C. tonkinensis formed a weakly supported
monophyletic clade [46]. After that, Chanderbali et al.
used a nuclear marker 26S ribosomal DNA sequence and
four chloroplast regions (psbA-trnH, rpll6, trnL-trnF, and
trnT-trnL) to recover a Caryodaphnopsis clade, which
included C. bilocellata and C. tonmentosa[44]. Rohwer
etal. (2005), using the chloroplast sequence trnKintron
[47], found a weakly supported group comprising C. bilo-
cellata, C. tonmentosa, and Neocinnamomum mekon-
gense. Nie etal. (2007) displayed a clade comprising C.
tonmentosaand N. mekongensebased on ITS, trnL-trnF,
rpll6, and psbA-trnH regions [48]. Recently, Li et al.
(2016) used nuclear barcoding markers ITS and RPB2
and found that a monophyleticCaryodaphnopsis clade
[45], which comprised species from two geographical
groups, was strongly supported. In those phylogenetic
analyses, the relationships among five South American
species were well resolved, i.e., an unidentified Caryo-
daphnopsis species and its sister group containing C.
burger, C. fosteri, and C. inaequalis, followed by C.cogol-
loi[41]. However, the relationships among species in Asia
have not been resolved due to low sequence divergence
in the ITSand RPB2 markers. e separation of three
individuals of C. tonkinensis into two branches may rep-
resent sample misidentifications or indicate intraspecific
diversity [45].
In this study, we completed the assembly and annota-
tion of the mitogenome of C. henryi. Data from 21Car-
yodaphnopsis individuals in Asia were collected. e
goals of this study were to (1) determine the first com-
plete mitogenome in the Lauraceae family; (2) reveal
the genomic characteristics and structural features of C.
henryi; and (3) reconstruct the nuclear, chloroplast, and
mitochondrial phylogenies of the Caryodaphnopsisspe-
cies in Asia.
Methods
Plant material andgeographic distributions
Fresh leaves and silica-gel dried materials were collected
from ten Caryodaphnopsis species from China and Viet-
nam. Distribution data was compiled using herbarium
records, and the voucher specimens were deposited in
the Herbarium of Guangxi Normal University (Table1).
Figure1 depicts the fruits of six Caryodaphnopsis spe-
cies. In addition, the plastome sequence of C. henryi was
deposited in the Lauraceae Chloroplast Genome Data-
base (LCGDB, LAU00015,https:// lcgdb. wordp ress. com)
[20]. And the complete mitogenome sequence of C. hen-
ryi was deposited in NCBI (OR987149).
Table 1 Sampled species of Caryodaphnopsis and their voucher specimens in this study
Species Herbarium Voucher Geographic Origin Latitude Longitude
Caryodaphnopsis laotica Airy Shaw GXNU SONG Yu SY34973 Hekou, Yunnan 104.607492 23.102
Caryodaphnopsis laotica Airy Shaw GXNU SONG Yu SY36893 Hekou, Yunnan 104.048425 22.739892
Caryodaphnopsis sp. 1 GXNU SONG Yu SY37063 Hekou, Yunnan 103.969734 22.708797
Caryodaphnopsis sp. 1 GXNU SONG Yu SY36821 Hekou, Yunnan 104.068275 22.767897
Caryodaphnopsis sp. 2 GXNU SONG Yu SY35907 Hekou, Yunnan 104.031533 22.67455
Caryodaphnopsis sp. 2 GXNU SONG Yu SY34883 Hekou, Yunnan 104.032433 22.662531
Caryodaphnopsis sp. 3 GXNU SONG Yu SY36729 Malipo, Yunnan 104.848122 22.969744
Caryodaphnopsis sp. 3 GXNU SONG Yu SY36734 Malipo, Yunnan 104.843201 22.984373
Caryodaphnopsis tonkinensis (Lec.) Airy Shaw GXNU SONG Yu SY37141 Hekou, Yunnan 103.938156 22.672583
Caryodaphnopsis tonkinensis (Lec.) Airy Shaw GXNU SONG Yu SY36875 Hekou, Yunnan 103.938283 22.673356
Caryodaphnopsis tonkinensis (Lec.) Airy Shaw GXNU SONG Yu SY34707 Hekou, Yunnan 103.938522 22.673214
Caryodaphnopsis tonkinensis (Lec.) Airy Shaw GXNU SONG Yu SY34705 Hekou, Yunnan 103.938621 22.673386
Caryodaphnopsis latifolia W. T. Wang GXNU SONG Yu SY35963 Hekou, Yunnan 103.981613 22.714413
Caryodaphnopsis latifolia W. T. Wang GXNU SONG Yu SY35972 Hekou, Yunnan 103.969734 22.708797
Caryodaphnopsis malipoensis Bing Liu & Y. Yang GXNU SONG Yu SY36712 Malipo, Yunnan 104.848489 22.974842
Caryodaphnopsis malipoensis Bing Liu & Y. Yang GXNU SONG Yu SY36715 Malipo, Yunnan 104.828323 22.987118
Caryodaphnopsis bilocellata van der Werff & Dao GXNU SONG Yu SY37158 Hekou, Yunnan 103.960899 22.69406
Caryodaphnopsis bilocellata van der Werff & Dao GXNU SONG Yu SY35356 Hekou, Yunnan 103.960750 22.69325
Caryodaphnopsis metallica Kosterm GXNU SONG Yu SY37885 Vietnam 104.0557 22.6575
Caryodaphnopsis henryi Airy Shaw GXNU SONG Yu SY34716 Honghe, Yunnan 103.108022 23.038376
Caryodaphnopsis henryi Airy Shaw GXNU SONG Yu SY34708 Honghe, Yunnan 103.09825 23.027934
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 4 of 18
Yangetal. BMC Plant Biology (2024) 24:616
DNA extraction andsequencing
High-quality genomic DNA of ten Caryodaph-
nopsis leaves were delivered to Tianjin Novogene
Company for Illumina library preparation and second-
generation sequencings. Genomic DNA was isolated
from 2g of fresh or silica-dried leaves using the CTAB
technique using 4% CTAB [49], 1% PVP, and 0.2% DL
dithiothreitol. e cleaved DNA fragments were tilized
to build 500 bp short-insert libraries, according to the
manufacturer’s handbook (Illumina). Each DNA sample
received > 4.0Gb of data from a Genome Analyzer (Illu-
mina HiSeq 2500) at BGI-Shenzhen after being indexed
by tags and pooled in one lane. A total of 27.9 Gb of
sequence reads with a length of 150bp were obtained for
C. henyri using second-generation sequencing. Young
leaves from C. henryi was extracted and sequenced using
Oxford Nanopore PromethION platforms for third-gen-
eration sequencings. High-quality genomic DNA was
extracted from the leaves using the SDS method. After
library construction using SQK-LSK109 (Oxford Nanop-
ore Technology), DNA sequencing was performed using
Oxford Nanopore sequencing based on the promethION
platform and 20.7Gb of raw data with an average reads
size of 27,600bp were produced.
Genome assembly andannotation
e unlooped mitogenome, complete plastome, and
nrDNA sequences for the Caryodaphnopsis samples
were assembled using GetOrganelle 1.7.5 [50]. To assem-
ble a complete mitogenome of Caryodaphnopsis henryi,
the Illumina sequencing data of C. henryi were initially
assembled using GetOrganelle [50]. After obtaining the
Nanopore third-generation sequencing reads of C. hen-
ryi, the adaptors were first trimmed using Porechop,
and then, by aligning the trimmed reads to the scaf-
folds assembled by GetOrganelle using BLAST + with
the parameter -evalue 1e-200 [51], the subset of long
sequences that was similar to the mitochondria was
obtained. Finally, these long reads and the mitochondria-
related short reads that were extended by GetOrganelle
were used together for hybrid assembly, which was per-
formed by the Unicycler pipeline [52]. In the assembly
result of C. henryi, two putative mitochondrial sequences
were obtained, including a linear sequence of length
Fig. 1 Fruits of six Caryodaphnopsis species (A: C. tonkinensis, B: C. henryi, C: C. malipoensis, D: C. sp. 1, E: C. sp. 2, F: C. sp. 3)
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 5 of 18
Yangetal. BMC Plant Biology (2024) 24:616
968,798bp, and a circular sequence of length 199,231bp.
Mitogenomes were annotated using GeSeq [53], with
Liriodendron tulipifera (KC821969) and Magnolia bion-
dii (MN206019) as references. Subsequently, a detailed
annotation was performed with references in Geneious
Prime [54]. e circular mitogenome map was visualized
using OGDRAW [55].
Repeat andHomologous DNA Analysis
REPuter (https:// bibis erv. Cebit ec. uni- biele feld. de/ reput
er) [56] was used to visualize forward, palindrome,
reverse and complement sequences in the mitogenome
of Caryodaphnopsis henryi, with a minimum repeat size
of 30 bp, hamming distance of three and a sequence
identity > 90%. And Tandem Repeats Finder (TRF) pro-
grams (https:// tandem. bu. edu/) [57] was used to visu-
alize tandem sequences with default parameters. e
simple sequence repeats (SSRs) in the mitogenome of
C. henryi was identified using MISA-web (http:// pgrc.
ipkga tersl eben. de/ misa/), with a motif size of one to six
nucleotides and thresholds of 8, 5, 5, 4, 4 and 4, respec-
tively. BLASTN was used to detect transferred DNA
fragments by analysing sequence similarity between the
plastome and the mitogenome, with an e-value cut-off of
1e-5. e results were visualized using the Circos module
in TBtools v2.012 [58]. Mauve v.2.4.0 software was used
for determining the mitogenome rearrangements among
Caryodaphnopsis henryi, Hernandia nymphaeifolia
(ON023262), and Magnolia biondii (MN206019). RAW-
Graphs (https:// app. rawgr aphs. io/) was used to describe
the collinearity relationships among the gene orders in
the mitogenomes of C. henryi, H. nymphaeifolia, and M.
biondii.
Phylogenectic analysis
All the sequence matrices were aligned with MAFFT
program (version 7.31) [59] and manually modified
with Geneious (version 9.1.7) [54]. ree datasets of
mitochondrial, chloroplast, and nuclear ribosomal cis-
tron sequences were comprised of the following cases:
the mitochondrial dataset had 41 protein-coding genes,
nine intron sequences, and ten intergenic regions; the
chloroplast dataset used complete chloroplast genome
sequences; and the nrDNA dataset was ETS-18S-ITS1-
5.8S-ITS2-26S. A maximum likelihood (ML) analysis was
carried out with IQ-TREE (version 2.1.2) [60] using 1000
ultrafast bootstrap replicates. e DNA substitution
modelswere chosen as TVM+I+G (mtDNA), GTR+I+G
(cpDNA), and GTR+G (nrDNA). e bayesian infer-
ence (BI) analysis based on the GTR+F+I (mtDNA),
GTR+F+I+G4 (cpDNA), and GTR+F+I (nrDNA) mod-
els was performed with MrBayes (version 3.2.7) [61].e
BI analysis started with a random tree andsampled every
1000 generations. e first 20% of the trees was discarded
as burnin, and the remainingtrees were used to generate
a majorityrule consensus tree [62].Visualizing and edit-
ing phylogenetic trees were performed with FigTree soft-
ware(version 1.4.0).
Results
Organelle genome features
e DNA of C. henryi was extracted and sequenced using
the Illumina HiSeq 2500 and Oxford Nanopore Pro-
methION platforms for second- and third-generation
sequencing, respectively. A total of 27.9Gb raw reads of
150bp in length and about 20.7Gb Nanopore long read
data with an average read size of 27,600bp were used for
genome assembly. We successfully assembled the whole
mitogenome and chloroplast of C. henryi by using Illu-
mina short reads and Nanopore long reads, which con-
sists of one big linear contig and two tiny circular contigs
with lengths of 968,798bp, 199,231bp, and 154,938bp,
respectively. With a total length of 1,168,029bp, the over-
all base composition of the entire mitogenome is as fol-
lows: A: 26.7%, T: 26.5%, G: 23.4%, C: 23.4%, and G + C
content is 46.8%. e positions of all the genes identi-
fied in the C.henryi mitogenome and the functional cat-
egorization of these genes are presented (Fig. 2A). e
mitogenome contains 65 unique genes, including 41
protein-coding genes (PCGs), 21 transfer RNA (tRNA)
genes, and 3 ribosomal RNA (rRNA) genes (Table2). e
chloroplast genome, with a length of 154,938 bp (39%
G + C content), contains 113 unique genes, including 79
protein-coding genes, 30 tRNA genes, and 4 rRNA genes
(Fig.2B).
Repeat elements andDNA transfer analysis
In the mitogenome of C. henryi, we detected 2233
repeats, and these repeats include 1093 forward repeats
of 30–366bp, 982 palindromic repeats of 30–25,242bp,
40 reverse repeats of 30-39 bp, 37 complement repeats of
30-38bp, and 81 tandem repeats of 2–53bp (Fig.3A). A
total of 368 potential SSRs were detected in the mitog-
enome of C. henryi, of which 279 are mononucleotides,
66 are dinucleotides, nine are trinucleotides, eight are
tetranucleotides, five are pentanucleotides, and one is
hexanucleotides. Of the mononucleotide repeats, A/T
(86.74%) occupied the main proportion (Fig.3B).
e C. henryi mitogenome sequence was approxi-
mately 7.5 times longer than its chloroplast genome.
Between the mitogenome and plastome we found a total
of 50 homologous DNA fragments (TableS1, Fig.4). e
length of fragments ranged from 39 to 5262bp. e total
insert fragments were 23,583 bp in length, accounting
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 6 of 18
Yangetal. BMC Plant Biology (2024) 24:616
for 2.02% of the length of mitogenome. Six tRNAgenes
were located in these fragments (trnH-GUG, trnM-CAU,
trnN-GUU, trnV-GAC, trnW-CCA, trnP-UGG). We also
detected that the fragments of chloroplast genes, such as
rrnS and trnD-GUC, were located in the mitogenome.
Mitochondrial genome comparisons
We performed synteny and rearrangement analy-
ses between C. henryi mitogenome sequences and two
published mitogenome sequences of H. nymphaeifolia and
M. biondii. Frequent rearrangement events were detected
in both coding segments and noncoding regions (Fig-
ureS1). For the PCGs, eleven segments (Fig.5) including
matR-nad1, nad1-ccmB-rps11, nad5-nad3-rps12, cob-
rps14-rpl5, rpl2-rps19-rps3-rpl16, rps1-rps7, cox2-nad6-
nad5-nad7, sdh4-cox3-atp8, atp4-nad4L, nad1-nad5, and
rps13-nad1 were extensively conserved between C. hen-
ryi and M. biondii mitogenomes, while seven segments
Fig. 2 Gene maps of the Caryodaphnopsis henryi mitogenome (A) and chloroplast genome (B). The annotation of the genomes was performed
using GeSeq. The genes that are drawn outside of the circle are transcribed clockwise, whereas those that are drawn inside the circle are transcribed
counter clockwise
Table 2 Genes, separated by category, encoded by Caryodaphnopsis henryi mitogenome
A single asterisk (*) preceding gene names indicate intron-containing genes
Group of genes Name of gene
Maturases matR
Transport membrane protein mttB
NADH dehydrogenase *nad1, *nad2, nad3, *nad4, nad4L, *nad5, nad6, *nad7, nad9
ATP synthase atp1, atp4, atp6, atp8, atp9
Cytochrome c biogenesis ccmB, *ccmC, ccmFC, ccmFN
Cytochrome c oxidase cox1, *cox2, cox3
Ubiquinol cytochrome c reductase cob
Ribosomal proteins (SSU) rps1, rps2, *rps3, rps4, rps7, *rps10, rps11, rps12, rps13, rps14,rps19
Ribosomal proteins (LSU) *rpl2, rpl5, rpl10, rpl16
Succinate dehydrogenase sdh3, sdh4
Ribosomal RNA rrn5, rrnL, rrnS
Transfer RNA trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-GCC, trnH-GUG,
trnI-CAU, trnK-UUU, trnM-CAU, trnN-GUU, trnN-GUU, trnP-UGG, trnP-UGG,
trnP-UGG, trnQ-UUG, trnS-GCU, rnS-UGA, trnV-GAC, trnW-CCA, trnY-GUA
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 7 of 18
Yangetal. BMC Plant Biology (2024) 24:616
including rps11-nad9, rps19-rps3-rpl16-rpl10, nad5-nad7,
rpl5-rps14-cob, sdh4-cox3-atp8, nad5-nad3-rps12, and
sdh3-atp4-nad4L were extensively conserved between C.
henryi and H. nymphaeifolia mitogenomes.
Phylogeny ofmitochondrial sequences
With the reference mitogenome of C. henryi, we fur-
ther assembled 60 mitochondrial regions, including
41 mitochondrial protein-coding gene sequences, nine
intron sequences, and ten intergenic region sequences
for 21 individuals of ten Caryodaphnopsis species in
Asia. e mitochondrial matrix (Table 3) based on
the 60 regions comprises 166,057 characters, and 363
of which (depending on the consensus threshold) are
parsimony-informative characters (PICs). e mito-
chondrial matrix was used to reconstruct phylogenetic
trees, with two Neocinnamomum species serving as
outgroups (Fig.6A). e 22 Caryodaphnopsis individu-
als were divided into four distinct groups. e group I
only included one C. burger individual (ML-BS = 100%,
BI-PP = 1.00). e group II included two C. henryi
individuals (ML-BS = 95%, BI-PP = 1.00). e group
III included individuals of C. bilocellata, C. latifolia,
and a suspected new species C. sp. 2 (ML-BS = 97%,
BI-PP = 1.00). And the group IV included individuals of
C. laotica, C. malipoensis,C.metallica, C. tonkinensis,
and two suspected new species C. sp. 1 andC. sp. 3(ML-
BS = 97%, BI-PP = 1.00).
Phylogeny ofplastome sequences
e complete chloroplast genomes of 21 individuals from
tenCaryodaphnopsis species in Asia were newlydeter-
mined in the present study.ey were all assembled into
single circular genomes with a typical quadripartite struc-
ture, including one LSC with the lengths of 86,035 bp
(C. henryi) to 91,966 bp (C. sp. 2), one SSC with the
lengths of 17,310bp (C. sp. 3) to 17,701bp (C. henryi),
and a pair of IR with the lengths of 19,694 (C. sp. 2) to
25,601bp (C. henryi) (Table4). e chloroplast genome
alignment has 155,629 characters, 705 (0.45%) of which
are PICs. e matrix of complete plastomes was used
to reconstruct a phylogenetic tree of Caryodaphnopsis
Fig. 3 Number and distribution of long repeats (A) and SSRs (B) in mitogenome sequence of Caryodaphnopsis henryi
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 8 of 18
Yangetal. BMC Plant Biology (2024) 24:616
(Fig. 6B). Five well-supported groups were identified
within the Caryodaphnopsis: the group I included one
C. burger individualand two C. henryiindividuals(ML-
BS = 100%, BI-PP = 1.00), the group II included four indi-
viduals of C. laotica and C. tonkinensis(ML-BS = 98%,
BI-PP = 1.00),thegroup III only included one individual
of C. metallica (ML-BS=98%, BI-PP=1.00), the group
IV includedother two individuals of C. tonkinensis and
individuals of a suspected new species C. sp. 1 (ML-BS =
71%,BI-PP = 0.41), and the group V includedindividu-
alsof C. bilocellata, C. latifolia, C.malipoensis, and two
suspected new species C. sp. 2 and C. sp. 3 (ML-BS =
71%, BI-PP = 0.41).
Phylogeny ofnuclear ribosomal cistron sequences
e nrDNA sequence of 21 individuals from ten Car-
yodaphnopsis species in Asia were newly determind
in the study.e lengths of nrDNA sequences ranged
from 6482bp (C. bilocellata) to 6537bp (C. metallica)
(Table5). ree rRNA genes and three transcribed spac-
ers were found in these nrDNA sequences. Forthe 26S
large-subunit rRNA (26S) region, the length varied from
3386 to 3388bp; for the 18S small-subunit rRNA (18S)
region, 1811bp; for the 5.8S rRNA (5.8S) region, 159bp;
for the external transcribed spacer (ETS) region, from
653 to 656bp; for the ITS1 region, from 214 to 271bp;
and for the ITS2 region, from 213 to 222bp. e nuclear
ribosomal matrix is 6,672 bp and contains 175 (2.62%)
PICs.e 22 Caryodaphnopsis individuals were divided
into sixgroups(Fig.6C).e group I includedthe only
one individual of C. burger (ML-BS = 100%, BI-PP =
1.00). e group II includedthe two individuals of C. hen-
ryi (ML-BS = 90%, BI-PP = 0.95). e group III included
the only oneindividual of C. metallica and two individu-
als of C. bilocellata (ML-BS = 98%, BI-PP = 0.99). e
groupIV included the two individuals of C. malipoensis
(ML-BS = 83%, BI-PP = 1.00). e group V includedthe
individuals of C. latifolia and C. tonkinensis (ML-BS =
94%, BI-PP = 1.00). And the group VI included theindi-
viduals of C. laotica and three suspected new species C.
sp. 1, C. sp. 2, and C. sp. 3 (ML-BS = 94%, BI-PP= 1.00).
Fig. 4 Homological sequences between mitogenome and plastome of C. henryi. The blue circular segment represents the mitogenome, the green
circular segment represents the plastome, and the line represents the homologous fragment. Different colors in the inner circle represent gene
density
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 9 of 18
Yangetal. BMC Plant Biology (2024) 24:616
Discussion
General features ofmitogenome
is study presents thecomplete mitogenome for woody
plants in the family Lauraceaeobtained by Illuminaand
Nanopore sequencing technologies (Fig. 2A). To date,
there are now three orders and eight families whose
mitogenomes have been sequenced within the magnoli-
ids. e mitogenome of Caryodaphnopsis henryi, witha
length of 1,168,029bp, is larger than bothmitogenomes
of Hernandia nymphaeifolia and Magnolia biondii
[63].e length of mitochondrial genes is similar among
C.henryi, M. biondii,and H. nymphaeifolia. A total of 65
mitochondrial genes in C.henryi, with a total length of
41,938bp, is 800bp smaller than those of M.biondiiand
49bp larger than those of H. nymphaeifolia. e mito-
chondrial intronic and intergenic regions of C. henryi,
with a total length of 1,126,191bp, are 201,829bp larger
than those of M. biondiiand 632,275bp larger than those
Fig. 5 Gene order in the mitogenomes of Hernandia nymphaeifolia, Magnolia biondii, and Caryodaphnopsis henryi. H. nymphaeifolia mitochondrial
genes are shown on the left, C. henryi mitochondrial genes in the middle, and M. biondii mitochondrial genes on the right, with different colors
signifying the relevant collinear sections
Table 3 The 60 mitochondrial segments were used to reconstruct the phylogenetic relationships
Types Regions
Intergenic regions nad4-cox2, cox2-nad6, rps14-cob, rps7-atp6, rps13-nad1, nad5-rps4, cox3-atp8, nad1-ccmB, atp1-sdh4, nad5-nad7
Intron regions ccmFC-ccmFC, cox2-cox2, nad2-nad2, nad4-nad4, nad5-nad5, nad7-nad7, rpl2-rpl2, rps3-rps3, rps10-rps10
PCGs atp1, atp4, atp6, atp8, atp9, ccmB, ccmC, ccmFC, ccmFN, cob, cox1, cox2, cox3, matR, mttB, nad1, nad2, nad3, nad4, nad4L, nad5,
nad6, nad7, nad9, rpl10, rpl16, rpl2, rpl5, rps1, rps10, rps11, rps12, rps13, rps14, rps19, rps2, rps3, rps4, rps7, sdh3, sdh4
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 10 of 18
Yangetal. BMC Plant Biology (2024) 24:616
Fig. 6 Molecular phylogenetic trees of eleven species of Caryodaphnopsis based on mitochondrial (A), complete plastomes (B), and nrDNA (C)
sequences using unpartitioned Bayesian inference (BI) and maximum likelihood (ML). The trees were rooted with thesequences of Neocinnamomum
fargesii and N. lecomtei. Numbers associated with the branches are ML bootstrap values (BS) and BI posterior probabilities (PP)
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 11 of 18
Yangetal. BMC Plant Biology (2024) 24:616
Table 4 Summary of ten complete plastomes of Caryodaphnopsis
Types C. henryi C. tonkinensis C. metallica C.sp.3 C. malipoensis C. bilocellata C. latifolia C. laotica C. sp.1 C. sp.2
Total cpDNA size (bp) 154,938 148,829 148,977 149,299 149,314 148,970 148,970 148,838 148,977 149,027
Length of LSC region (bp) 86,035 91,762 91,910 91,917 91,932 91,912 91,912 91,771 91,935 91,966
Length of IR region (bp) 25,601 19,695 19,700 20,036 20,036 19,695 19,695 19,695 19,695 19,694
Length of SSC region (bp) 17,701 17,677 17,667 17,310 17,311 17,668 17,668 17,677 17,652 17,673
Total GC content 39.00% 39.00% 39.10% 39.00% 39.00% 39.00% 39.00% 39.00% 39.00% 39.00%
Total number of genes (unique) 131(113) 128(113) 128(113) 128(113) 128(113) 128(113) 128(113) 128(113) 128(113) 128(113)
Protein Coding Genes 86 83 84 84 84 84 84 84 84 84
tRNA 37 36 36 36 36 36 36 36 36 36
rRNA 8 8 8 8 8 8 8 8 8 8
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 12 of 18
Yangetal. BMC Plant Biology (2024) 24:616
Table 5 Summary of ten complete nrDNAs of Caryodaphnopsis
Types C. henryi C. tonkinensis C. metallica C.sp.3 C. malipoensis C. bilocellata C. latifolia C. laotica C. sp.1 C. sp.2
External transcribed spacer (bp) 653 653 654 654 654 656 654 654 654 654
18S small subunit rRNA (bp) 1811 1811 1811 1811 1811 1811 1811 1811 1811 1811
Internal transcribed spacer 1 (bp) 271 266 214 266 264 256 266 267 257 266
5.8S rRNA (bp) 159 159 159 159 159 159 159 159 159 159
Internal transcribed spacer 2 (bp) 213 222 222 213 213 213 215 213 213 213
26S large subunit rRNA (bp) 3388 3387 3386 3387 3387 3387 3388 3387 3387 3387
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 13 of 18
Yangetal. BMC Plant Biology (2024) 24:616
of H. nymphaeifolia. ere is no substantial difference in
the number of mitochondrial genes, variations in non-
coding DNA content are statistically linked to variations
in mitogenome size [64]. In addition, siginificant length
variation of mitochondrial intergenic regions has also
been reported in nine species in Piperales [23].
e size variation of mitogenomes in land plants can
be influenced by a variety of factors, including retrotrans-
poson proliferation, the generation of repetitive DNA
through homologous recombination, the incorpora-
tion of foreign sequences via intracellular transfer from
the chloroplast or nuclear genome, or horizontal trans-
fer of mitochondrial DNA [63, 64]. is variety has been
reported in many plant species, with mitogenome sizes
ranging from 66kb in Viscum scurruloideum [65] to as
large as 11Mb in Silene conica [66]. However, in different
species, the increase in mitogenome size could be caused
by different factors [67].
On the one hand, a total of 2233 repeats and 368 SSRs
were identified in the mitogenome of Caryodaphnopsis
henryi (Fig.3B). e mitogenome exhibited a significant
number of dispersed repeats, primarily consisting of tan-
dem, forward, and palindromic repeats (Fig. 3A). ese
repeats are critical for the recombination of the mitog-
enome, as they are one of the causes of variation affect-
ing the size and structure of the mitogenome [65]. e
presence of repeated sequences in the mitogenome can
increase the possibility of recombination, leading to vari-
ations in the genome structure, which in turn could relate
to gene expression and function [66].
On the other hand, the structure and evolutionary pro-
cessof plantmitogenomemake it more prone to accept-
ing and integrating foreign DNA [64]. Horizontal gene
transfer from chloroplasts to mitochondria has been
reported multiple times, but the length and number of
transfer fragments vary significantly between species.
In this study, we found 50 homologous DNA fragments
in Caryodaphnopsis henryi (Fig. 4), transferred from
the chloroplast genome to the mitogenome. us, the
length variation of intergenic regions might contribute
to the length difference of the mitogenome inmagnoli-
ids lineages, primarily due to frequent recombination of
repeated sequences and integration of foreign ones dur-
ing evolution [67].
Genome rearrangement events, such as gene order
changes, can reflect evolutionary distance and niche
adaptation between species [68]. ese events are
responsible for creating extant species with conserved
genes in different positions across genomes, and close
species tend to have a similar set of genes or share
most of them [69, 70]. Gene synteny analysis revealed
a succession of rearrangements in the mitogenomes of
Magnolia biondii, Hernandia nymphaeifolia, and Car-
yodaphnopsis henryi (Fig. 5). Only six gene clusters in
Fig. 7 Phylogenies obtained from the three different datasets: a mitochondrial; b nuclear ribosomal; c chloroplast
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 14 of 18
Yangetal. BMC Plant Biology (2024) 24:616
mitogenomewere found to be highly conserved acrossC.
henryi, H. nymphaeifolia, and M. biondii. In addition,
unlike H. nymphaeifolia, the mitogenomes of C. henryi
and M. biondii contained elevengene clusters. Although
C. henryi has a closer relationship with H. nymphaeifo-
lia, the number of conserved gene clusters between C.
henryi and H. nymphaeifolia arelessthan those between
C. henryi and M. biondii. e location of protein-coding
genes may be poorly conserved in plant mitogenomes.
e genome rearrangement events revealed by gene col-
linearity analysis can indeed reflect the evolutionary dis-
tance and niche adaptation between species [
71, 72].
Cytonuclear discordance
Cytonuclear discordance, which shows markedly different
phylogenetic patterns between nuclear markers and cyto-
plasmic genes such as mitochondrial and chloroplast genes,
has been observed in various plant populations and is often
attributed to processes such as hybridization and incom-
plete lineage sorting [30, 73, 74]. e species in thegenus
ofCaryodaphnopsis, with different positions in the chloro-
plast and mitochondrial phylogenies relative to the nuclear
phylogeny(Fig. 7). Our phylogenetic analyses revealed sig-
nificantcytonuclear discordance in thegenus ofCaryodaph-
nopsis. e species of C. bilocellata and C. metallica are
generally grouped together in the nuclear phylogeny, with
different positions in the mitochondrial and chloroplast
phylogenies. e speciesof C. sp. 1, C. sp. 2, C. sp. 3, andC.
laoticaare grouped together in the nuclearphylogeny, with
different positionsin the mitochondrial and chloroplast phy-
logenies. is finding is comparable with prior studies on
nuclear and cytoplasmic genes inconsistencies in other plant,
including in the apple genus Malus [
73], balsam poplars [30], the Australian plant genus
Adenanthos [74]. is inconsistency may reveal complex
patterns of gene flow that these species may have experi-
enced over the course of their evolution [75]. In addition,
four individuals of the C. tonkinensis species are clustered
together in nuclear phylogeny but separated in different
clades of the mitochondrial and chloroplast phylogenies.
is separation of C. tonkinensis may represent intraspecific
Fig. 8 The geographic distribution and the fruit feature of Caryodaphnopsis are represented in the phylogenetic tree based on their mitochondrial,
chloroplast, and nrDNA phylogenetic trees
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 15 of 18
Yangetal. BMC Plant Biology (2024) 24:616
diversity, indicating that Caryodaphnopsis may have a spe-
cies complex.
Mitochondrial and chloroplast capture in plants is a
phenomenon that occurs when a plant species acquires
these organelles from another species through hybridi-
zation [76, 77]. In our study, the species of Caryodaph-
nopsis, with different positions in the nuclear phylogeny,
are grouped together in the mitochondrial and chloro-
plast phylogenies. e individuals of C. latifolia and C.
bilocellata collected from Hekou, China. Based on the
mtDNA and cpDNA data, our phylogenomic analy-
sisshows sisterhood of the species of C. latifolia and the
species of C. bilocellata.Our phylogeny appears to reflect
theorganellar capture from another species.Maybe the
overlap of their geographic distributions results in mito-
chondrial and chloroplast capture. e overlapping geo-
graphic (Fig.8) distribution of species can lead to gene
flow and hybridization, potentially resulting in gene trans-
fer between mitochondria and chloroplasts, which can
affect their clustering on the phylogenetic tree [78, 79].
Distribution sites of Caryodaphnopsis species shows an
interesting pattern of genetic diversity across regions with
comparable species richness. Malipo county of China has
only two Caryodaphnopsis species, which share similar
chloroplast and mitochondrial genomes (Fig.9). In con-
trast, Hekou county of China has six Caryodaphnopsis
species with multiple types of chloroplast, mitochondrial,
and nrDNA sequences. e genetic diversity within and
between species could trace implications for evolutionary
processes, including adaptation to environmental stress,
natural selection, and disease susceptibility [80]. e high
genetic diversity observed in Hekou suggests that it may
be a center of Caryodaphnopsis species distribution in
Asia and a source of genetic resources for future conser-
vation and breeding efforts. e phenomenon of higher
genetic diversity in areas with greater species richness
has been observed in other plant groups, such as tropical
rainforests and alpine regions [8183].
Conclusions
We assembled the complete mitogenome sequence of
Caryodaphnopsis henryi, a tropical tree in the family
Lauraceae. e whole mitogenome of C. henryi consists
of one big linear contig, with length of 968,798bp, and
one tiny circular contig, with length of 199,231bp. e
mitogenome contains 65 genes, including 41 protein-
coding genes, 21 tRNA genes, and three rRNA genes.
ere are 50 homologous DNA fragments between
Fig. 9 Distribution of Caryodaphnopsis species in this study. Each site of the species is represented by a square point. The color of the square
corresponds to the species’ grouping with nrDNA data. The circle is divided into three parts, representing the groupings with nrDNA, mtDNA,
and cpDNA data respectively. Same color indicates the species within the consistent group of the phylogenetic topologies. The world map
was downloaded from the website of the Resource and Environment Science and Data Center (http:// www. resdc. cn)
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 16 of 18
Yangetal. BMC Plant Biology (2024) 24:616
the mitogenome and plastome of C. henryi. Com-
parative genomic analysis indicated that the sizes and
geneorders of the three sequenced mitogenomesof C.
henryi, Magnolia biondii, and Hernandia nymphaeifo-
lia differed greatly. We found significant incongruence
between the mitochondrial and nuclear or chloroplast
phylogenies in a Caryodaphnopsis group.e study also
revealed that Caryodaphnopsis species with sympatry
often cluster together in the chloroplast and mitochon-
drial phylogenetic trees.
Abbreviations
PCGs Protein-Coding Genes
tRNA Transfer RNA Genes
rRNA Ribosomal RNA Genes
SSRs Simple Sequence Repeats
cpDNA Chloroplast DNA
nrDNA Nuclear Ribosomal Cistron
mtDNA Mitochondrial DNA
PICs Parsimony-Informative Characters
ML Maximum Likelihood
BI Bayesian Inference
LSC Large Single-Copy Region
SSC Small Single-Copy Region
IRs Inverted Repeats
Supplementary Information
The online version contains supplementary material available at https:// doi.
org/ 10. 1186/ s12870- 024- 05050-3.
Supplementary Material 1.
Supplementary Material 2.
Acknowledgements
The authors would like to thank Dr. Bing Liu at Institute of Botany, Chinese
Academy of Sciences (CAS) for species collection.
Authors’ contributions
S.T.Y., S.J.W., and Y.S. designed the work. Y.Y.Q. and J.P.H. prepared the datasets.
S.T.Y., Y.Y.Q., D.Z., J.P.H., Y.H.T, S.J.W., and Y.S. contributed materials/analysis tools.
S.T.Y. wrote the manuscript. D.Z., J.P.H., S.J.W., and Y.S. revised the manuscript.
All authors approved the final manuscript.
Funding
This work was supported by the Guangxi Key Laboratory of Landscape
Resources Conservation and Sustainable Utilization in Lijiang River Basin,
Guangxi Normal University (Grant No. LRCSU21Z0103) and Key Laboratory
of Ecology of Rare and Endangered Species and Environmental Protection
(Guangxi Normal University), Ministry of Education (AB21220057). This work
was also supported by the National Natural Science Foundation of China
(No. 32260060, 31970223) and the Special Program for Technology Bases and
Talents of Guangxi (Grant No. 2022AC20002).
Availability of data and materials
All relevant phylogenomic matrices were deposited in the the manuscript’s
supplementary files. The assembled mitochondrial genome sequence was
submittted to National Center for Biotechnology Information with accession
number OR987149 (https:// www. ncbi. nlm. nih. gov).
Declarations
Ethics approval and consent to participate
Not applicable.
Consent for publication
Not applicable.
Competing interests
The authors declare no competing interests.
Author details
1 Key Laboratory of Ecology of Rare and Endangered Species and Environmen-
tal Protection (Ministry of Education) and Guangxi Key Laboratory of Land-
scape Resources Conservation and Sustainable Utilization in Lijiang River
Basin, Guangxi Normal University, Guilin 541004, Guangxi, China. 2 Southwest
Forestry University, Kunming 650224, Yunnan, China. 3 Southeast Asia Biodiver-
sity Research Institute, Chinese Academy of Sciences & Center for Integrative
Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy
of Sciences, Menglun, Mengla, Yunnan 666303, China. 4 Guangxi Key Labora-
tory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi
Zhuang Autonomous Region and Chinese Academy of Sciences, Guangxi
Institute of Botany, Guilin 541006, China.
Received: 9 December 2023 Accepted: 19 April 2024
References
1. Cazzolla Gatti R, Reich PB, Gamarra JGP, Crowther T, Hui C, Morera A,
et al. The number of tree species on Earth. Proc Natl Acad Sci U S A.
2022;119(6):e2115329119.
2. Yang J, Guo YF, Chen XD, Zhang X, Ju MM, Bai GQ, et al. Framework
phylogeny, evolution and complex diversification of Chinese oaks. Plants
(Basel). 2020;9(8):1024.
3. Liu R, Wang H, Yang JB, Corlett RT, Randle CP, Li DZ, Yu WB. Cryptic species
diversification of the Pedicularis siphonantha complex (Orobanchaceae)
in the mountains of Southwest China since the Pliocene. Front Plant Sci.
2022;13:811206.
4. Pinheiro F, Dantas-Queiroz MV, Palma-Silva C. Plant species complexes
as models to understand speciation and evolution: a review of South
American studies. Crit Rev Plant Sci. 2018;37(1):54–80.
5. Struck TH, Feder JL, Bendiksby M, Birkeland S, Cerca J, Gusarov VI, et al.
Finding evolutionary processes hidden in cryptic species. Trends Ecol
Evol. 2018;33(3):153–63.
6. Scherz MD, Glaw F, Hutter CR, Bletz MC, Rakotoarison A, Kohler J, Vences
M. Species complexes and the importance of data deficient classifica-
tion in red list assessments: the case of Hylobatrachus frogs. Plos One.
2019;14(8):e0219437.
7. Alagona PS. Species complex: classification and conservation in Ameri-
can environmental history. Isis. 2016;107(4):738–61.
8. Jorger KM, Schrodl M. How to describe a cryptic species? Practical chal-
lenges of molecular taxonomy. Front Zool. 2013;10(1):59.
9. Malmstrom CM. Ecologists study the interactions of organisms and their
environment. Nat Educ Knowl. 2010;3(10):88.
10. Sijimol K, Dev SA, Sreekumar VB. DNA barcoding supports existence of
morphospecies complex in endemic bamboo genus Ochlandra Thwaites
of the Western Ghats, India. J Genet. 2020;99(1):68.
11. Pereira DS, Hilario S, Goncalves MFM, Phillips AJL. Diaporthe species on
palms: molecular reassessment and species boundaries delimitation in
the D. arecae Species Complex. Microorganisms. 2023;11(11):2717.
12. Curtu AL, Sofletea N, Toader AV, Enescu MC. Leaf morphological and genetic
differentiation between Quercus robur L. and its closest relative, the drought-
tolerant Quercus pedunculiflora K. Koch. Ann Forest Sci. 2011;68:1163–72.
13. Zhang HJ, Feng T, Landis JB, Zhang X, Meng A, Deng T, Sun H, Wang
HC. Circumscription of the Sibbaldia procumbens complex (Potentilleae:
Rosaceae) in China based on evidence from simple sequence repeat
markers and morphology. Bot J Linn Soc. 2019;191(3):305–14.
14. Li R, Yang JB, Yang SX, Li DZ. Phylogeny and taxonomy of the Pyrenaria
complex (Theaceae) based on nuclear ribosomal ITS sequences. Nord J
Bot. 2012;29:780–7.
15. Bi CW, Lu N, Xu YQ, He CP, Lu ZH. Characterization and analysis of the
mitochondrial genome of common bean (Phaseolus vulgaris) by com-
parative genomic approaches. Int J Mol Sci. 2020;21(11):3778.
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 17 of 18
Yangetal. BMC Plant Biology (2024) 24:616
16. Rocha EP, Cornet E, Michel B. Comparative and evolutionary analysis of the
bacterial homologous recombination systems. Plos Genet. 2005;1(2):e15.
17. Christensen AC. Plant mitochondrial genome evolution can be explained
by DNA repair mechanisms. Genome Biol Evol. 2013;5(6):1079–86.
18. Meslier V, Quinquis B, Da Silva K, Plaza Onate F, Pons N, Roume H, Podar
M, Almeida M. Benchmarking second and third-generation sequencing
platforms for microbial metagenomics. Sci Data. 2022;9(1):694.
19. Song Y, Yu WB, Tan YH, Jin JJ, Wang B, Yang JB, Liu B, Corlett RT. Plastid
phylogenomics improve phylogenetic resolution in the Lauraceae. J Syst
Evol. 2020;58(4):423–39.
20. Song Y, Yu WB, Tan YH, Liu B, Yao X, Jin JJ, Padmanaba M, Yang JB, Corlett
RT. Evolutionary comparisons of the chloroplast genome in Lauraceae
and insights into loss events in the Magnoliids. Genome Biol Evol.
2017;9(9):2354–64.
21. Song Y, Xia SW, Tan YH, Yu WB, Yao X, Xing YW, Corlett RT. Phylogeny and
biogeography of the Cryptocaryeae (Lauraceae). Taxon. 2023;72(6):1244–61.
22. Van de Paer C, Bouchez O, Besnard G. Prospects on the evolutionary
mitogenomics of plants: A case study on the olive family (Oleaceae). Mol
Ecol Resour. 2018;18(3):407–23.
23. Yu RX, Chen XD, Long LJ, Jost M, Zhao R, Liu LM, Mower JP,
dePamphilisde CW, Wanke S, Jiao YN. De novo assembly and compara-
tive analyses of mitochondrial genomes in Piperales. Genome Biol Evol.
2023;15(3):evad041.
24. Zhang X, Shan YY, Li JL, Qin QL, Yu J, Deng HP. Assembly of the complete
mitochondrial genome of Pereskia aculeata revealed that two pairs of
repetitive elements mediated the recombination of the genome. Int J
Mol Sci. 2023;24(9):8366.
25. Bianconi ME, Dunning LT, Curran EV, Hidalgo O, Powell RF, Mian S, Leitch
IJ, Lundgren MR, Manzi S, Vorontsova MS, et al. Contrasted histories of
organelle and nuclear genomes underlying physiological diversification
in a grass species. Proc Biol Sci. 2020;287(1938):20201960.
26. Liu Y, Johnson MG, Cox CJ, Medina R, Devos N, Vanderpoorten A, Hede-
nas L, Bell NE, et al. Resolution of the ordinal phylogeny of mosses using
targeted exons from organellar and nuclear genomes. Nat Commun.
2019;10(1):1485.
27. Toews DPL, Brelsford A. The biogeography of mitochondrial and nuclear
discordance in animals. Mol Ecol. 2012;21(16):3907–30.
28. Liu JX, Shi MM, Zhang ZL, Xie HB, Kong WJ, Wang QL, Zhang XX, Shi LC,
et al. Phylogenomic analyses based on the plastid genome and concat-
enated nrDNA sequence data reveal cytonuclear discordance in genus
Atractylodes (Asteraceae: Carduoideae). Front Plant Sci. 2022;13:1045423.
29. Lee-Yaw JA, Grassa CJ, Joly S, Andrew RL, Rieseberg LH. An evaluation
of alternative explanations for widespread cytonuclear discordance in
annual sunflowers (Helianthus). New Phytol. 2019;221(1):515–26.
30. Huang DI, Hefer CA, Kolosova N, Douglas CJ, Cronk QCB. Whole plastome
sequencing reveals deep plastid divergence and cytonuclear discord-
ance between closely related balsam poplars, Populus balsamifera and P.
Trichocarpa (Salicaceae). New Phytol. 2014;204(3):693–703.
31. Airy-Shaw HK. Notes on two asiatic genera of Lauraceae. Bullet Miscell
Info (Royal Gardens, Kew). 1940;2:74–7.
32. Kostermans AJGH. A monograph of Caryodaphnopsis Airy Shaw. Rein-
wardtia. 1974;9(1):123–37.
33. Cao ZY, Qu YY, Song Y, Xin PY. Comparative genomics and phylogenetic
analysis of chloroplast genomes of Asian Caryodaphnopsis taxa (Laura-
ceae). Gene. 2024;907:148259.
34. van der Werff H, Richter HG. Caryodaphnopsis Airy-Shaw (Lauraceae), a
Genus New to the Neotropics. Syst Bot. 1985;10(2):166–73.
35. Li XW, Li J. Notes on the taxonomy and distribution of the genus
Caryodaphnopsis of Lauraceae and to discuss the characteristics of its
area-type. Plant Diversity. 1991;13(01):1–3.
36. Wu CY, Wang WT. A preliminary report on floristic studies of tropical and
subtropical region of Yunnan. Acta Phytotaxonomica Sinica. 1957;6:183–254.
37. Airy Shaw HK. A new species of Caryodaphnopsis (Lauraceae). Harv Pap
Bot. 1960;14:250–1.
38. van der Werff H. A new species of Caryodaphnopsis (Lauraceae) from
Vietnam. Novon. 1999;9(4):584–6.
39. Liu B, Yang Y, Ma K. A new species of Caryodaphnopsis Airy Shaw (Laura-
ceae) from southeastern Yunnan China. Phytotaxa. 2013;118(1):1–8.
40. Van der Werff H. A new species of Caryodaphnopsis (Lauraceae) from
Peru. Syst Bot. 1986;11(3):415–8.
41. van der Werff H. Eight new species and one new combination of neo-
tropical Lauraceae. Ann Mo Bot Gard. 1988;75(2):402–19.
42. van der Werff H. New Species of Lauraceae from Ecuador and Peru. Ann
Mo Bot Gard. 1991;78(2):409–23.
43. Van der Werff H. A new species of Caryodaphnopsis (Lauraceae) from
Harvard. Botany. 2012;17(1):39–41.
44. Chanderbali AS, van der Werff H, Renner SS. Phylogeny and historical
biogeography of Lauraceae: evidence from the chloroplast and nuclear
genomes. Ann Mo Bot Gard. 2001;88(1):104–34.
45. Li L, Madriñán S, Li J. Phylogeny and biogeography of Caryodaphnopsis
(Lauraceae) inferred from lowcopy nuclear gene and ITS sequences.
Taxon. 2016;65(3):433–43.
46. Rohwer JG. Toward a phylogenetic classification of the Lauraceae: evi-
dence from matK sequences. Syst Bot. 2000;25(1):60–71.
47. Rohwer JG, Rudolph B. Jumping genera: The phylogenetic positions of
Cassytha, Hypodaphnis, and Neocinnamomum (Lauraceae) based on
different analyses of trnK intron sequences. Ann Missouri Bot Garden.
2005;92(2):153–78.
48. Nie ZL, Wen J, Sun H. Phylogeny and biogeography of Sassafras (Laura-
ceae) disjunct between eastern Asia and eastern North America. Plant
Syst Evol. 2007;267(1–4):191–203.
49. Doyle JJ, Dickson EE. Preservation of plant samples for DNA restriction
Endonuclease analysis. Taxon. 1987;36(4):715–22.
50. Jin JJ, Yu WB, Yang JB, Song Y, dePamphilis CW, Yi TS, Li DZ. GetOrganelle:
a fast and versatile toolkit for accurate de novo assembly of organelle
genomes. Genome Biol. 2020;21(1):241.
51. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K,
Madden TL. BLAST+: architecture and applications. BMC Bioinformatics.
2009;10:421.
52. Wick RR,Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial
genome assemblies from short and long sequencing reads. Plos Comput
Biol. 2017;13(6):e1005595.
53. Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R,
Greiner S. GeSeq – versatile and accurate annotation of organelle
genomes. Nucleic Acids Res. 2017;45(W1):W6–W11.
54. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton
S, Cooper A, Markowitz S, Duran C, et al. Geneious Basic: an integrated
and extendable desktop software platform for the organization and
analysis of sequence data. Bioinformatics. 2012;28(12):1647–9.
55. Lohse M, Drechsel O, Bock R. OrganellarGenomeDRAW (OGDRAW): a tool
for the easy generation of high-quality custom graphical maps of plastid
and mitochondrial genomes. Curr Genet. 2007;52(5–6):267–74.
56. 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.
57. Benson G. Tandem repeats finder: a program to analyze DNA sequences.
Nucleic Acids Res. 1999;27(2):573–80.
58. Chen CJ, Wu Y, Li JW, Wang X, Zeng ZH, Xu J, Liu YL, Feng JT, Chen H, He
YH, Xia R. TBtools-II: A “One for all, All for one” bioinformatics platform for
biological big-data mining. Mol Plant. 2023;16(11):1733-42.
59. Katoh K, Standley DM. MAFFT multiple sequence alignment software
version 7: improvements in performance and usability. Mol Biol Evol.
2013;30(4):772–80.
60. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and
effective stochastic algorithm for estimating maximum-likelihood phy-
logenies. Mol Biol Evol. 2015;32(1):268–74.
61. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference
under mixed models. Bioinformatics. 2003;19(12):1572–4.
62. Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior
Summarization in Bayesian Phylogenetics Using Tracer 1.7. Syst Biol.
2018;67(5):901–4.
63. Dong SS, Liu M, Liu Y, Chen F, Yang T, Chen L, Zhang XT, Guo X, Fang DM,
Li LZ, et al. The genome of Magnolia biondii Pamp. provides insights into
the evolution of Magnoliales and biosynthesis of terpenoids. Hortic Res.
2021;8(1):38.
64. Rice DW, Alverson AJ, Richardson AO, Young GJ, Sanchez-Puerta
MV, Munzinger J, Barry K, Boore JL, et al. Horizontal transfer of entire
genomes via mitochondrial fusion in the angiosperm Amborella. Science.
2013;342:1468–73.
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
Page 18 of 18
Yangetal. BMC Plant Biology (2024) 24:616
65. Guo WH, Grewe F, Fan WS, Young GJ, Knoop V, Palmer JD, Mower JP.
Ginkgo and Welwitschia mitogenomes reveal extreme contrasts in gym-
nosperm mitochondrial evolution. Mol Biol Evol. 2016;33(6):1448–60.
66. Gualberto JM, Newton KJ. Plant mitochondrial genomes: dynamics and
mechanisms of mutation. Annu Rev Plant Biol. 2017;68:225–52.
67. Woloszynska M, Bocer T, Mackiewicz P, Janska H. A fragment of chloro-
plast DNA was transferred horizontally, probably from non-eudicots, to
mitochondrial genome of Phaseolus. Plant Mol Biol. 2004;56(5):811–20.
68. Siqueira G, Brito KL, Dias U, Dias Z. Heuristics for genome rearrangement
distance with replicated genes. IEEE/ACM Trans Comput Biol Bioinform.
2021;18(6):2094–108.
69. Mao M, Gibson T, Dowton M. Evolutionary dynamics of the mitochondrial
genome in the evaniomorpha (hymenoptera)-a group with an intermedi-
ate rate of gene rearrangement. Genome Biol Evol. 2014;6(7):1862–74.
70. Zhang Y, Gong L, Lu XT, Miao ZL, Jiang LH, Liu BJ, Liu LQ, Li PF, Zhang X,
Lü ZM. Comparative mitochondrial genome analysis of Varunidae and its
phylogenetic implications. Acta Oceanol Sin. 2022;41(6):119–31.
71. Du YH, Zou JR, Yin ZQ, Chen TJ. Pan-chromosome and comparative
analysis of Agrobacterium fabrum reveal important traits concerning the
genetic diversity, evolutionary dynamics, and niche adaptation of the
species. Microbiol Spectr. 2023;11(2):e0292422.
72. Ben Moussa H, Pedron J, Hugouvieux-Cotte-Pattat N, Barny MA. Two
species with a peculiar evolution within the genus Pectobacterium
suggest adaptation to a new environmental niche. Environ Microbiol.
2023;25(11):2465–80.
73. Liu BB, Ren C, Kwak M, Hodel RGJ, Xu C, He J, Zhou WB, Huang CH, Ma
H, Qian GZ, et al. Phylogenomic conflict analyses in the apple genus
Malus s.l. reveal widespread hybridization and allopolyploidy driving
diversification, with insights into the complex biogeographic history in
the Northern Hemisphere. J Integr Plant Biol. 2022;64(5):1020–43.
74. Nge FJ, Biffin E, Thiele KR, Waycott M. Reticulate evolution, ancient
Chloroplast Haplotypes, and rapid radiation of the Australian plant genus
Adenanthos (Proteaceae). Front Ecol Evol. 2021;8:616741.
75. Mao Y, Peng TT, Shao F, Zhao QY, Peng ZG. Molecular evolu-
tion of the hemoglobin gene family across vertebrates. Genetica.
2023;151(3):201–13.
76. Kawabe A, Nukii H, Furihata HY. Exploring the history of chloroplast
capture in Arabis using whole chloroplast genome sequencing. Int J Mol
Sci. 2018;19(2):602.
77. Baldwin E, McNair M, Leebens-Mack J. Rampant chloroplast cap-
ture in Sarracenia revealed by plastome phylogeny. Front Plant Sci.
2023;14:1237749.
78. Lin QS, Banerjee A, Stefanovic S. Mitochondrial phylogenomics of Cuscuta
(Convolvulaceae) reveals a potentially functional horizontal gene transfer
from the host. Genome Biol Evol. 2022;14(6):evac091.
79. Filip E, Skuza L. Horizontal gene transfer involving chloroplasts. Int J Mol
Sci. 2021;22(9):4484.
80. Stange M, Barrett RDH, Hendry AP. The importance of genomic
variation for biodiversity, ecosystems and people. Nat Rev Genet.
2021;22(2):89–105.
81. Kuria MW. Evaluation of genetic diversity in Strychnos henningsii selected
from nine populations in Kenya based on RAPD markers. East Afr J Agri
Biotechnol. 2023;6(1):406–21.
82. Chen X, Feng Y, Chen S, Yang K, Wen XY, Sun Y. Species delimitation and
genetic relationship of Castanopsis hainanensis and Castanopsis wenchan-
gensis (Fagaceae). Plants (Basel). 2023;12(20):3544.
83. Born C, Alvarez N, McKey D, Ossari S, Wickings EJ, Hossaert-McKey M,
Chevallier MH. Insights into the biogeographical history of the lower
Guinea forest domain: evidence for the role of refugia in the intraspecific
differentiation of Aucoumea klaineana. Mol Ecol. 2011;20(1):131–42.
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in pub-
lished maps and institutional affiliations.
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
1.
2.
3.
4.
5.
6.
Terms and Conditions
Springer Nature journal content, brought to you courtesy of Springer Nature Customer Service Center GmbH (“Springer Nature”).
Springer Nature supports a reasonable amount of sharing of research papers by authors, subscribers and authorised users (“Users”), for small-
scale personal, non-commercial use provided that all copyright, trade and service marks and other proprietary notices are maintained. By
accessing, sharing, receiving or otherwise using the Springer Nature journal content you agree to these terms of use (“Terms”). For these
purposes, Springer Nature considers academic use (by researchers and students) to be non-commercial.
These Terms are supplementary and will apply in addition to any applicable website terms and conditions, a relevant site licence or a personal
subscription. These Terms will prevail over any conflict or ambiguity with regards to the relevant terms, a site licence or a personal subscription
(to the extent of the conflict or ambiguity only). For Creative Commons-licensed articles, the terms of the Creative Commons license used will
apply.
We collect and use personal data to provide access to the Springer Nature journal content. We may also use these personal data internally within
ResearchGate and Springer Nature and as agreed share it, in an anonymised way, for purposes of tracking, analysis and reporting. We will not
otherwise disclose your personal data outside the ResearchGate or the Springer Nature group of companies unless we have your permission as
detailed in the Privacy Policy.
While Users may use the Springer Nature journal content for small scale, personal non-commercial use, it is important to note that Users may
not:
use such content for the purpose of providing other users with access on a regular or large scale basis or as a means to circumvent access
control;
use such content where to do so would be considered a criminal or statutory offence in any jurisdiction, or gives rise to civil liability, or is
otherwise unlawful;
falsely or misleadingly imply or suggest endorsement, approval , sponsorship, or association unless explicitly agreed to by Springer Nature in
writing;
use bots or other automated methods to access the content or redirect messages
override any security feature or exclusionary protocol; or
share the content in order to create substitute for Springer Nature products or services or a systematic database of Springer Nature journal
content.
In line with the restriction against commercial use, Springer Nature does not permit the creation of a product or service that creates revenue,
royalties, rent or income from our content or its inclusion as part of a paid for service or for other commercial gain. Springer Nature journal
content cannot be used for inter-library loans and librarians may not upload Springer Nature journal content on a large scale into their, or any
other, institutional repository.
These terms of use are reviewed regularly and may be amended at any time. Springer Nature is not obligated to publish any information or
content on this website and may remove it or features or functionality at our sole discretion, at any time with or without notice. Springer Nature
may revoke this licence to you at any time and remove access to any copies of the Springer Nature journal content which have been saved.
To the fullest extent permitted by law, Springer Nature makes no warranties, representations or guarantees to Users, either express or implied
with respect to the Springer nature journal content and all parties disclaim and waive any implied warranties or warranties imposed by law,
including merchantability or fitness for any particular purpose.
Please note that these rights do not automatically extend to content, data or other material published by Springer Nature that may be licensed
from third parties.
If you would like to use or distribute our Springer Nature journal content to a wider audience or on a regular basis or in any other manner not
expressly permitted by these Terms, please contact Springer Nature at
onlineservice@springernature.com
... Mitochondria are maternally inherited organelles that contain genetic information distinct from that of the nucleus. The study of mitochondrial phylogeny can reveal different evolutionary patterns compared to nuclear genome, which is significant for understanding hybridization and incomplete lineage sorting during species evolution [81,82]. The comparison of the mitogenome of V. diffusa with those of 23 species from the same order, along with 2 species from the Zygophyllaceae family as an outgroup, revealed that V. diffusa and species from the Salicaceae family were grouped together. ...
Article
Full-text available
Background Viola diffusa is used in the formulation of various Traditional Chinese Medicines (TCMs), including antiviral, antimicrobial, antitussive, and anti-inflammatory drugs, due to its richness in flavonoids and triterpenoids. The biosynthesis of these compounds is largely mediated by cytochrome P450 enzymes, which are primarily located in the membranes of mitochondria and the endoplasmic reticulum. Results This study presents the complete assembly of the mitogenome and plastome of Viola diffusa. The circular mitogenome spans 474,721 bp with a GC content of 44.17% and encodes 36 unique protein-coding genes, 21 tRNA, and 3 rRNA. Except for the RSCU values of 1 observed for the start codon (AUG) and tryptophan (UGG), the mitochondrial protein-coding genes exhibited a codon usage bias, with most estimates deviating from 1, similar to patterns observed in closely related species. Analysis of repetitive sequences in the mitogenome demonstrated potential homologous recombination mediated by these repeats. Sequence transfer analysis revealed 24 homologous sequences shared between the mitogenome and plastome, including nine full-length genes. Collinearity was observed among Viola diffusa species within the other members of Malpighiales order, indicated by the presence of homologous fragments. The length and arrangement of collinear blocks varied, and the mitogenome exhibited a high frequency of gene rearrangement. Conclusions We present the first complete assembly of the mitogenome and plastome of Viola diffusa, highlighting its implications for pharmacological, evolutionary, and taxonomic studies. Our research underscores the multifaceted importance of comprehensive mitogenome analysis.
Article
Full-text available
Due to cryptic diversification, phenotypic plasticity and host associations, multilocus phy-logenetic analyses have become the most important tool in accurately identifying and circumscribing species in the Diaporthe genus. However, the application of the genealogical concordance criterion has often been overlooked, ultimately leading to an exponential increase in novel Diaporthe spp. Due to the large number of species, many lineages remain poorly understood under the so-called species complexes. For this reason, a robust delimitation of the species boundaries in Diaporthe is still an ongoing challenge. Therefore, the present study aimed to resolve the species boundaries of the Diaporthe arecae species complex (DASC) by implementing an integrative taxonomic approach. The Genealogical Phylogenetic Species Recognition (GCPSR) principle revealed incongruences between the individual gene genealogies. Moreover, the Poisson Tree Processes' (PTPs) coalescent-based species delimitation models identified three well-delimited subclades represented by the species D. arecae, D. chiangmaiensis and D. smilacicola. These results evidence that all species previously described in the D. arecae subclade are conspecific, which is coherent with the morphological indis-tinctiveness observed and the absence of reproductive isolation and barriers to gene flow. Thus, 52 Diaporthe spp. are reduced to synonymy under D. arecae. Recent population expansion and the possibility of incomplete lineage sorting suggested that the D. arecae subclade may be considered as ongoing evolving lineages under active divergence and speciation. Hence, the genetic diversity and intraspecific variability of D. arecae in the context of current global climate change and the role of D. arecae as a pathogen on palm trees and other hosts are also discussed. This study illustrates that species in Diaporthe are highly overestimated, and highlights the relevance of applying an integrative taxonomic approach to accurately circumscribe the species boundaries in the genus Diaporthe.
Article
Full-text available
Castanopsis is one of the most common genus of trees in subtropical evergreen broad-leaved forests and tropical monsoon rainforests in China. Castanopsis hainanensis and Castanopsis wenchangensis are endemic to Hainan Island, but they were once confused as the same species due to very similar morphologies. In this study, nuclear microsatellite markers and chloroplast genomes were used to delimit C. hainanensis and C. wenchangensis. The allelic variations of nuclear microsatellites revealed that C. hainanensis and C. wenchangensis were highly genetically differentiated with very limited gene admixture. Both showed higher genetic diversity within populations and lower genetic diversity among populations, and neither had further population genetic structure. Furthermore, C. wenchangensis and C. hainanensis had very different chloroplast genomes. The independent genetic units, very limited gene admixture, different distribution ranges, and distinct habitats all suggest that C. wenchangensis and C. hainanensis are independent species, thus they should be treated as distinct conservation units.
Article
Full-text available
Introgression can produce novel genetic variation in organisms that hybridize. Sympatric species pairs in the carnivorous plant genus Sarracenia L. frequently hybridize, and all known hybrids are fertile. Despite being a desirable system for studying the evolutionary consequences of hybridization, the extent to which introgression occurs in the genus is limited to a few species in only two field sites. Previous phylogenomic analysis of Sarracenia estimated a highly resolved species tree from 199 nuclear genes, but revealed a plastid genome that is highly discordant with the species tree. Such cytonuclear discordance could be caused by chloroplast introgression (i.e. chloroplast capture) or incomplete lineage sorting (ILS). To better understand the extent to which introgression is occurring in Sarracenia, the chloroplast capture and ILS hypotheses were formally evaluated. Plastomes were assembled de-novo from sequencing reads generated from 17 individuals in addition to reads obtained from the previous study. Assemblies of 14 whole plastomes were generated and annotated, and the remaining fragmented assemblies were scaffolded to these whole-plastome assemblies. Coding sequence from 79 homologous genes were aligned and concatenated for maximum-likelihood phylogeny estimation. The plastome tree is extremely discordant with the published species tree. Plastome trees were simulated under the coalescent and tree distance from the species tree was calculated to generate a null distribution of discordance that is expected under ILS alone. A t-test rejected the null hypothesis that ILS could cause the level of discordance seen in the plastome tree, suggesting that chloroplast capture must be invoked to explain the discordance. Due to the extreme level of discordance in the plastome tree, it is likely that chloroplast capture has been common in the evolutionary history of Sarracenia.
Article
Full-text available
Pereskia aculeata is a potential new crop species that has both food and medicinal (antinociceptive activity) properties. However, comprehensive genomic research on P. aculeata is still lacking, particularly concerning its organelle genome. In this study, P. aculeata was studied to sequence the mitochondrial genome (mitogenome) and to ascertain the assembly, informational content, and developmental expression of the mitogenome. The findings revealed that the mitogenome of P. aculeata is circular and measures 515,187 bp in length with a GC content of 44.05%. It contains 52 unique genes, including 33 protein-coding genes, 19 tRNA genes, and three rRNA genes. Additionally, the mitogenome analysis identified 165 SSRs, primarily consisting of tetra-nucleotides, and 421 pairs of dispersed repeats with lengths greater than or equal to 30, which were mainly forward repeats. Based on long reads and PCR experiments, we confirmed that two pairs of long-fragment repetitive elements were highly involved with the mitogenome recombination process. Furthermore, there were 38 homologous fragments detected between the mitogenome and chloroplast genome, and the longest fragment was 3962 bp. This is the first report on the mitogenome in the family Cactaceae. The decoding of the mitogenome of P. aculeata will provide important genetic materials for phylogenetic studies of Cactaceae and promote the utilization of species germplasm resources.
Article
Full-text available
Adaptation to various altitudes and oxygen levels is a major aspect of vertebrate evolution. Hemoglobin is an erythrocyte protein belonging to the globin superfamily, and the α-, β-globin genes of jawed vertebrates encode tetrameric ((α2β2) hemoglobin, which contributes to aerobic metabolism by delivering oxygen from the respiratory exchange surfaces into cells. However, there are various gaps in knowledge regarding hemoglobin gene evolution, including patterns in cartilaginous fish and the roles of gene conversion in various taxa. Hence, we evaluated the evolutionary history of the vertebrate hemoglobin gene family by analyses of 97 species representing all classes of vertebrates. By genome-wide analyses, we extracted 879 hemoglobin sequences. Members of the hemoglobin gene family were conserved in birds and reptiles but variable in mammals, amphibians, and teleosts. Gene motifs, structures, and synteny were relatively well-conserved among vertebrates. Our results revealed that purifying selection contributed substantially to the evolution of all vertebrate hemoglobin genes, with mean dN/dS (ω) values ranging from 0.057 in teleosts to 0.359 in reptiles. In general, after the fish-specific genome duplication, the teleost hemoglobin genes showed variation in rates of evolution, and the β-globin genes showed relatively high ω values after a gene transposition event in amniotes. We also observed that the frequency of gene conversion was high in amniotes, with fewer hemoglobin genes and higher rates of evolution. Collectively, our findings provide detail insight into complex evolutionary processes shaping the vertebrate hemoglobin gene family, involving gene duplication, gene loss, purifying selection, and gene conversion.
Article
The biogeographical history of many lineages within the Lauraceae remains poorly known because of the difficulty of assigning macrofossils to living genera, poor pollen preservation, and the absence of sufficiently resolved or well-supported phylogenies. Here, we utilize plastid genome sequencing to reinvestigate the phylogenetic and biogeographic history of trees in the tribe Cryptocaryeae, an important component of broad-leaved forests worldwide, with around 800 species that rely on vertebrate frugivores to disperse their seeds. A new time-calibrated phylogeny with high support for 176 species was used to infer the biogeographic history and speciation rates based on inferences of BAMM analyses. A monophyletic Cryptocaryeae with Aspidostemon, Beilschmiedia, Cryptocarya, Dahlgrenodendron, and Eusideroxylon clades was confirmed. The five clades of Cryptocaryeae were estimated to share a common ancestor in tropical Africa or Asia in the Early Cretaceous around 123 Ma. The Beilschmiedia and Cryptocarya clades were estimated to have originated in South America around 66 Ma. Extant subclades of the Beilschmiedia clade could colonize Australia by 35 Ma and extant subclades of the Cryptocarya clade could colonize Australia by 42 Ma. Diversification rates of the Beilschmiedia clade accelerated 14 and 12 Ma after its origin and diversification rates of the Cryptocarya clade accelerated 18 Ma after its origin. Over 45% extant Cryptocaryeae species originated in the three periods of accelerated differentiation in the Miocene of Asia and Australia. Long-distance dispersal has had a major influence on biogeography, with dispersal to Asia likely occurring seven times, Zealandia six times, America three times, Australia three times, Africa twice, and Oceania at least once. Over 70% extant Cryptocaryeae species which diverged before the Quaternary grow in the Southern Hemisphere, while 90% extant Cryptocaryeae species which diverged in the Quaternary grow in the Northern Hemisphere. The Cryptocaryeae originated in and diversified with the first angiosperm-dominated broad-leaved evergreen forests, from the Cretaceous to the Paleogene. Long-distance seed dispersal, probably by birds, although possibly also by flotation, has allowed the tribe to track these forests in space and time, despite a failure to adapt to cold, dry, or highly seasonal environments.
Article
Strychnos henningsii is a traditional medicinal plant distributed throughout the tropical and subtropical areas. It belongs to the family Strychnaceae but formally in the family Loganiaceae. In order to understand the genetic variation across the populations and geographical regions of this plant, RAPD markers were used to assess the genetic diversity in nine populations of this species in Kenya. Two hundred and seventy samples were randomly selected from the nine populations, each comprising thirty individuals. The genetic variation within and among populations was evaluated using RAPD Primers. RAPD markers detected an average of 38.97% polymorphism in all populations studied. The most polymorphic population revealed was Kitui with 75 (55.15 %) polymorphic loci, while Baringo was the least polymorphic population with 25 (25.74%) polymorphic loci detected. The markers also revealed twenty-five specific population loci, which could be responsible for specific population traits. A higher molecular variance was revealed among the population (54%; p<0.001) than within populations 46%; p<0.001). According to Nei’s unbiased genetic matrix, the most genetically close populations were Taita-Taveta and Kitui with the highest genetic identity of 0.955, while Ngong and Baringo populations were the most genetically distant populations with a genetic identity of 0.836. Clustering analysis grouped the nine populations into two groups. Cluster I comprised Kitui, Taveta, Karura, Marsabit, Ngong, Nyeri and Narok. Cluster II consisted of Jirore and Baringo. These results were supported by the principal Coordinate Analysis. However, the clustering analysis did not correlate to the geographical areas of plant collection. The values for genetic diversity (H) and Shannon index (I) obtained from this study ranged from 0.0867-0.1483 and 0.1289 -0.2337, respectively, indicating that a low genetic diversity exists among the S. henningsii genotypes. It is recommended that all existing populations be conserved and further studied conducted using codominance markers to provide more insight into the genetic variation that exists within and among S. henningsii genotypes
Article
Historically, research on Soft Rot Pectobacteriacea (SRP) has focused on economically important crops and ornamentals and knowledge of these bacteria outside the plant context remains poorly investigated. Recently, two closely related species Pectobacterium aquaticum and Pectobacterium quasiaquaticum were isolated from water and have not been isolated from any plant yet. To identify the distinctive characteristics of these two species, we performed a comparative genomic analysis of 80 genomes representing 19 Pectobacterium species and performed an evolutionary reconstruction. Both water species underwent a reduction in genome size associated with a high pseudogene content. A high gene loss was predicted at the emergence of both species. Among the 199 gene families missing from both P. aquaticum and P. quasiaquaticum genomes but present in at least 80% of other Pectobacterium genomes, COG analysis identified many genes involved in nutrient transport systems. In addition, many type II secreted proteins were also missing in both species. Phenotypic analysis revealed that both species had reduced pectinolytic activity, a biofilm formation defect, were highly motile and had reduced virulence on several plants. These genomic and phenotypic data suggest that the ecological niche of P. aquaticum and P. quasiaquaticum may differ from that of other Pectobacterium species.