The complete plastome sequence of Illigera grandiflora

Abstract

Illigera grandiflora, a kind of traditional medicinal liana, belongs to the Illigera Blume of the Hernandiaceae. In this study, we reported the characteristics of complete plastome for I. grandiflora. Its total plastome was 156,138 bp in length, comprising a large single-copy region(LSC) of 84,931 bp, a small single-copy region (SSC) of 18,544 bp, and a pair of inverted repeat (IR) regions of 26,549 bp. The overall GC content was 39.16% (LSC, 37.77%; SSC, 33.89%; IR, 43.21%). The plastome encoded 134 genes, including 83 protein-coding genes, 42 transfer RNA genes, and 10 ribosomal RNA genes. The relationships in our phylogeny showed that the two Illigera species are located in the same clade, with Hernandia nymphaeifolia being the next sister group, followed by Wilkiea huegeliana.

Full text

RAPID COMMUNICATION
The complete plastome sequence of Illigera grandiflora
Yaya Qu
a,b,c
, Linyi Yang
a,b,c
, Zhenghai Sun
a,b,c
, Luyao Ma
a,b,c
, Jing Xin
a,b,c
, Yu Song
d
and Peiyao Xin
a,b,c
a
Southwest Research Center for Landscape Architecture Engineering, State Forestry and Grassland Administration, Southwest Forestry
University, Kunming, PR China;
b
Yunnan Province South and Southeast Asia Joint R&D Center of Economic Forest Full Industry Chain,
Southwest Forestry University, Kunming, PR China;
c
Key Laboratory of Forest Resources Conservation and Utilization in the Southwest
Mountains of Ministry of Education, Southwest Forestry University, Kunming, PR China;
d
Center for Integrative Conservation, Xishuangbanna
Tropical Botanical Garden, Chinese Academy of Sciences, Jinghong, PR China
ABSTRACT
Illigera grandiflora, a kind of traditional medicinal liana, belongs to the Illigera Blume of the
Hernandiaceae. In this study, we reported the characteristics of complete plastome for I. grandiflora. Its
total plastome was 156,138 bp in length, comprising a large single-copy region(LSC) of 84,931 bp, a
small single-copy region (SSC) of 18,544bp, and a pair of inverted repeat (IR) regions of 26,549bp. The
overall GC content was 39.16% (LSC, 37.77%; SSC, 33.89%; IR, 43.21%). The plastome encoded 134
genes, including 83 protein-coding genes, 42 transfer RNA genes, and 10 ribosomal RNA genes. The
relationships in our phylogeny showed that the two Illigera species are located in the same clade, with
Hernandia nymphaeifolia being the next sister group, followed by Wilkiea huegeliana.
ARTICLE HISTORY
Received 29 January 2021
Accepted 26 June 2021
KEYWORDS
Illigera; plastome;
phylogenetic relationship
Illigera grandiflora W.W.Sm. & Jeffrey, an evergreen liana with
2–6 m tall, inhabits forests at an altitude of 800–2100 m and
is widely distributed in India, north Myanmar, and southwest-
ern China (Chinese Flora Editorial Board, Chinese Academy of
Sciences 2008). The root and stem of I. grandiflora was used
to treat dropsy and traumatic injury (Gao 2007; Huang 1985),
and previous studies have revealed the major chemical com-
ponents of the plants of the genus Illigera Blume are alka-
loids and terpenoids. Li et al. (2019) have isolated a new
dibenzopyrrocoline alkaloid, together with five known ones
from I. grandiflora, three of them exhibited the moderate
inhibitory activity against acetylcholinesterase (AChE) or
butyrylcholinesterase (BChe), it has showed great medical
potential. But there are few studies of I. grandiflora on gen-
omic at present. Recent studies (Xin et al. 2020) have finished
the complete chloroplast genomes sequencing of Illigera cel-
ebica (LAU199). In order to compare the chloroplast differen-
ces among different species and to better understand its
phylogenetic relationships between them and other Laurales
species, we reported the characteristics of complete plastome
for I. grandiflora, and then reconstructed a phylogenetic tree.
Fresh leaves of I. grandiflora were collected from
Cangyuan Wa Autonomous County, Yunnan, China: (23.2N,
99.4E) for genomic DNA extraction using modified CTBA
method (Cai et al. 2014), and was then sequenced by
Illumina Hiseq 2000 platform at BGI-Shenzhen. A specimen
was deposited at XTBG’s Biodiversity Research Group (contact
Song-Yu, songyu@xtbg.ac.cn) under the voucher number
SY5852. Aligning, assembly (reference sequences are
LAU00199 and MN990581), and annotation were conducted
by MAFFT v.7 online program (https://mafft.cbrc.jp/align-
ment/server/) (Katoh and Standley 2013), GetOrganelle soft-
ware (Jin et al. 2018), and Geneious R8.1.3 (Kearse et al.
2012) respectively. The plastid genome phylogenetic relation-
ships were reconstructed based on a maximum-likelihood
(ML) analysis with the GTR þFþR2 model by iqtree version
1.6.7.1 program using 1000 bootstrap replicates (Nguyen
et al. 2015).
The plastome of I. grandiflora (MW755975) is a circular
DNA molecule with a length of 156,138 bp, which is 15 bp
larger than Illigera celebiea (LAU00199). The complete plas-
tome contains a large singlecopy region (LSC, 84,931 bp), a
small single-copy region (SSC, 18,544 bp), and a pair of
inverted repeats (IRs, 26,549 bp). The overall GC content is
39.16%, the corresponding values of the LSC, SSC,and IR
regions are 37.77%, 33.89%, and 43.21% respectively. The
plastome encoded a set of 120 genes, of which 76 are pro-
tein-coding genes, 36 are transfer RNA genes, and 8 are
rRNA genes.
The ML tree was built on complete plasomes of 22 related
species, Liriodendron chinense (KU170538) was treated as the
out-group (Figure 1). The phylogenetic tree was divided into
CONTACT Peiyao Xin xpytgyx@163.com Southwest Research Center for Landscape Architecture Engineering, State Forestry and Grassland Administration,
Southwest Forestry University, Kunming, PR China; Yunnan Province South and Southeast Asia Joint R&D Center of Economic Forest Full Industry Chain,
Southwest Forestry University, Kunming, PR China; Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of Ministry of
Education, Southwest Forestry University, Kunming, PR China
ß2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited.
MITOCHONDRIAL DNA PART B
2021, VOL. 6, NO. 8, 2406–2407
https://doi.org/10.1080/23802359.2021.1951625

three mian clades corresponding to four families:
Hernandiaceae, Monimiaceae, Lauraceae, and Calycanthaceae.
Most relationships had high internal support. Phylogenetic
analysis based on all plastomes supported that sisterhood of
I. grandiflora and I. celebiea, with H. nymphaeifolia
(MG838431) being the next sister group, followed by W.
huegeliana (KT716505). In addition, we reconfirmed the
sisterhood of Lauraceae and a clade containing
Hernandiaceae and Monimiaceae (Song et al. 2020).
Disclosure statement
No potential conflict of interest was reported by the author(s).
Funding
This research was supported by the Key Research and Development
Program of Yunnan Provincial Science and Technology Planning
Project [2018BB005].
Data availability statement
The genome sequence data that support the findings of this study are
openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/)
under the accession no. MW755975. The associated BioProject, SRA, and
Bio-Sample numbers are PRJNA715651, SAMN18388833, and
SRR14018806, respectively.
References
Cai WJ, Xu DB, Lan X, Xie HH, Wei JG. 2014. A new method for the
extraction of fungal genomic DNA. Agric Res Appl. 152:1–5.
Chinese Flora Editorial Board, Chinese Academy of Sciences. 2008. Flora
of China. Vol. 7. J B Sci Press(Beijing); p. 1153–1926.
Gao Z. 2007. It is made up of plant extracts such as Sinomenium spp.,
Aconitum carmichaeli Debx. and Paeonia lactiflora Pall to treat arthritis
and pain. Drugs Clin. 22 (04):181–182.
Huang X. 1985. A new species and medicinal plant of the same genus
from Illigera BI of Guangxi. Guihaia. 5(1):17–20.
Jin JJ, Yu WB, Yang JB, Song Y, Yi TS, Li DZ. dePamphilis CW, Yi TS, Li
DZ. 2020. GetOrganelle: a fast and versatile toolkit for accurate
de novo assembly of organelle genomes. Genome Biology. 21(1):241.
Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment soft-
ware version 7: improvements in performance and usability. Mol Biol
Evol. 30(4):772–780.
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton
S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious Basic: an inte-
grated and extendable desktop software platform for the organization
and analysis of sequence data. Bioinformatics. 28(12):1647–1649.
Li XJ, Dong JW, Gan D, Zhou DJ, Cai XY, Cai L, Ding ZT. 2019.
(-)-Grandiflorimine, a new dibenzopyrrocoline alkaloid with cholin-
esterase inhibitory activity from Illigera grandiflora. Nat Prod Res.
35(5):763–769.
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast
and effective stochastic algorithm for estimating maximum-likelihood
phylogenies. Mol Biol Evol. 32(1):268–274.
Song Y, Yu WB, Tan YH, Jin JJ, Wang B, Yang JB, Liu B, Corlett RT. 2020.
Plastid phylogenmics improve phylogenetic resolution in the
Lauraceae. J Syst Evol. 58(4):423–439.
Xin YX, Xin J, Yao GQ, Qu YY, Feng FY, Song Y, Sun ZH. 2020. The com-
plete chloroplast genome sequence of Illigera celebica. Mitochondrial
DNA B Resour. 5(3):2454–2455.
Figure 1. The ML phylogenetic tree for I. grandiflora based on other 21 species (11 in Lauraceae, 2 in Hernandiaceae, 1 in Monimiaceae, 6 in Calycanthaceae, and 1
in Magnoliaceae) plastid genomes; the complete plastome sequences were from Lauraceae Chloroplast Genome Database (https://lcgdb.wordpress.com/) (13 spe-
cies those numbers ending with LAU) and NCBI (other 9 species).
MITOCHONDRIAL DNA PART B 2407