The complete chloroplast genome sequence of Illigera celebica

Abstract

Illigera celebica is an evergreen woody vine that belongs to genus Illigera Bl in the family Hernandiaceae and has medicinal value. The complete chloroplast genome of I. celebica was sequenced to determine its phylogenetic location with respect to the other species under the Laurales. Its whole chloroplast genome is 156,123 bp in length, and comprises a large single-copy region (LSC, 84,913 bp), a small single-copy region (SSC,18,775 bp), and a pair of inverted repeats (IRs, 26,217 bp). The overall GC content is 39.2% (LSC, 37.8%; SSC, 33.9%; IR, 43.4%). Maximum likelihood phylogenetic analysise (TVM + F + R2 model) was conducted using 15 complete chloroplast genomes of Laurales, and the results confirmed that Hernandia nymphaeifolia and Wilkiea huegeliana were located in the same lineage.

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MITOGENOME ANNOUNCEMENT
The complete chloroplast genome sequence of Illigera celebica
Yaxuan Xin
a,b
, Jing Xin
a,b
, Guoqiong Yao
a,b
, Yaya Qu
a,b
, Fayu Feng
a,b
, Yu Song
c
and Zhenghai Sun
a,b
a
South and Southeast Asia Joint R&D Center of Economic Forest Full Industry Chain of Yunnan Province, Southwest Forestry University,
Kunming, PR China;
b
International Technologial Cooperation Base of High Effective Economic Forestry cultivating of Yunnan Province,
Southwest Forestry University, Kunming, PR China;
c
Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese
Academy of Sciences, Jinghong, PR China
ABSTRACT
Illigera celebica is an evergreen woody vine that belongs to genus Illigera Bl in the family
Hernandiaceae and has medicinal value. The complete chloroplast genome of I. celebica was sequenced
to determine its phylogenetic location with respect to the other species under the Laurales. Its whole
chloroplast genome is 156,123 bp in length, and comprises a large single-copy region (LSC, 84,913 bp),
a small single-copy region (SSC,18,775bp), and a pair of inverted repeats (IRs, 26,217bp). The overall
GC content is 39.2% (LSC, 37.8%; SSC, 33.9%; IR, 43.4%). Maximum likelihood phylogenetic analysise
(TVM þFþR2 model) was conducted using 15 complete chloroplast genomes of Laurales, and the
results confirmed that Hernandia nymphaeifolia and Wilkiea huegeliana were located in the
same lineage.
ARTICLE HISTORY
Received 23 May 2020
Accepted 30 May 2020
KEYWORDS
Illigera; genome;
phylogenetic relationship
Illigera celebica is a kind of evergreen woody vine that
belongs to genus Illigera Bl in the family Hernandiaceae.
I. celebica is widely distributed in Yunnan, Guangxi, and
Guangdong provinces (Chinese Flora Editorial Board, Chinese
Academy of Sciences 1982) of south China, and in other
countries, such as Vietnam, Thailand, and Cambodia (http://
foc.iplant.cn/). The root and stem of I. celebica can dispel
wind, dehumidify, and relieve pain (Huang 1985; Gao 2007).
At present, genus Illigera has no clear phylogenetic system.
Therefore, the complete chloroplast genome of I. celebica
was obtained by high-throughput sequencing to reconstruct
a phylogenetic tree to better understand the relationships of
I. celebica and other Laurales species.
The healthy young leaves of I. celebica were freshly picked
from Xishuangbanna Tropical Botanical Garden (XTBG) in
Yunnan, China (101.2713E longitude, 21.9170N latitude;
540 m). DNA was extracted using modified CTBA method (Cai
et al. 2014) and the specimens were stored in XTBG’s
Biodiversity Research Group (Registry No. SWFU-SY36764).
The whole chloroplast genome was sequenced according to
the method of Yang et al. (2014). The whole nine pairs of
universal primers were sequenced by remote polymerase
chain reaction for next-generation sequencing. The publicly
available chloroplast genome of Eusideroxylon zwageri
(Accession No.MF939351) was used as reference. The chloro-
plast genome of I. celebica was assembled using the
GetOrganelle software (Jin et al. 2018) and annotated
through the Geneious 8.1.3 software (Biomatters Ltd.,
Auckland, New Zealand).
The chloroplast genome of I. celebica (LAU00199) with a
length of 156,123bp, which is 1,639 and 1,454 bp smaller
than those of Hernandia nymphaeifolia (157,762 bp,
MG838431) and E. zwageri (157,577 bp, MF939351). It was
also 22,963 bp large than that of Wilkiea huegeliana
(133,160 bp, KT716505). The results showed that the com-
plete genome of I. celebica is composed of a large single-
copy region (LSC, 84,913 bp), a small single-copy region (SSC,
18,775 bp), and a pair of inverted repeats (IRs, 26,217 bp). The
overall GC content is 39.2% (LSC, 37.8%; SSC, 33.9%; IR,
43.4%). The chloroplast genome of I. celebica contains 112
unique genes, which are composed of 76 protein-coding
genes, 8 are rRNA genes, and 37 tRNA genes.
The evolutionary relationship between I. celebica and
other Laurales species was determined based on the com-
plete sequence of the chloroplast genome of I. celebica and
the reconstruction of a phylogenetic tree from the thirteen
published chloroplast genomes of family Lauraceae
(Figure 1). In addition, Liriodendron chinense (Accession
Number: KU170538) was treated as an outgroup. A max-
imum-likelihood (ML) analysis based on the TVM þFþR2
model was performed with iqtree version 1.6.7 program
using 1000 bootstrap replicates (Nguyen et al. 2015). The
CONTACT Zhenghai Sun sunzhenghai1978@163.com South and Southeast Asia Joint R&D Center of Economic Forest Full Industry Chain of Yunnan
Province, Southwest Forestry University, Kunming, PR China; International Technologial Cooperation Base of High Effective Economic Forestry cultivating of
Yunnan Province, Southwest Forestry University, Kunming, PR China
ß2020 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
2020, VOL. 5, NO. 3, 2454–2455
https://doi.org/10.1080/23802359.2020.1778562

ML phylogenetic tree of Liriodendron chinense showed
100% bootstrap values at each node, confirmed that
H. nymphaeifolia and Wilkiea huegeliana belong to the same
lineage (Song et al. 2019).
Disclosure statement
The authors report no conflict of interest.
Funding
This research was supported by the Construction Project of Doctor
Station of Forestry First-level Discipline in Yunnan Province.
Data availability statement
The chloroplast data of the I. celebica will be submitted to Laurales
Chloroplast Genome Database (https://lcgdb.wordpress.com). Accession
numbers are LAU00199.
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. 1982. Flora
of China. Vol. 31. J B Sci Press(China); p. 476.
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 Clinic. 22(4):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. 2018. GetOrganelle: a simple
and fast pipeline for de novo assemble of a complete circular chloro-
plast genome using genome skimming data. bioRxiv. 256479. doi:10.
1101/256479.
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. 2019.
Plastid phylogenmics improve phylogenetic resolution in the
Lauraceae. J Sytemat Evol. doi:10.1111/jse.12536.
Yang JB, Li DZ, Li HT. 2014. Highly effective sequencing whole chloro-
plast genomes of angiosperms by nine novel universal primer pairs.
Mol Ecol Resour. 14(5):1024–1031.
Figure 1. The ML phylogenetic tree for I. celebica based on other 14 species (two in Cryptocarya, two in Endiandra, one in Eusideroxylon, one in Hernandia, one in
Wilkiea, three in Calycanthus, two in Chimonanthus, and one in Idiospermum) chloroplast genomes.
MITOCHONDRIAL DNA PART B 2455