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The complete chloroplast genome of the endangered tree Parashorea chinensis (Dipterocarpaceae)

Mitochondrial DNA Part B

March 2019
4(1):1163-1164

DOI:10.1080/23802359.2019.1591236

License
CC BY-NC 4.0

Authors:

Yongshuai Sun

Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences

The complete chloroplast genome sequence of Parashorea chinensis, an endangered large tree species in the northern edge of tropical Asia, is determined in this study. The total genome size is 152,002 bp, containing a large single copy (LSC) region (84,094 bp) and a small single copy region (20,003), which were separated by two inverted repeat (IRs) regions (23,954 bp). The overall GC contents of the plastid genome were 37.1%. In total, 116 unique genes were annotated and they consisted of 81 protein-coding genes, 31 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 20 chloroplast genomes indicates that P. chinensis is closely related to P. macrophylla.

ML phylogenetic tree of the 18 Malvales based on the available chloroplast genome sequences in GenBank, and the chloroplast sequence of Parashorea chinensis. The tree is rooted with the Brassicales (Arabidopsis thaliana and Carica papaya). Bootstraps (10,000 replicates) are shown at the nodes.

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MITOGENOME ANNOUNCEMENT

The complete chloroplast genome of the endangered tree Parashorea chinensis

(Dipterocarpaceae)

Xing-Fu Zhu and Yongshuai Sun

CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China

ABSTRACT

The complete chloroplast genome sequence of Parashorea chinensis, an endangered large tree species

in the northern edge of tropical Asia, is determined in this study. The total genome size is 152,002bp,

containing a large single copy (LSC) region (84,094 bp) and a small single copy region (20,003), which

were separated by two inverted repeat (IRs) regions (23,954bp). The overall GC contents of the plastid

genome were 37.1%. In total, 116 unique genes were annotated and they consisted of 81 protein-cod-

ing genes, 31 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 20 chloroplast

genomes indicates that P. chinensis is closely related to P. macrophylla.

ARTICLE HISTORY

Received 25 January 2019

Accepted 2 March 2019

KEYWORDS

Chloroplast; Parashorea

chinensis; phylogen-

etic analysis

Parashorea chinensis is a large tree species (up to 80 m tall)

in the family Dipterocarpaceae. It is found in southern China

and in northern Vietnam. It has been overexploited and now

is threatened by habitat loss (Li et al. 2007). The plant is clas-

sified as endangered in the IUCN Red List of Threatened

Species (Qin et al. 2017). Consequently, the genetic and gen-

omic information is urgently needed to promote its system-

atics research and the development of conservation value of

P. chinensis. Here, we made the first report of a complete

plastome for P. chinensis (GenBank accession num-

ber: MK424049).

The total genomic DNA was extracted from dry leaves col-

lected from Ningming (Guangxi, China, E107.0981,

N22.2456) and Voucher herbarium specimens were depos-

ited at the Herbarium of Xishuangbanna Tropical Botanical

Garden. Genomic DNA was extracted from the fresh leaves

using the modified CTAB method (Doyle and Doyle 1987).

Total DNA was used for the shotgun library construction.

After cluster generation, libraries were sequenced on an

Illumina Hiseq 4000 platform and 150 bp paired-end reads

were generated. The filtered reads were assembled using the

program GetOrganelle v1.5 (Jin et al. 2018) with the refer-

ence chloroplast genome of P. macrophylla (GenBank acces-

sion number: MH791330.1), annotated by Dual Organellar

GenoMe Annotator (DOGMA; Wyman et al. 2004) and GeSeq

(Tillich et al. 2017).

The complete chloroplast genome of P. chinensis is

152,002 base pairs (bp) in length and contains two inverted

repeat (IRa and IRb) regions of 23,954 bp, which was

separated by a large single-copy (LSC) region of 84,094 bp

and a small single-copy (SSC) region of 20,003 bp. The

overall GC contents of the plastid genome were 37.1%.

The new sequence possesses total 116 genes, including

four ribosomal RNA genes, 31 tRNA genes, and 81 protein-

coding genes. In these genes, six tRNA genes (i.e. trnE-

UUC, trnA-UGC, trnL-UAA, trnS-CGA, trnV-UAC, and trnY-

AUA) and seven protein-coding genes (clpP, ndhA, ndhB,

rpl2, rps16, rpoC1 and ycf1) contained one intron, and the

ycf3 gene have two introns. Most of the genes occurred as

a single copy, whereas four rRNA genes (i.e. 4.5S, 5S, 16S,

and 23S rRNA), seven tRNA genes (i.e. trnA-UGC, trnE-UUC,

trnL-CAA, trnM-CAU, trnN-GUU, trnR-ACG, and trnV-GAC)

and six protein-coding genes (i.e. rpl2, rpl23, ycf2, ndhB,

rps7, and rps12) occur in double.

To understand the phylogenetic position of Parashorea

within the order Malvales, we downloaded the complete

chloroplast genomes of 19 species from the NCBI GenBank

database, including 17 species in Malvales and two species in

Brassicales. The sequences were aligned using MAFFT v7.307

(Katoh and Standley 2013), and RAxML (Stamatakis 2014) was

used to construct a maximum likelihood tree with

Arabidopsis thaliana and Carica papaya as outgroups. All

nodes in the complete plastome trees were strongly sup-

ported. The phylogenetic tree showed that P. chinensis was

closely related to P. macrophylla (Figure 1). This published

P. chinensis chloroplast genome will provide useful informa-

tion for phylogenetic and evolutionary studies in

Dipterocarpaceae and Malvales.

CONTACT Yongshuai Sun sunyongshuai@xtbg.ac.cn CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese

Academy of Sciences, Mengla 666303, China

ß2019 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-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits

unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

MITOCHONDRIAL DNA PART B

2019, VOL. 4, NO. 1, 1163–1164

https://doi.org/10.1080/23802359.2019.1591236

Disclosure statement

No potential conflict of interest was reported by the authors.

Funding

This research was supported by the National Natural Science Foundation

of China (no. 31500194).

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Figure 1. ML phylogenetic tree of the 18 Malvales based on the available chloroplast genome sequences in GenBank, and the chloroplast sequence of Parashorea

chinensis. The tree is rooted with the Brassicales (Arabidopsis thaliana and Carica papaya). Bootstraps (10,000 replicates) are shown at the nodes.

1164 X.-F. ZHU AND Y. SUN

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Article

Nov 1986
PHYTOCHEMISTRY

Automatic annotation of organellar genomes with DOGMA

Article

Dec 2004

GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data

Jan 2018

Yang J-B Song
Y Yi
T-S Li

Jin J-J, Yu W-B, Yang J-B, Song Y, Yi T-S, Li D-Z. 2018. GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data. bioRxiv. 256479.