极小种群濒危植物广西火桐、丹霞梧桐的叶绿体基因组特征

doi:10.17520/biods.2020263

生物多样性 ›› 2021, Vol. 29 ›› Issue (5): 586-595. DOI: 10.17520/biods.2020263

• 研究报告: 植物多样性 • 上一篇下一篇

极小种群濒危植物广西火桐、丹霞梧桐的叶绿体基因组特征

陆奇丰¹, 黄至欢², 骆文华¹^,^*()

1.广西壮族自治区中国科学院广西植物研究所, 广西桂林 541006
2.南华大学建筑学院, 湖南衡阳 421001

收稿日期:2020-06-30 接受日期:2020-09-10 出版日期:2021-05-20 发布日期:2021-02-01
通讯作者: 骆文华
作者简介:* E-mail: luowenhua2004@163.com
基金资助:
国家自然科学基金(31960083);国家自然科学基金(31700196);国家科技基础资源调查专项(2017FY100100)

Characterization of complete chloroplast genome in Firmiana kwangsiensis and F. danxiaensis with extremely small populations

Qifeng Lu¹, Zhihuan Huang², Wenhua Luo¹^,^*()

1 Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, Guangxi 541006
2 School of Architecture, University of South China, Hengyang, Hunan 421001

Received:2020-06-30 Accepted:2020-09-10 Online:2021-05-20 Published:2021-02-01
Contact: Wenhua Luo

摘要/Abstract

摘要：

广西火桐(Firmiana kwangsiensis)和丹霞梧桐(F. danxiaensis)是我国南方特有物种, 其分布范围狭窄, 种群数量少。为了解其叶绿体基因组结构及系统发生关系, 本文通过高通量测序方法获得广西火桐和丹霞梧桐的浅层基因组数据, 通过生物信息学方法对叶绿体全基因组进行组装, 并对其结构特征进行分析。结果表明: 广西火桐和丹霞梧桐的叶绿体基因组大小分别为160,836 bp和161,253 bp, 具有典型被子植物叶绿体基因组环状四分体结构, 包含长度分别为89,700 bp、90,142 bp的大单拷贝区(large single copy, LSC), 长度分别为19,970 bp、20,067 bp的小单拷贝区(small single copy, SSC)及长度分别为25,583 bp、25,522 bp的2个反向重复序列区(inverted repeat sequence, IR)。两个物种的叶绿体基因组共注释得到131个基因, 包括86个蛋白编码基因、37个tRNA基因和8个rRNA基因。广西火桐的叶绿体基因组中共检测出26个正向重复序列、2个反向重复序列、21个回文重复序列、21个串联重复序列和98个简单重复序列; 丹霞梧桐叶绿体基因组中共检测出23个正向重复序列、5个反向重复序列、21个回文重复序列、30个串联重复序列和107个简单重复序列。系统发生分析结果表明5种梧桐属(Firmiana)植物构成两个强烈支持的分支(支持率100%), 一个分支为广西火桐、美丽火桐(F. pulcherrima)和火桐(F. colorata), 其中广西火桐与美丽火桐构成姐妹群; 另一分支是互为姐妹群的丹霞梧桐和云南梧桐(F. major)。综上所述, 广西火桐和丹霞梧桐的叶绿体基因组结构、基因排列及重复序列具有较高的相似性, 系统进化树将5种梧桐属物种分为两个分支, 其中广西火桐和美丽火桐最近; 而丹霞梧桐与云南梧桐关系最近。本研究鉴定的SSR位点可为梧桐属物种系统发生、进化关系的研究提供遗传信息。

关键词: 广西火桐, 丹霞梧桐, 叶绿体全基因组, 高通量测序, 重复序列, 系统发生分析

Abstract

Aims: Firmiana kwangsiensis and F. danxiaensis are endemic plant species with narrow distribution and small population in southern China, which have important ecological and economic value. However, our knowledge of the chloroplast genome level of F. kwangsiensis and F. danxiaensis are still limited. Also, the phylogenetic relationships among the Firmiana genus remain unclear.
Methods: The genome skimming sequencing data of F. kwangsiensis and F. danxiaensis were obtained by using the high-throughput sequencing, and the complete chloroplast genomes were assembled and then the structures were analyzed by bioinformatics methods.
Results: The results revealed that complete chloroplast genomes of the F. kwangsiensis and F. danxiaensis show a typical quadripartite structure of 160,836 bp and161,253 bp in length, consisting of a large single copy region (89,700 bp and 90,142 bp) and a small single copy region (19,970 bp and20,067 bp) that were separated by a pair of inverted repeat regions (25,583 bp and 25,522 bp each). The annotation results showed that chloroplast genomes of both species contain 131 genes, including 86 protein-coding, 37 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) genes. In F. kwangsiensis, 26 forward repeats, two reverse repeats, 21 palindromic repeats, 23 tandem repeats, and 98 simple sequence repeats were found, and 23 forward repeats, five reverse repeats, 21 palindromic repeats, 30 tandem repeats, and 107 simple sequence repeats were found in F. danxiaensis. Phylogenetic analyses revealed that five Firmiana species were clustered into two branches with strong supports. Firmiana kwangsiensis, F. pulcherrima and F. colorata formed a branch, and the F. kwangsiensis was a sister relationship to F. pulcherrima in this branch, the other branch was F. danxiaensis and F. major.
Conclusion: The structures, gene arrangement and repeat sequences in F. kwangsiensis and F. danxiaensis chloroplast genome were high similar. Phylogenetic analyses revealed that five Firmiana species were clustered into two clades, F. kwangsiensis was closely related to F. pulcherrima, and F. danxiaensis was closely related to F. major. In addition, the SSRs in this study will provides important genetic information for phylogenetic, evolution for Firmiana species.

Key words: Firmiana kwangsiensis, Firmiana danxiaensis, chloroplast genome, high-throughput sequencing, repeat sequence, phylogenetic analysis

陆奇丰, 黄至欢, 骆文华 (2021) 极小种群濒危植物广西火桐、丹霞梧桐的叶绿体基因组特征. 生物多样性, 29, 586-595. DOI: 10.17520/biods.2020263.

Qifeng Lu, Zhihuan Huang, Wenhua Luo (2021) Characterization of complete chloroplast genome in Firmiana kwangsiensis and F. danxiaensis with extremely small populations. Biodiversity Science, 29, 586-595. DOI: 10.17520/biods.2020263.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2020263

https://www.biodiversity-science.net/CN/Y2021/V29/I5/586

图/表 5

图1 广西火桐和丹霞梧桐叶绿体基因组的基因图谱

Fig. 1 Gene map of the Firmiana kwangsiensis and F. danxiaensis chloroplast genome

表1 广西火桐和丹霞梧桐的叶绿体基因组特征比较

Table 1 Comparison of chloroplast genome characteristics of Firmiana kwangsiensis and F. danxiaensis

基因组特征 Genome characteristics	广西火桐 F. kwangsiensis	丹霞梧桐 F. danxiaensis
序列全长 Genome size (bp)	160,836	161,253
LSC区长度 LSC length (bp)	89,700	90,142
SSC区长度 SSC length (bp)	19,970	20,067
IR区长度 IR length (bp)	25,583	25,522
GC含量 GC content (%)	37.04	36.87
LSC区GC含量 GC content of LSC (%)	34.92	34.68
SSC区GC含量 GC content of SSC (%)	31.46	31.24
IR区GC含量 GC content of IR (%)	42.93	42.97
A碱基占比 A base content (%)	30.98	31.13
T碱基占比 T base content (%)	31.98	31.99
C碱基占比 C base content (%)	18.87	18.61
G碱基占比 G base content (%)	18.17	18.26
基因总数 Total genes	131	131
编码蛋白基因数 No. of protein coding sequences	86	86
tRNA	37	37
rRNA	8	8

图2 广西火桐和丹霞梧桐的叶绿体基因组SSR分析。(A)不同SSR类型的数量; (B)大单拷贝区(LSC); 反向重复区(IR)和小单拷贝区(SSC)的SSR数量; (C)基因间隔区(IGS)、基因编码区(CDS)及内含子(intron)的SSR数量。

Fig. 2 SSR analysis of the chloroplast genomes of Firmiana kwangsiensis and F. danxiaensis. (A) Number of SSRs in different types; (B) Number of SSRs in the LSC (large single copy), SSC (small single copy), and IR (inverted repeat region); (C) Number of SSRs in the intergenic regions (IGS), protein-coding gene (CDS) and introns.

图3 广西火桐和丹霞梧桐的叶绿体基因组重复序列分析。(A)不同重复序列类型的分布数量; (B)串联重复序列长度的分布范围; (C)正向、反向和回文重复序列长度的分布范围。

Fig. 3 Repeat sequences analysis of Firmiana kwangsiensis and F. danxiaensis chloroplast genome. (A) Number of different types of repeats; (B) Size of tandem repeats in specific range; (C) Size of forward, reverse and palindromic repeats in specific range.

图4 基于叶绿体全基因组序列最大似然法构建的15个物种的系统发生树

Fig. 4 Phylogenetic tree of 15 species based on chloroplast genome using maximum likelihood (ML) method

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极小种群濒危植物广西火桐、丹霞梧桐的叶绿体基因组特征

Characterization of complete chloroplast genome in Firmiana kwangsiensis and F. danxiaensis with extremely small populations

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