木犀科植物叶绿体基因组结构特征和系统发育关系

doi:10.11983/CBB18191

植物学报 ›› 2019, Vol. 54 ›› Issue (4): 441-454.DOI: 10.11983/CBB18191

木犀科植物叶绿体基因组结构特征和系统发育关系

赵月梅¹,杨振艳²,赵永平¹,李筱玲¹,赵志新¹,赵桂仿^3,^*()

1 商洛学院生物医药与食品工程学院, 商洛 726000
2 中国科学院昆明植物研究所, 东亚植物多样性与生物地理学重点实验室, 昆明 650201
3 西北大学生命科学学院, 西部资源生物与现代生物技术教育部重点实验室, 西安 710069

收稿日期:2018-09-06 接受日期:2019-04-23 出版日期:2019-07-10 发布日期:2020-01-08
通讯作者: 赵桂仿
基金资助:
商洛市博士科技创新团队(SK2017-45);商洛学院高层次人才引进项目(17SKY029)

Chloroplast Genome Structural Characteristics and Phylogenetic Relationships of Oleaceae

Yuemei Zhao¹,Zhenyan Yang²,Yongping Zhao¹,Xiaoling Li¹,Zhixin Zhao¹,Guifang Zhao^3,^*()

1 College of Biopharmaceutical and Food Engineering, Shangluo University, Shangluo 726000, China
2 Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
3 Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China

Received:2018-09-06 Accepted:2019-04-23 Online:2019-07-10 Published:2020-01-08
Contact: Guifang Zhao

摘要/Abstract

摘要：

木犀科11属19个种叶绿体基因组的一般特征和变异特征的比较分析显示, 结果表明, 该科叶绿体基因组大小为154-165 kb, 其差异主要是大单拷贝(LSC)长度的差异所致。Jasminum属3个物种的叶绿体基因组长度与其余物种有较大差异, 该属clpP基因内含子和accD基因丢失。共线性分析表明, Jasminum属3个物种多个基因出现基因重排现象, 倒位可能是重排的主要原因。Jasminum属在IRb/SSC和SSC/IRa边界的基因均与其它物种不同; 重复序列与SSR数量检测结果表明, Jasminum属与其余物种在数量及重复长度上差异较大。基于CDS数据构建的系统发育树表明, Abeliophyllum distichum和Forsythia suspensa为木犀科中较早分化的类群。

关键词: 木犀科, 叶绿体基因组, 结构特征, 系统发育

Abstract:

In this study, the chloroplast genomes from 19 species (11 genera) in Oleaceae were compared to reveal the general characteristics and structural variations. The chloroplast genome sizes in Oleaceae were 154-165 kb, and the differences were mainly caused by the length of large single-copy regions. The chloroplast genome sizes of 3 species from the genus Jasminum differed greatly from that for other species; in addition, the introns from the clpP and accD genes were lost in Jasminum. Synteny analyses showed several gene rearrangements in 3 Jasminum species that were probably caused by inversions. The boundary genes between IRb/small single copy (SSC) and SSC/IRa regions in 3 Jasminum species differed from others. Repeat sequences and simple sequence repeat detection demonstrated that Jasminum had significant differences in repeat number and repeat length as compared with other genera. On the basis of shared protein-coding genes among 19 species, Abeliophyllum distichum and Forsythia suspensa were the early-diverging clades in Oleaceae.

Key words: Oleaceae, chloroplast genomes, structural characteristics, phylogeny

赵月梅,杨振艳,赵永平,李筱玲,赵志新,赵桂仿. 木犀科植物叶绿体基因组结构特征和系统发育关系. 植物学报, 2019, 54(4): 441-454.

Yuemei Zhao,Zhenyan Yang,Yongping Zhao,Xiaoling Li,Zhixin Zhao,Guifang Zhao. Chloroplast Genome Structural Characteristics and Phylogenetic Relationships of Oleaceae. Chinese Bulletin of Botany, 2019, 54(4): 441-454.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB18191

https://www.chinbullbotany.com/CN/Y2019/V54/I4/441

图/表 7

Table 1 List of 19 species in Oleaceae, GenBank accession number and structural features of chloroplast genomes

表2 叶绿体基因组中含内含子蛋白编码基因的编码区长度和基因全长

Table 2 Length of coding region and complete gene of intron-contained protein-coding genes of chloroplast genomes

Species	petD	rps12	clpP	rpoC1	rps16
1	483/1196	372/908	591/2047	2064/2821	267/1132
2	483/1218	372/908	591/2043	2073/2834	267/1147
3	483/1230	375/911	591/2045	2052/2820	267/1134
4	483/1261	381/917	591/2043	2073/2827	267/1153
5	483/1134	372/908	591/2045	2052/2811	255/1147
6	483/1148	372/908	591/2053	2073/2830	267/1136
7	483/1217	372/908	591/2039	2073/2834	267/1142
8	483/1196	372/908	588/2045	2064/2822	267/1131
9	483/1196	381/917	660	2076/2844	267/1162
10	483/1203	387/923	786	2052/2808	267/1154
11	483/1213	387/923	786	2052/2807	267/1161
12	483/1215	381/917	591/2041	2073/2833	267/1143
13	483/1217	372/908	591/2043	2073/2830	267/1143
14	483/1215	372/908	591/2046	2073/2832	267/1141
15	483/1213	371/907	591/2043	2073/2831	267/1142
16	483/1213	372/908	591/2044	2073/2831	267/1142
17	483/1215	373/909	591/2041	2073/2833	267/1141
18	483/1203	372/908	591/2047	2073/2834	267/1147
19	483/1199	372/913	591/2041	2073/2784	237/1115

图1 19种木犀科植物叶绿体基因组中重复序列类型和比例 (A) 3种重复类型的数目; (B) 3种重复类型的比例; (C) SSR类型的比例; (D) SSR的数目和类型

Figure 1 The type and percentage of repeated sequences in the chloroplast genomes of 19 species in Oleaceae (A) Number of three type repeats; (B) Percentage of three type repeats; (C) Percentage of SSR types; (D) Number and types of SSRs

图2 木犀科19个物种的叶绿体基因组的四部分边界比较

Figure 2 Comparison of the border regions of the chloroplast genomes from 19 species in Oleaceae

图3 木犀科19个物种叶绿体基因组的比对分析物种编号1-19同表1。以Abeliophyllum distichum叶绿体基因组序列为参考序列(x轴), 各物种叶绿体基因组与参考序列一致度范围为50%-100%(y轴)。箭头表示基因及转录方向。

Figure 3 Graphic view of the alignment of chloroplast genomes from 19 species in Oleaceae The species number 1-19 same as Table 1. Sequence identity varying between 50% and 100% are drawn on the y axis of the plot, the x axis corresponds to the coordinates on the Abeliophyllum distichum chloroplast genome. Arrows indicate the annotated genes and their transcriptional direction.

图4 木犀科19种植物的叶绿体基因组共线性分析物种编号1-19同表1。

Figure 4 Synteny analyses of chloroplast genomes from 19 species in Oleaceae The species number 1-19 same as Table 1.

图5 基于木犀科19个物种共有蛋白编码基因构建的系统发育树每个节点附近的数字分别表示ML树的自展支持率和BI树的后验概率。以Cornus controversa、Echites umbellatus和Catharanthus roseus为外类群。ML: 最大似然法; BI: 贝叶斯法

Figure 5 Phylogenetic relationship of 19 species in Oleaceae inferred from ML and BI analyses based on shared protein-coding genes The numbers near each node are bootstrap support values in ML and posterior probability in BI. The outgroups are Cornus controversa, Echites umbellatus and Catharanthus roseus. ML: Maximum likelihood; BI: Bayesian inference

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木犀科植物叶绿体基因组结构特征和系统发育关系

Chloroplast Genome Structural Characteristics and Phylogenetic Relationships of Oleaceae

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