2024年2月29日 星期四
祁连圆柏叶绿体基因组序列特征分析
Analysis on chloroplast genome sequence characteristics of Juniperus przewalskii
2023年 第32卷 第3期 页码[1-11]    下载全文[14.5MB]  
摘要

基于Oxford Nanopore PromethION测序仪对祁连圆柏(Juniperus przewalskii Komarov)叶绿体基因组的测序结果,对原属于圆柏属(Sabina Mill.)、现属于刺柏属(Juniperus Linn.)的祁连圆柏和高山柏(Juniperus squamata Buchanan-Hamilton ex D. Don)等5个树种的叶绿体基因组进行了序列对比和反向重复区(IR)边界分析,并对柏科(Cupressaceae)15个树种进行了系统发育分析。结果表明:祁连圆柏叶绿体基因组为环状四分体结构,但四分体结构不明显,基因组全长127 317 bp,共编码118个基因;密码子共23 708个,且偏好使用A或U;简单重复序列共289个,以AA或TT为主;长重复序列共38个,其中正向重复序列最为丰富。参与比较分析的5个树种的叶绿体基因组具有高度相似性,存在显著变异的区域主要集中在非编码序列;5个树种的IR区表现出明显缩减现象,长度在257~265 bp之间。系统发育分析结果显示:原属于圆柏属的物种与刺柏属物种亲缘关系较近,且2个属内的部分物种在系统发育树中的位置出现交错现象,其中祁连圆柏与高山柏聚为一支,亲缘关系最近。综合研究结果表明:祁连圆柏叶绿体基因组偏小,表现为不典型的四分体结构,IR区发生明显缩减;在叶绿体基因组编码的氨基酸序列中,Leu数量最多,AAA(编码Lys)是使用最多的密码子;原属于圆柏属的物种叶绿体基因组具有高度保守性,高变异区域只存在于单拷贝区域,鉴定出的accD、ycf1和ycf2 3个存在显著变异的基因可作为高变异区,为界定密切相关的分类群提供丰富的系统发育信息。

Abstract

Based on the sequencing result of chloroplast genome of Juniperus przewalskii Komarov by using Oxford Nanopore PromethION sequencer, sequence alignment and inverted repeat (IR) region boundary analysis were conducted for chloroplast genomes of five tree species including J. przewalskii and  Juniperus squamata Buchanan-Hamilton ex D. Don, which originally belong to Sabina Mill. and now belong to Juniperus Linn., and phylogenetic analysis was performed for 15 tree species in Cupressaceae. The results show that the chloroplast genome of J. przewalskii is a loop tetrad structure, but the tetrad structure is not evident, and the total length of genome is 127 317 bp, encoding 118 genes in total; there are 23 708 codons in total, and A or U is preferred; there are 289 simple repeat sequences in total, and are mainly AA or TT; there are 38 long repeat sequences in total, in which forward repeat sequence is the most abundant. There are high similarities among chloroplast genomes of five tree species participated in comparative analysis, and the regions with significant variation are mainly concentrated in noncoding sequence; IR regions of five tree species show an obvious reduction phenomenon, and the lengths are within 257-265 bp. The phylogenetic analysis result shows that species originally belong to Sabina has a relatively close genetic relationship with species in Juniperus, and the positions of some species in two genera in the phylogenetic tree show an interlaced phenomenon, in which J. przewalskii and J. squamata are clustered into one branch, and their genetic relationship is the closest. The comprehensive study result shows that the chloroplast genome of J. przewalskii is relatively small, which shows a nontypical tetrad structure, and the IR regions are obviously reduced; in the amino acid sequences encoded by chloroplast genome, Leu is the most abundant amino acid, and AAA (encoding Lys) is the most-used codon; the chloroplast genomes of species originally belong to Sabina are highly conserved, high variation regions only exist in single copy region, and three identified genes with significant variation namely accD, ycf1, and ycf2 can be regarded as  high variation regions, which can provide rich phylogenetic information for  defining closely-associated taxonomic groups.

关键词祁连圆柏; 叶绿体基因组; 刺柏属; 序列比对; 系统发育树
Key wordsJuniperus przewalskii Komarov; chloroplast genome; Juniperus Linn.; sequence alignment; phylogenetic tree
作者赵明1, 张宏斌1, 李伟2, 赵祜1, 刘建海1, 赵国生1, 赵兴鹏1, 吕东1
所在单位1. 甘肃省祁连山水源涵养林研究院, 甘肃 张掖 734000; 2. 北京林业大学生物科学与技术学院, 北京 100083
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基金项目甘肃省科技计划项目创新基地和人才计划(22JR10KA026); 国家自然科学基金项目(31860210; 31860221)