2024年2月22日 星期四
星毛唐松草叶绿体基因组特征及系统发育分析
Analyses on characteristics of chloroplast genome and phylogeny of Thalictrum cirrhosum
2023年 第32卷 第3期 页码[24-32]    下载全文[8.5MB]  
摘要

对星毛唐松草(Thalictrum cirrhosum Lévl.)叶绿体基因组的碱基组成和基因类型等特征进行分析,并与同属近缘种黏唐松草(Thalictrum viscosum C. Y. Wu)、丝叶唐松草(Thalictrum foeniculaceum Bunge)、朝鲜唐松草(Thalictrum coreanum H. Lév.)和芸香唐松草〔Thalictrum thalictroides (Linn.) Eames et Boivin〕的叶绿体基因组进行比较和系统发育分析。结果显示:星毛唐松草叶绿体基因组中AT含量(61.6%)明显高于GC含量(38.4%),反向重复区(IR)的GC含量最高(43.2%);注释到的133个基因中20个基因含有2份拷贝,17个基因含有2个内含子,仅clpP1基因含有3个内含子;根据基因对应的产物,133个基因可分为17类,其中,蛋白质编码基因中核糖体蛋白小亚基和光系统Ⅱ亚基的编码基因数量最多(14);叶绿体基因组中共检测到58个SSR位点,其中,由T、A和C组成的单核苷酸SSR位点最多(51),占总SSR位点数的88%。星毛唐松草及其4个近缘种叶绿体基因组的大单拷贝区(LSC)、小单拷贝区(SSC)和IR区分别包含409、84和260个多态性位点,核苷酸多态性平均值分别为0.009 4、0.014 0和0.002 1;IR区序列变异较小,表明IR区相对保守。星毛唐松草及其4个近缘种的叶绿体基因组结构、基因数量和GC含量均较为相似,非编码序列变异程度均明显高于编码序列,但在IR区的边界处有一定差异。聚类分析结果显示:唐松草属(Thalictrum Linn.)植物聚为一支,其中,星毛唐松草与黏唐松草的亲缘关系最近。综合研究结果表明:星毛唐松草叶绿体基因组的碱基组成偏向使用A或T,trnV-UAC基因、ndhF和ndhD基因以及ycf1基因对应的3个区域为星毛唐松草及其4个近缘种的核苷酸多态性热点区域;星毛唐松草及其4个近缘种的叶绿体基因组特征较为相似,ycf1、ndhF、rpl2和rps19基因的收缩或扩张可能是唐松草属植物叶绿体基因组IR区存在差异的主要原因;叶绿体基因组可为唐松草属植物的分类及鉴定提供可靠依据。

Abstract

Characteristics including base composition and gene type of chloroplast genome of Thalictrum cirrhosum Lévl. were analyzed, and comparison and phylogenetic analysis with those of related species in the same genus namely Thalictrum viscosum C. Y. Wu, Thalictrum foeniculaceum Bunge, Thalictrum coreanum H. Lév., and Thalictrum thalictroides (Linn.) Eames et Boivin were carried out. The results show that AT content (61.6%) in chloroplast genome of T. cirrhosum is obviously higher than  GC content (38.4%), and GC content in the inverted repeat region (IR) is the highest (43.2%); 20 out of 133 annotated genes contain two copies, and 17 genes contain two introns, while only clpP1 gene contains three introns; based on the products of genes, 133 genes can be divided into 17 categories, in which, the number of genes that encode  small subunit of ribosome protein and subunit of photosystem Ⅱ are the most (14) among protein-coding genes; there are 58 SSR loci in the chloroplast genome, in which, the single nucleotide SSR loci consisting of T, A, and C are the most (51), which accounts for 88% of total number of SSR loci. The large single copy region (LSC), small single copy region (SSC), and IR region of the chloroplast genomes of T. cirrhosum and its four related species contain 409, 84, and 260 polymorphic loci, respectively, and the averages of nucleotide polymorphism are 0.009 4, 0.014 0, and 0.002 1, respectively; the sequence variation of IR region is small, indicating that the IR region  is relatively conservative. The structures, gene numbers, and GC contents of chloroplast genomes of T. cirrhosum and its four related species are all relatively similar, and the variation degree of noncoding sequences is obviously higher than that of coding sequences, but there are some differences in the boundaries of IR regions. The cluster analysis result shows that Thalictrum Linn. species can be clustered into one branch, in which, T. cirrhosum has the closest genetic relationship with T. viscosum. The comprehensive study result shows that the base composition of chloroplast genome of T. cirrhosum prefers A or T, the three regions corresponding to trnV-UAC gene, ndhF and ndhD genes, and ycf1 gene were nucleotide polymorphism hotspots of T. cirrhosum and its four related species; the characteristics of chloroplast genomes of T. cirrhosum and its four related species are relatively similar, and contraction or expansion of ycf1, ndhF, rpl2, and rps19 genes are the main reason for the differences in IR regions of chloroplast genomes of Thalictrum species; the chloroplast genome can provide reliable basis for the classification and identification of Thalictrum species.

关键词星毛唐松草; 叶绿体基因组; 序列比对; 系统发育分析
Key wordsThalictrum cirrhosum Lévl.; chloroplast genome; sequence alignment; phylogenetic analysis
作者侯哲, 娄晓鸣, 李昂, 黄长兵
所在单位苏州农业职业技术学院, 江苏 苏州 215008
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基金项目四川省自然科学基金项目(2022NSFSC1141); 江苏省特色花卉工程中心基金项目(苏发改高技发[2020]1460号); 江苏省省级作物种质资源库(球宿根花卉)项目(JS-ZW-K05); 苏州农业职业技术学院博士提升计划(BS[2022]08)