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为探究癞屑化松萝(Usnea lapponica)线粒体基因组特征及松萝属(Usnea)线粒体基因组进化水平，本研究通过对癞屑化松萝的线粒体基因组进行测序、组装和注释，获得该物种的完整线粒体基因组，并与松萝属其他物种线粒体基因组进行比较研究。癞屑化松萝线粒体基因组是一个大小为61 782 bp的闭合环状DNA分子，其碱基组成具有AT偏好性，共有41个基因，包括14个蛋白质编码基因、 2个核糖体RNA基因和25个转运RNA基因；松萝属物种线粒体基因排列和共线性分析显示各物种之间发生了基因重排与同源基因簇丢失现象；重复序列分析显示癞屑化松萝含有丰富的重复序列，松萝属线粒体基因组重复序列数目差异较大，多为正向重复和回文重复，简单重复序列(simple sequence repeats, SSR)主要为二核苷酸和五核苷酸，且A+T含量较高；松萝属线粒体基因组所共有的14个蛋白质编码基因中，只有cox2的Ka/Ks值大于1,其正在接受正选择压力，其余13个蛋白质编码基因正在接受纯化选择压力；共线性分析、重复序列分析以及系统发育分析共同显示癞屑化松萝与亚棕松萝(Usnea subfusca)亲缘关系更近。本研究揭示了癞屑化松萝的线粒体基因组序列信息，丰富了地衣基因组研究数据，为松萝属基因组比较、遗传分化、资源保护以及系统发育提供数据支持。
Abstract：The aim of this study was to explore the characteristics of mitochondrial genome of Usnea lapponica and the evolution level of the mitochondrial genome of Usnea. In this study, the mitochondrial genome of U. lapponica was sequenced, assembled and annotated to obtain the complete mitochondrial genome of this species, which was compared with that of other species of Usnea. The mitochondrial genome of U. lapponica was a closed circular DNA molecule with a size of 61 782 bp, and the base composition showed an AT preference. There were 41 genes, including 14 protein-coding genes, 2 ribosomal RNA genes and 25 transporter RNA genes. Gene sequencing and colinearity analysis in U. lapponica showed that gene rearrangement and homologous gene cluster loss occurred among species. Repetitive sequence analysis showed that there were abundant repetitive sequences in U. lapponica. The number of repetitive sequences in the Usnea mitochondrial genome varied greatly, most of which were forward and palindrome repeats. Simple sequence repeats(SSR) were mainly di-nucleotide and penta-nucleotide, and the content of A+T was high. Among the 14 protein-coding genes shared by the mitochondrial genome of Usnea, only cox2 had a Ka/Ks value over 1 which was under positive selection pressure, and the remaining 13 protein-coding genes were under purification selection pressure. Colinearity analysis, repeat sequence analysis and phylogenetic analysis showed that there were a closer relationship between U. lapponica and U. subfusca. This study revealed the mitochondrial genome sequence information of U. lapponica, enriched the lichen genome research data, and provided data support for genome comparison, genetic differentiation, resource protection and phylogenetic development of Usnea.
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基本信息:
DOI：10.13417/j.gab.042.000073
中图分类号:Q943.2
引用信息:
[1]方津津,图尔荪阿依·排祖拉,古丽米热·艾尼瓦尔,等.癞屑化松萝(Usnea lapponica)线粒体基因组特征及其系统进化研究[J].基因组学与应用生物学,2023,42(01):73-83.DOI:10.13417/j.gab.042.000073.
基金信息:
国家自然科学基金项目(31760052); 新疆少数民族科技人才特殊培养计划科研项目(2022D03005)共同资助
2022-12-09
2022-12-09
2022-12-09