广西植物2025，Vol.45Issue(5)：809-823,15.DOI:10.11931/guihaia.gxzw202308065
高山植物唐古红景天叶绿体基因组特征及系统发育分析
Characteristics of chloroplast genome and phylogenetic analysis of alpine plant Rhodiola tangutica(Crassulaceae)
摘要
Abstract
In order to explore the structure characteristics,gene information and phylogenetic relationship of the chloroplast genome for Rhodiola tangutica,which is an important medicinal plant growing in Northwest China,this study sequenced its complete chloroplast genome using Illumina NovaSeq6000,and analyzed the genome structure,gene function and genetic relationship of the chloroplast genome using multiple bioinformatics analysis softwares such as GeSeq,PGA,NOVOPlasty,IRscope and MISA.The results were as follows:(1)The chloroplast genome of R.tangutica had a quadripartite circular structure of 150 863 bp in length,including LSC(82 121 bp),SSC(16 996 bp)and IR(25 873 bp).Total GC content was 37.8%,and which of the IR regions was the highest(42.9%).The genome encoded 131 genes in total,including 85 PCGs,38 tRNAs and 8 rRNAs.(2)Among the 32 471 codons,cysteine(Cys)had the smallest percentage(1.18%),while isoleucine(Ile)had the highest percentage(8.24%).There were 29 codons with the value of RSCU above one.(3)The analysis of IR regions showed that both rps19 and ndhF were expanded into the IRB region.(4)Phylogenetic analysis indicated that R.tangutica and R.quadrifida had the closest relationship.Estimation of divergence time indicated that the origin of Rhodiola species was around 15.50 Mya(95%HPD:6.0-21.0 Mya).This study clarified the chloroplast genome characteristics of R.tangutica and obtained a reasonable phylogenetic relationship of Rhodiola.This study provides a theoretical reference for the study of genetic diversity,the discussion of adaptive evolutionary mechanism and the protection of germplasm resources of Rhodiola.关键词
红景天属/唐古红景天/叶绿体基因组/系统发育/密码子偏好性Key words
Rhodiola/Rhodiola tangutica/chloroplast genome/phylogeny/codon preference分类
农业科技引用本文复制引用
曲荣举,靳佳瑞,才让扎西,毛轩睿,刘玉萍,苏旭,胡夏宇,杨萍,李小莉,孙成林..高山植物唐古红景天叶绿体基因组特征及系统发育分析[J].广西植物,2025,45(5):809-823,15.基金项目
第二次青藏高原综合科学考察研究项目(2019QZKK0502) （2019QZKK0502）
青海省自然科学基金面上项目(2022-ZJ-913). （2022-ZJ-913）
