世界科学技术-中医药现代化2025，Vol.27Issue(1)：36-55,20.DOI:10.11842/wst.20240604002
5种黄精属植物叶绿体基因组从头组装及系统发育研究
De Novo Assembly and Phylogenetic Study of Chloroplast Genomes of Five Species of Genus Polygonatum
摘要
Abstract
Objective Five chloroplast(cp)genomes from members of genus Polygonatum were assembled by hybrid assembly technique,and their intraspecic and interspecific differences were analyzed by comparative genomic method.Codon usage patterns and influencing factors were determined,and the cp genome data were applied to understand the phylogenomic relationships in the entire genus Polygonatum along with the available data.Methods In this study,the chloroplast genomes of 5 species of genus Polygonatum were assembled using Unicycler software.Sequence alignment,collinearity analysis,boundary analysis and other methods were used to evaluate the interspecific differences of these five species.Nucleotide polymorphism analysis was used to discover the high-variation sites of the five species and their related species,predict the distribution of different long repeat sequences and SSRs,and then analyze the use bias of Polygonatum code.Finally,phylogenetic tree was constructed with the coding sequences of other 47 genus Polygonatum and their closely related species to explore their phylogenetic relationships in this study.Results ①Chloroplast genomes of 155 408-155 623 bp were assembled from five species of Polygonatum.A total of 132-133 genes were annotated,and 369 long repeats and 1553 simple repeats were detected.②The contraction and expansion of chloroplast genomes in 8 species were not obvious at the IRs boundary,and the size and distribution of individual genes at the LSC-IRs-SSC boundary,such as ndhF gene and ycf1 gene,were slightly different.No interspecific or intraspecific rearrangement was observed in 8 species.③ The high-variation regions of the 8 chloroplast genomes are mainly located in two single-copy regions,the duplicate copy region is relatively conserved,and the coding region is more conserved than the non-coding region.High nucleotide polymorphic loci rps16-trnQ,trnS-trnG,trnTUGU-trnL,ndhF-rpl32 and rpl32-trnL are located in the single copy region and most of them are gene spacer regions.④ The codon preference results showed that the codon preference of the five species was similar and mainly affected by selection pressure,and the third base of the codon played A dominant role and mainly ended in A/U.RSCU clustering heat map shows that PK and PZ,PCB and PS have close relationship.⑤ Phylogenetic trees divided 52 species into five branches:Ⅰ,Ⅱ,Ⅲ,ⅣandⅤ.PS,PK,PCB,PCZ and PZ were divided into ⅣandⅤbranches,among which PK and PZ were most closely related,while PCZ was more distant than the other four,was divided into the Ⅴbranch alone.Conclusion This study provided a reference for the phylogenetic research and molecular marker development of the medicinal plants of the Polygonum genus.关键词
黄精属/叶绿体基因组/混合组装/密码子偏好性/紫杆多花黄精Key words
Genus Polygonatum/Chloroplast genome/Hybrid assembly/Codon usage bias/Polygonatum cyrtonema of purple stalk分类
农业科技引用本文复制引用
李伟,朱明玉,曾宇灵,文萱,黄楚彤,法欣悦,森林,胡志刚,刘义飞..5种黄精属植物叶绿体基因组从头组装及系统发育研究[J].世界科学技术-中医药现代化,2025,27(1):36-55,20.基金项目
国家自然科学基金委员会青年基金项目(31500260):中国阴地蕨属药用草本植物系统学及分子进化研究,负责人:森林 （31500260）
刘合钢全国名老中医药专家传承工作室建设项目,负责人:刘合刚. （）
