江苏农业学报2025，Vol.41Issue(10)：1907-1919,13.DOI:10.3969/j.issn.1000-4440.2025.10.004
基于全基因组的假蒟叶绿体进化:特征及系统发育分析
Evolutionary characteristics and phylogenetic analysis of chloroplasts in Piper sarmentosum based on whole genome sequencing
摘要
Abstract
To elucidate the genomic information of Piper sarmentosum,this study conducted de novo sequencing,assembly,and annotation of its chloroplast genome,followed by a comprehensive analysis of its genomic structure,gene composition,repetitive sequence characteristics,simple sequence repeat(SSR)loci,and phylogenetic relationships.The results showed that the total length of the chloroplast genome sequence of Piper sarmentosum was 161 389 bp,exhibiting a typical quadripartite structure consisting of a large single-copy(LSC)region,a small single-copy(SSC)region,and two inverted repeat(IRa and IRb)regions.The over-all G+C content was 38.30%,and the genome contained 82 protein-coding genes.A total of 16 forward repeats,24 palindromic repeats,two reverse repeats,and two comple-mentary repeats were identified during the analysis of its dispersed repetitive sequences.Meanwhile,51 SSR loci were detected,with A/T nucleotides being the predominant repeat type.The results of codon usage bias analysis revealed that codons encoding leucine(Leu)were the most frequently used,while those encoding cysteine(Cys)were the least fre-quent.Among the high-frequency codons,most ended with A or U.Through comparative analysis of chloroplast genome IR boundaries within the genus,it was found that the IR boundary regions of Piper were relatively conserved,with only minor variations.Six highly variable regions were detected in the Piper genus through nucleotide polymorphism analysis:rps16(ex-on1)-trnQ,psbZ-trnG,rps4-trnT,petA-psbJ,psbJ-psbL,and ndhF-rpl32.These regions can be utilized to develop molecu-lar markers for phylogenetic and DNA barcoding research in Piper.Phylogenetic analysis based on chloroplast genomes of Piperales plants confirmed that Piper sarmentosum was closely related to Piper betle,Piper hainanense,and Piper mutabile.The results of this study provide valuable information for the phylogeny and chloroplast genetic engineering of this important plant with both medicinal and edible values.关键词
假蒟/胡椒属/叶绿体基因组/密码子偏好性/系统发育分析Key words
Piper sarmentosum/Piper L./chloroplast genome/codon usage bias/phylogenetic analysis分类
农业科技引用本文复制引用
林锦杭,耿晓姗,郭艺鹏,刘秦..基于全基因组的假蒟叶绿体进化:特征及系统发育分析[J].江苏农业学报,2025,41(10):1907-1919,13.基金项目
国家自然科学基金项目(32101691) （32101691）
广西自然科学基金项目(2025GXNSFAA069625) （2025GXNSFAA069625）
2023年度广西高校中青年教师基础能力提升项目(2023KY05604) （2023KY05604）
