热带作物学报2025，Vol.46Issue(10)：2346-2354,9.DOI:10.3969/j.issn.1000-2561.2025.10.006
爪哇香茅叶绿体基因组的组装与序列分析
Assembly and Sequence Analysis of the Chloroplast Genome of Cymbopogon winterianus
摘要
Abstract
In this study,Cymbopogon winterianus was used as the experimental material,and the DNA sequence of C.winterianus was sequenced using the Illumina NovaSeq 6000 sequencing platform.The sequencing data were assembled with GetOrganelle v1.7.7.0 software to construct the chloroplast genome.Referring to the known chloroplast genome of C.flexuosus,the chloroplast genome of C.winterianus was annotated,and the genomic characteristics were analyzed and a phylogenetic tree was constructed.The chloroplast genome of C.winterianus was 139 823 bp in length,with a typical circular quadripartite structure.The GC content was 38.45％,and the AT content was 61.55％.It included a large single-copy region(LSC)with a length of 82 214 bp,a pair of inverted repeat regions(IR)with a length of 21 368 bp,and a small single-copy region(SSC)of 14 873 bp.A total of 130 genes were annotated in the chloroplast genome of C.winterianus(including 85 mRNA genes,37 tRNA genes,and 8 rRNA genes).In addition,among the annotated genes,there were 16 double-copy genes,accounting for 12.31％,including 7 tRNA genes,4 self-replication genes,4 rRNA genes,2 protein genes with unknown functions,and 1 NADH dehydrogenase subunit gene.A total of 144 SSR loci were detected in the chloroplast genome of C.winterianus,with mononucleotide repeats being absolutely dominant,mainly A/T.After comparing the boundaries of the inverted repeat sequences of four Cymbopogon species,it was found that C.flexuosus,C.pospischilii,and C.winterianus exhibited extremely high homology in gene structure and species.Among them,the ndhH gene was located in the small single-copy region(SSC),and the ndhF gene was located in the boundary region between the SSC and IRb.However,C.winterianus had an additional rps3 gene in the LSC region compared with C.flexuosus and C.pospischilii.Phylogenetic tree analysis showed that C.winterianus had the closest genetic relation-ship with C.pospischilii and C.citratus(MK593547.1).This study completed the assembly and annotation of the com-plete chloroplast genome of C.winterianus,analyzed the characteristics of the chloroplast genome of C.winterianus,and preliminarily explored the phylogenetic position of C.winterianus within the genus Cymbopogon.It would lay a good foundation for the phylogenetic,genetic diversity,and genomic studies of Cymbopogon plants,as well as for the discovery and utilization of important functional genes.关键词
爪哇香茅草/叶绿体基因组/组装/注释/进化树分析Key words
Cymbopogon winterianus/chloroplast genome/assembly/annotation/phylogenetic tree analysis分类
农业科技引用本文复制引用
罗佳霖,窦秋玉,郭大中,陈浩文,罗丽晶,李佳屹,范源洪..爪哇香茅叶绿体基因组的组装与序列分析[J].热带作物学报,2025,46(10):2346-2354,9.基金项目
云南省重大科技专项计划项目(No.2019ZG00903) （No.2019ZG00903）
国家科技资源共享服务平台项目(No.NTPGRC2024-015). （No.NTPGRC2024-015）
