九翅豆蔻叶绿体基因组特征及其密码子偏好性分析  

Analysis of Chloroplast Genome Characteristics and Its Code Usage Bias of Amomum maximum

作　　者：傅武祥 郭雨桐 张雪梅[2] 马占霞 FU Wuxiang;GUO Yutong;ZHANG Xuemei;MA Zhanxia(West Yunnan University of Applied Sciences College of Tea(Pu′er),Pu′er,665000;College of Agronomy and Biotechnology,Yunnan Agricultural University,Kunming,650201;Xishuangbanna Tropical Botanical Garden,Chinese Academy of Sciences,Menglun,666303)

机构地区：[1]滇西应用技术大学普洱茶学院,普洱665000 [2]云南农业大学农学与生物技术学院,昆明650201 [3]中国科学院西双版纳热带植物园,勐仑666303

出　　处：《基因组学与应用生物学》2024年第1期17-30,共14页Genomics and Applied Biology

基　　金：滇西应用技术大学教学质量工程项目(21JK16);云南省教育厅科学研究基金项目(2022J1045)共同资助。

摘　　要：为探究九翅豆蔻(Amomum maximum)叶绿体全基因组(chloroplast DNA,cpDNA)特征和密码子使用偏好性,本研究利用Illumina HiSeq测序平台对九翅豆蔻叶绿体全基因组进行测序,通过组装与注释得到叶绿体基因组全序列,使用MISA、IQTREE和CodonW等软件对九翅豆蔻叶绿体全基因组的微卫星位点(microsatellite site)、密码子偏好性及系统发育进行分析。结果表明,九翅豆蔻完整叶绿体全基因组长度为163602 bp,基因组平均G+C含量为36.1%,其大单拷贝(large single copy,LSC)区和小单拷贝(small single copy,SSC)区长度分别为88626 bp和15426 bp,两个反向重复(inverted repeat,IR)区长度为29775 bp。九翅豆蔻叶绿体基因组共编码132个基因,包含86个蛋白编码基因、38个tRNA基因和8个rRNA基因。叶绿体基因组序列上共检测到132个简单重复序列(simple sequence repeat,SSR)位点。其中单核苷酸、二核苷酸、三核苷酸、四核苷酸和五核苷酸数量分别为65、35、5、24、3个,绝大多数属于单碱基重复的A/U类型。系统发育分析显示九翅豆蔻在豆蔻属(Amomum)植物中单独聚为一支。这为九翅豆蔻种质资源鉴定、评价及物种形成机制研究奠定了基础。To explore the characteristics and codon usage bias of the whole chloroplast genome(chloroplast DNA,cpDNA)of Amomum maximum,this study used the Illumina HiSeq sequencing platform to sequence the whole chloroplast genome of A.maximum,and obtained the complete chloroplast genome sequence through assembly and annotation.The microsatellite sites,codon bias and phylogeny of the chloroplast genome of A.maximum were analyzed by software such as MISA,IQTREE and CodonW.The results showed that the complete chloroplast genome of A.maximum was 163602 bp in length,with an average G+C content of 36.1%.The lengths of the large single copy(LSC)region and the small single copy(SSC)region were 88626 bp and 15426 bp,respectively,and the two inverted repeat(IR)regions were 29775 bp.The chloroplast genome of A.maximum encoded 132 genes,including 86 protein-coding genes,38 tRNA genes and 8 rRNA genes.A total of 132 simple sequence repeat(SSR)sites were detected on the chloroplast genome sequence.Among them,the numbers of mononucleotide,dinucleotide,trinucleotide,tetranucleotide and pentanucleotide were 65,35,5,24 and 3,respectively,most of which belonged to the A/U type of single base repeat.Phylogenetic analysis showed that A.maximum was clustered as a separate branch in the genus Amomum.This laid a foundation for the research of identification,evaluation and species formation mechanism of A.maximum germplasm resources.

关 键 词：九翅豆蔻 叶绿体基因组 微卫星位点 密码子偏好性 系统发育分析 

分 类 号：S567.239[农业科学—中草药栽培]