'湘辣14号'辣椒叶绿体全基因组特征及进化关系分析
Analysis of Chloroplast Genome Characteristics and Evolutionary Relationship of Capsicum annuum'Xiangla No.14'
何刀山 1何海燕 1谢维 1罗治国 1张铁军 2秦雅林 3李鹏1
作者信息
- 1. 湘潭市农业科学研究所,湖南 湘潭 411134
- 2. 湘潭市雨湖区响水乡农业中心,湖南 湘潭 411134
- 3. 湖南人文科技学院农业与生物技术学院,湖南 娄底 417000
- 折叠
摘要
以'湘辣14号'辣椒幼嫩叶片为材料,采用Illumina NovaSeq 6000平台对其进行测序,获得'湘辣 14 号'叶绿体全基因组序列,利用生物信息学对'湘辣14号'叶绿体基因组结构特征、重复序列、密码子使用偏性、IR边界、核苷酸多样性以及进化关系进行分析.结果表明,'湘辣14号'叶绿体基因组全长为156 817 bp,为典型的四分体结构,总GC含量为37.72%.共注释132个基因,包括87个蛋白编码基因、8个rRNA基因、37个tRNA基因.在'湘辣14号'叶绿体基因组中鉴定到 61 个分散重复序列和 190 个简单重复序列(simple sequence repeat,SSR)位点,其中单核苷酸重复最多,主要以A/T为主,占总SSR数量的53.16%.密码子分析表明,'湘辣14号'叶绿体基因组密码子第三位碱基偏向使用A/U.IR区相对LSC和SSC更为保守,部分基因存在收缩和扩张现象.共在'湘辣14号'叶绿体基因组中获得5个高变异区:clpP、rpl20、cemA、rpl32、ycf1.进化关系分析说明,'湘辣14号'与辣椒C.annuum(OP919650.1)和C.annuum(JX27081.1)的亲缘关系较近,属于辣椒属植物.本研究为'湘辣14号'的性状改良和分子标记研究提供了数据支撑.
Abstract
Based on Illumina NovaSeq 6000 sequencing,the entire chloroplast genome sequence of Capsicum annuum cv'Xiangla No.14'was obtained,and its chloroplast genome structure and features,repeat sequence,codon usage bias,IR boundary,nucleotide diversity and evolutionary relationship were determined using bioinformatics method.The'Xiangla No.14'chloroplast genome displayed a typical quadripartite structure with a size of 156 817 bp,and the whole GC content was 37.72%.A total of 132 genes were annotated,comprising 87 protein-coding genes,8 rRNA genes,37 tRNA genes in'Xiangla No.14'chloroplast genome.In total of 61dispersed repeats and 190 SSR were detected in'Xiangla No.14'chloroplast genome.The most type was single nucleotide repeats,which mainly included A and T,accounting for 53.16%of the total number of SSR.Codon analysis showed that the third base of the chloroplast genome of'Xiangla No.14'was biased towards A/U.The IR region was more conservative than LSC and SSC regions,and some genes existed expansion and contraction.Five mutation hotspots,namely,clpP,rpl20,cemA,rpl32,and ycf1 were obtained in'Xiangla No.14'chloroplast genome.Phylogenetic analysis revealed that'Xiangla No.14'was closely related with C.annuum(OP919650.1)and C.annuum(JX27081.1),which belonged to C.genus.The findings of this study provided data support for the characteristics improvement and molecular marker study of'Xiangla No.14'in the future.
关键词
'湘辣14号'/辣椒属/叶绿体基因组/基因组特征/进化关系Key words
'Xiangla No.14'/Capsicum genus/chloroplast genome/genome characteristics/evolutionary relationship引用本文复制引用
出版年
2024
国家科技期刊平台
NSTL
万方数据