韭(Allium tuberosum)叶绿体基因组及其特征分析

Chloroplast Genome and Characteristics Analysis of Allium tuberosum

以韭(Allium tuberosum)叶绿体基因组为研究对象,利用Illumina NovaSep高通量测序技术对韭叶绿体基因组进行测序,研究了韭叶绿体基因组结构、密码子偏好性、简单重复序列、叶绿体基因组的比较和系统发育,以期为韭分子标记开发、种质资源鉴定和开发利用提供参考依据。结果表明:韭叶绿体基因组全长154056bp,共注释133个基因,包括tRNA38个,rRNA8个,蛋白编码基因87个;韭cpDNA密码子偏爱以A或U结尾,Leu使用频率最高,Cys使用频率最低;在叶绿体基因组中共检测250个SSR位点,其中单核苷酸重复数量最多(164个),六核苷酸重复最少(1个);基因组IR边界未出现明显的扩张和收缩;系统发育分析显示,野韭和韭亲缘关系最近。

Taking the chloroplast genome of Allium tuberosum as the research object,the chloroplast genome was sequenced by Ilumina NovaSep sequencing platform and the structure,codon preference,simple repeat sequence,comparison and phylogeny of chloroplast genome were studied,in order to provide reference for the molecular marker development,identification and exploitation of the germplasm resources studies of A.tuberosum.The results showed that the chloroplast genome of A.tuberosum was 154056 bp in length with 133 genes annotated,including 38 tRNAs,8 rRNAs and 87 protein-coding genes.The codons in cpDNA of A.tuberosum tended to end with A or U,the frequency of Leu was the highest and that of Cys was the lowest.250 SSR loci were identified in the chloroplast genome sequence,with the highest number of single nucleotide repeats(164)and the lowest number of hexanucleotide repeats(one).There were no obvious expansion and contraction at the IR boundaries;phylogenetic analysis showed that A.tuberosum was most closely related to A.ramosum.