贵州九种猕猴桃属植物叶绿体基因组特征及比较分析

Chloroplast genome characteristics and comparative analysis of nine Actinidia species in Guizhou

关键词:  猕猴桃属, 叶绿体基因组, 简单序列重复, 序列比对, 系统发育

Key words:  Actinidia, chloroplast genome, simple sequence repeats, sequence alignment, phylogeny

摘要:

为明确猕猴桃属植物叶绿体基因组特征与系统发育关系,该文以贵州地区葛枣、革叶、京梨等9种猕猴桃为研究对象,基于二代测序数据开展叶绿体基因组组装、注释和比较基因组学分析,系统解析了其基因组特征与系统发育关系。结果表明:(1)9种猕猴桃属植物的叶绿体基因组均为双链环状分子,呈典型的四分体环状结构,序列全长为155 660～156 770 bp,总GC含量为37.21%～37.33%,基因组大小相似度较高。(2)除黄毛与条叶猕猴桃仅注释到129个基因以外,其他猕猴桃均注释得到130个基因,包括83个蛋白质编码基因、39个tRNA基因与8个rRNA基因。(3)密码子使用偏好性相近,第三位碱基以A/U结尾为主; 共鉴定出491个SSR位点,涵盖单核苷酸至六核苷酸6种重复类型。(4)比较基因组分析显示,大单拷贝(LSC)与小单拷贝(SSC)区序列变异高于反向重复(IR)区,非编码区变异较编码区更显著,共识别出9个突变基因片段,包括rps16-trnQ-UUG、ndhC-trnV-UAC和rbcL-accD等基因间隔区与基因区段。(5)系统发育树分为4支,葛枣猕猴桃遗传距离较远,中华与美味猕猴桃聚为一支,京梨、革叶、条叶和黄毛猕猴桃聚集为一支,阔叶与毛花猕猴桃亲缘关系最近。该研究为贵州省猕猴桃种质资源的鉴定与保护提供了叶绿体基因组层面的重要依据,也为该属植物的分类、系统进化及分子鉴定研究积累了关键数据基础与理论基础。

Abstract:

To elucidate the chloroplast genomic characteristics and phylogenetic relationships within the genus Actinidia, nine species distributed in Guizhou Province, including A. polygama, A. rubricaulis var. coriacea, and A. callosa var. henryi, were selected in this study. Based on next-generation sequencing data, we performed chloroplast genome assembly, annotation, and comparative genomic analysis to systematically investigate their genomic characteristics and phylogenetic relationships. The results were as follows:(1)The chloroplast genomes of all nine Actinidia species were double-stranded circular molecules with a typical quadripartite structure. Their full lengths ranged from 155 660 to 156 770 bp, and the overall GC content varied from 37.21% to 37.33%, indicating high similarity in genome size.(2)A total of 130 genes were annotated in most species, including 83 protein-coding genes, 39 tRNA genes, and 8 rRNA genes, except that 129 genes were annotated in A. fulvicoma and A. fortunatii.(3)Codon usage bias was similar among species, with a preference for A/U at the third codon position. A total of 491 simple sequence repeat(SSR)loci were identified, encompassing six repeat types ranging from mononucleotide to hexanucleotide.(4)Comparative genomic analysis revealed that sequence variation was higher in the large single copy(LSC)and small single copy(SSC)regions than in the inverted repeat(IR)region, and that non-coding regions exhibited more pronounced variation than coding regions. Nine divergent gene fragments were identified, including intergenic spacers such as rps16-trnQ-UUG, ndhC-trnV-UAC, and the rbcL-accD region.(5)Phylogenetic analysis resolved the nine species into four clades: A. polygama was phylogenetically distant from the others; A. chinensis and A. chinensis var. deliciosa clustered together; A. callosa var. henryi, A. rubricaulis var. coriacea, A. fortunatii, and A. fulvicoma formed a distinct clade; and A. latifolia showed the closest relationship with A. eriantha. This study has provided an important basis at the chloroplast genome level for the identification and conservation of kiwifruit germplasm resources in Guizhou Province, and has also accumulated key data and a theoretical basis for the taxonomy, phylogeny and molecular identification of this genus.