多花海棠叶绿体基因组分析

Chloroplast genome in Malus floribunda Siebold.

摘要:

多花海棠（Malus floribunda Siebold.）是世界范围内广泛栽培的苹果属物种，具有较高的观赏价值和育种意义。对其进行叶绿体基因组比较分析，有利于完善苹果属系统进化以及种质利用的研究内容。基于全基因组测序数据，组装获得一个完整的具有四分体结构的多花海棠叶绿体基因组。该基因组包括大单拷贝区（88 142 bp）、反向重复区B （26 353 bp）、小单拷贝区（19 189 bp）与反向重复区A （26 353 bp），共计160 037 bp。多花海棠叶绿体全基因组共注释到111个基因，包括78个蛋白编码基因、29个tRNA基因和4个rRNA基因。此外，在其基因组中识别到大量的重复序列，与三叶海棠和变叶海棠略有差异。通过计算相对同义密码子使用度，发现其高频密码子共30种，并且密码子具有偏向A/T结尾的使用模式。种间序列比对、边界分析的结果表明，大单拷贝区序列变异较大，8种苹果属植物SC区与IR区扩张收缩情况整体上较为相似。基于叶绿体基因组序列的系统进化分析，将多花海棠、湖北海棠和变叶海棠聚为一类。多花海棠叶绿体基因组的研究可为今后遗传标记开发与种质资源利用等提供数据支持。

关键词:多花海棠;叶绿体基因组;系统进化;生物信息学;比较基因组学分析

Abstract:

Malus floribunda Siebold. (Malus) is widely cultivated all over the world, which is of high ornamental value and breeding significance. Comparative analysis of the chloroplast genome can help enrich the phylogenetic relationship and facilitate germplasm utilization of Malus. Based on the whole genome sequencing data, a complete chloroplast genome (M. floribunda) with tetrad structure was assembled. The chloroplast genome (160 037 bp) was composed of a large single-copy (LSC) region (88 142 bp), inverted repeat (IR) B (26 353 bp), a small single-copy (SSC) region (19 189 bp), and IRA (26 353 bp). A total of 111 genes were annotated:78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. In addition, a large number of repeat sequences were identified in the genome, which was slightly different from that of M. sieboldii and M. toringoides. As for the relative synonymous codon usage, 30 high-frequency codons were found, and the codons tended to end with A/T. The results of interspecific sequence alignment and boundary analysis suggested the sequence variation of the LSC region was large, and the expansion and contraction of the SC region and IR region of the eight Malus species were generally similar. According to the phylogenetic analysis of chloroplast genome sequences, M. floribunda, M. hupehensis, and M. toringoides were grouped into one clade. The findings in this study can provide data support for the development of genetic markers and utilization of germplasm resources in the future.

Key words:Malus floribunda;chloroplast genome;phylogenetic;bioinformatics;comparative genomics analysis