牡荆属叶绿体基因组比较分析及系统发育分析（附录）

Comparative analysis of chloroplast genomes and phylogenetic analysis of Vitex

关键词:  牡荆属, 叶绿体基因组, 密码子偏好性, 系统发育, 唇形科, 马鞭草科

Key words:  Vitex, chloroplast genome, codon preference, phylogeny, Lamiaceae, Verbenaceae

摘要:

牡荆属(Vitex L.)广布于热带和亚热带地区,多为乔木或灌木,包含众多具有药用价值、观赏价值和生态价值的植物。为了解牡荆属的叶绿体基因组特征、系统位置及种间关系,该研究从头组装、注释获得穗花牡荆(V. agnus-castus)的叶绿体基因组,与牡荆属公布的11条叶绿体基因组序列进行基因组结构、密码子偏好性、高变区和重复序列分析,并进行系统发育分析。结果表明:(1)穗花牡荆叶绿体基因组呈典型的四段式结构,全长154 444 bp,其中大单拷贝(LSC)区、小单拷贝(SSC)区、反向重复(IR)区长度分别是85 229、17 915、51 400 bp,编码132个基因,包含87个蛋白编码基因、37个tRNA基因和8个rRNA基因。(2)牡荆属12个叶绿体基因组在长度、反向重复区边界位置、编码的基因及数目、GC含量方面均具有高保守性。(3)共检测到31个高频密码子和6个共有最优密码子,ENC-plot、PR2-plot和中性绘图分析表明密码子偏好性主要受自然选择的影响。(4)共检测到14个叶绿体基因组高变区和519个简单重复序列。(5)分子系统发育结果支持牡荆属隶属于唇形科牡荆亚科,而非马鞭草科。另外,系统发育推断也为存在争议的蔓荆(V. trifolia)、V. bicolor和单叶蔓荆(V. rotundifolia)之间关系的理解提供一定参考,建议将单叶蔓荆作为独立的种。该研究结果不仅丰富了穗花牡荆的遗传资源信息,增加了对牡荆属叶绿体基因组的理解,提供了牡荆属群体遗传学研究的候选分子标记,还证明了叶绿体基因组序列在牡荆属系统发育重建中的有效性。

Abstract:

Vitex L. is widely distributed in tropical and subtropical areas, mostly as woody trees or shrubs, and contains many plants with medicinal, ornamental and ecological values. To understand the characteristics of Vitex chloroplast genomes, the phylogenetic position and interspecific relationships of the genus, the chloroplast genome sequence of V. agnus-castus was firstly obtained by de novo assembly and annotation, the genome structure, codon preference, high variation region and repeat sequence were then analyzed with 11 published chloroplast genome sequences of Vitex, and then phylogenetic analysis was conducted. The results were as follows:(1)The chloroplast genome of V. agnus-castus was a typically quadripartite structure with a total length of 154 444 bp, in which the length of the large single copy(LSC)region, the small single copy(SSC)region and the inverted repeat(IR)region were 85 229, 17 915 and 51 400 bp, respectively. The chloroplast genome encoded 132 genes, including 87 protein-coding genes, 37 tRNA genes and 8 rRNA genes.(2)The 12 chloroplast genomes of Vitex were highly conserved in terms of genome length, boundary position of IR region, number of encoded genes and GC content.(3)A total of 31 high frequency codons and six common optimal codons were detected in 12 chloroplast genomes of Vitex. Further, the results of ENC-plot, PR2-plot and neutral plot analysis indicated that codon preference was mainly influenced by natural selection.(4)In addition, a total of 14 highly variable regions and 519 simple sequence repeats(SSRs)were detected in the 12 chloroplast genomes of Vitex.(5)The molecular phylogenetic inference in this study supported that Vitex belonged to the subfamily Viticoideae(Lamiaceae), not Verbenaceae. Moreover, phylogenetic inference also provided some understanding of the controversial relationships among V. trifolia, V. bicolor and V. rotundifolia, suggesting that V. rotundifolia was considered as a separate species. This study not only enriches the information of genetic resources of V. agnus-castus, increases the understanding of the chloroplast genomes of Vitex, provides candidate molecular markers for population genetics studies of Vitex, but also proves the effectiveness of chloroplast genome sequence in the phylogenetic reconstruction of Vitex.