基于质体基因组学方法研究广义玄参科的系统发育

Phylogeny of Scrophulariaceae sensu lato based on plastid genome

关键词:  广义玄参科, 系统发育基因组, 质体基因组, 唇形目

Key words:  Scrophulariaceae sensu lato, phylogenomic, plastid genome, Lamiales

摘要:

该研究利用GenBank数据库已公开发表的玄参科及相关类群的107属129个物种的质体基因组数据对广义玄参科的系统发育关系进行了分析。该文利用蛋白质编码基因构建了矩阵,并采用最大似然法及贝叶斯推断重建系统发育树。基于两种分析方法获得的系统发育树的拓扑结构完全一致且分辨率及支持率较高。在ML树中,总分支数为129个,其中支持率≥70%的分支数目为123个。结果表明:(1)广义玄参科不是一个单系类群,隶属于广义玄参科的51个物种(37属)分散于列当科、泡桐科、美丽桐科、通泉草科、母草科、狭义玄参科和车前科。(2)狭义玄参科为单系类群,除原隶属于广义玄参科的Bontia、Calamphoreus、Diocirea、Eremophila、Glycocystis、Leucophyllum、玄参属和毛蕊花属外,还包括了原隶属于马钱科的醉鱼草属和原隶属于苦槛蓝科的苦槛蓝属。(3)唇形目为一个单系,目下共形成了14个支持率高的单系分支,对应于14个科(其中美丽桐科和胡麻科仅包括一个物种,不包括在内),科间关系得到较好的解决,木犀科为最早分化出来的类群,其余的类群共同组成核心唇形目。在核心唇形目中,类群分化的次序依次为苦苣苔科、车前科、玄参科和母草科,其余的科聚成两个大的分支。其中,一个大分支包括5个科,紫葳科、马鞭草科和胡麻科形成中等支持率的一个亚支,其中紫葳科、马鞭草科为姐妹群; 爵床科和狸藻科亦形成中等支持率的一个亚支; 另一个大分支包括了6个科,类群分化的次序依次为唇形科、通泉草科、美丽桐科+透骨草科,泡桐科和列当科为姐妹群,为较进化的类群。该研究结果表明,传统意义上的玄参科不是一个自然类群,包括的种属分散于唇形目; 质体基因组适用于解决广义玄参科的系统发育关系,有待于扩大样本进一步研究。

Abstract:

Phylogenetic relationships of Scrophulariaceae s. l.(sensu lato)and the closely related groups were explored with 129 plastid genomes representing 107 genera. Plastome sequences were downloaded from the GenBank. Based on coding sequences(CDS), phylogenetic trees were reconstructed using maximum likelihood(ML)and Bayesian inference(BI)approaches. The ML and BI analyses shared the same topology and the main clades were consistently recovered with high support. Of the 129 total nodes, 123 were supported by ML bootstrap value ≥70%. The result were as follows:(1)Scrophulariaceae s. l. was confirmed as polyphyletic. Fifty-one species with representatives of 37 genera from the Scrophulariaceae s.l. were assigned to seven families. These were Orobanchaceae, Paulowniaceae, Wightiaceae, Mazaceae, Linderniaceae, Scrophulariaceae s. s.(sensu stricto), and Plantaginaceae.(2)Scrophulariaceae s.s. was a monophyletic group. In addition to the recognition of eight genera(including Bontia, Calamphoreus, Diocirea, Eremophila, Glycocystis, Leucophyllum, Scrophularia and Verbascum)comprised primarily of former members of Scrophulariaceae s.l., Buddleja which was originally placed in Loganiaceae, and Myoporum, traditionally placed in the Myoporaceae had been demonstrated to belong to this clade.(3)The Lamiales was monophyletic. Fourteen well-supported monophyletic clades were obtained corresponding to each family(Wightiaceae and Pedaliaceae for which only one species had been contained were not included). The relationships among the families were well resolved. Oleaceae formed a well-supported clade that was distinct from core Lamiales. Within the core Lamiales, four clades(Gesneriaceae, Plantaginaceae, Scrophulariaceae, and Linderniaceae)diverged before the remaining families grouping in two sister clades. Within one clade, two moderately to highly supported subclades were recovered. Lentibulariaceae was resolved as sister group to Acanthaceae, and Pedaliaceae was sister to Verbenaceae + Bignoniaceae. The other clade contained six families, with Lamiaceae, Mazaceae, Wightiaceae + Phrymaceae, and Paulowniaceae successively sister to Orobanchaceae. The results of our analyses indicate that the traditional Scrophulariaceae are an unnatural assemblage of plants distributed throughout the phylogenentic tree of Lamiales. Phylogenomics analyses based on plastid organelle have shown good potential for phylogenetic inference in Scrophulariaceae, more taxonomic sampling are needed to enhance our understanding of phylogenetic relationships of Scrophulariaceae in future studies.