Plastome phylogenomics of the early-diverging eudicot family Berberidaceae
Plastome phylogenomics of the early-diverging eudicot family Berberidaceae
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早期分化的双子叶植物小檗科的质体系统发育学
DOI：
10.1016/j.ympev.2018.07.021
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发表时间：
2018-11-01
影响因子：
4.1
通讯作者：
Wang, Hengchang
中科院分区：
文献类型：
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作者：
Sun, Yanxia;Moore, Michael J.;Wang, Hengchang
早分化双子叶植物小檗科的属间关系一直存在争议。为了解决这些关系，并更好地了解家庭内的质体组进化，我们测序了十个小檗科属的完整的质体组序列，结合这些与现有的6个质体的家庭，并进行了一系列的基因组分析的结果数据集。新测序的质体中有5个具有典型的被子植物质体的79个蛋白质编码基因、4个rRNA基因和30个tRNA基因。infA基因被发现是假的，在Bongardia，Diphylleia，八角莲和Vulgaveria; rps 7被发现是严重截短的Diphylleia，八角莲和鬼臼; clpP被发现是高度分歧的Vulgaveria;和类似的19 kb倒位检测到Bongardia。最大似然系统发育分析的79个基因，24个分类单元的数据集，包括几乎所有属的小檗科恢复四个染色体组（x = 6，7，8，10），解决了x = 8组的姐妹x = 10组，并支持单系的沼泽地包括x = 7，8，10。每个组内的通用关系都得到了高度支持。基于反向重复序列（IR）内的基因存在，在小檗科内共鉴定出7种质体IR类型。生物地理学分析表明，小檗科的起源和多样性可能受到其有利栖息地-温带森林分布的强烈影响。
The relationships among the genera of the early-diverging eudicot family Berberidaceae have long been controversial. To resolve these relationships and to better understand plastome evolution within the family, we sequenced the complete plastome sequences of ten Berberidaceae genera, combined these with six existing plastomes for the family, and conducted a series of phylogenomic analyses on the resulting data set. Five of the newly sequenced plastomes were found to possess the typical angiosperm plastome complement of 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. The infA gene was found to be pseudogenized in Bongardia, Diphylleia, Dysosma and Vancouveria; rps7 was found to be severely truncated in Diphylleia, Dysosma and Podophyllum; clpP was found to be highly divergent in Vancouveria; and a similar to 19 kb inversion was detected in Bongardia. Maximum likelihood phylogenetic analyses of a 79-gene, 24-taxon data set including nearly all genera of Berberidaceae recovered four chromosome groups (x = 6, 7, 8, 10), resolved the x = 8 group as the sister to the x = 10 group, and supported the monophyly of the Glade comprising x = 7, 8, 10. The generic relationships within each group were all resolved with high support. Based on gene presence within the Inverted Repeat (IR), a total of seven plastome IR types were identified within Berberidaceae. Biogeographical analysis indicated the origin and diversification of Berberidaceae has likely been strongly influenced by the distribution of its favored habitat: temperate forests.