PHYLOGENOMICS AND PLASTOME EVOLUTION OF THE CHLORIDOID GRASSES (CHLORIDOIDEAE: POACEAE)
PHYLOGENOMICS AND PLASTOME EVOLUTION OF THE CHLORIDOID GRASSES (CHLORIDOIDEAE: POACEAE)
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DOI：
10.1086/684526
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发表时间：
2016-03-01
影响因子：
2.3
通讯作者：
Kelchner, Scot A.
中科院分区：
文献类型：
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作者：
Duvall, Melvin R.;Fisher, Amanda E.;Kelchner, Scot A.
研究的优先权。完整质体的研究为我们理解禾本科植物的分子进化和叶绿体基因组学提供了信息，但本研究尚未包括Chloridoideae亚科。在以前的多位点研究中，特定的深分支，如在对应于犬齿亚科的大分支中，并不均匀。本研究对绿球藻亚科4族10属14种植物进行了质体染色体组全基因组分析。一个物种是桑格测序，和14个其他物种，包括外类群，测序与下一代测序合成方法。通过从头方法组装来自下一代序列的质体，并对整个质体的明确对齐的编码和非编码序列进行遗传学分析。完整的质体在Distichlis，Centropodia和Eragrostis tef中显示出罕见的基因组变化，这些变化具有潜在的染色体组学意义。系统基因组学分析显示，除了一个节点在犬齿亚目，其中一个短的内部分支连接长的终端分支的所有内组关系的一致强有力的支持。本分支内的决议被认为是依赖于分类群，并可能受到长分支吸引假象。我们的研究表明，在整个质体序列的系统发育信息的增加，很好地解决和强有力的支持部落和属的chloridoid草之间的关系。采样更多的物种，特别是在Centropodia 1 Ellisoelata分支和Cynodonteae，将进一步解决这些群体的关系，并澄清亚科的进化起源。
Premise of research. Studies of complete plastomes have proven informative for our understanding of the molecular evolution and phylogenomics of grasses, but subfamily Chloridoideae has not been included in this research. In previous multilocus studies, specific deep branches, as in the large clade corresponding to Cynodonteae, are not uniformly well supported.Methodology. In this study, a plastome phylogenomic analysis sampled 14 species representing 4 tribes and 10 genera of Chloridoideae. One species was Sanger sequenced, and 14 other species, including outgroups, were sequenced with next-generation sequencing-by-synthesis methods. Plastomes from next-generation sequences were assembled by de novo methods, and the unambiguously aligned coding and noncoding sequences of the entire plastomes were analyzed phylogenetically.Pivotal results. Complete plastomes showed rare genomic changes in Distichlis, Centropodia, and Eragrostis tef that were of potential phylogenomic significance. Phylogenomic analyses showed uniformly strong support for all ingroup relationships except one node in Cynodonteae in which a short internal branch connected long terminal branches. Resolution within this clade was found to be taxon dependent and possibly subject to long-branch attraction artifacts.Conclusions. Our study indicates that the increase in phylogenetic information in sequences of entire plastomes well resolves and strongly supports relationships among tribes and genera of chloridoid grasses. Sampling more species, especially in the Centropodia 1 Ellisochloa clade and Cynodonteae, will further address relationships in these groups and clarify the evolutionary origins of the subfamily.