Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes
Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes
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DOI：
10.1093/aobpla/plv046
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发表时间：
2015-01-01
期刊：
影响因子：
2.9
通讯作者：
Duvall, Melvin R.
中科院分区：
文献类型：
--
作者：
Saarela, Jeffery M.;Wysocki, William P.;Duvall, Melvin R.
整个质体基因组正在从整个绿色植物生命树中快速测序，这些系统发育分析正在增加分辨率，并支持早期单基因和多基因研究中存在差异或未解决的关系。冷季型禾本科是12个禾本科亚科中最大的一个，包括重要的温带禾本科、草坪草和牧草。虽然已经进行了大量的研究，一些“早期分歧”部落之间的关系冲突的研究，和一些亚族的Poeae之间的关系尚未得到解决。为了解决这些问题，我们对25个完整的质体进行了新的测序，这些质体显示了禾本科的典型重排。这些质体代表了Pooideae的9个族和11个亚族，并与亚科的20个现有质体进行了分析。最大似然（ML），最大简约（MP）和贝叶斯推理（BI）鲁棒地解决了子家族中最深的关系。完整的质体组数据提供了增加的节点支持相比，单独的蛋白编码数据的节点，没有最大限度地支持。继Brachyelytrum之后，Phaenospermateae，Brylkinieae-Meliceae和Ampelodesmeae-Stipeae是亚科其余部分的连续姐妹群。Ampelodesmeae嵌套在Stipeae中的质体树，与其phaenospermatoid和stipoid草（母本）之间的杂交起源一致。核心Pooideae是强有力的支持，包括Brachypodieae，一个Bromeae-Triticeae分支和Poeae。在Poeae内，Phalaridinae和Torreyoaculinae之间发现了一种新的姐妹群关系，并且该分支和Aveninae的相对分支顺序，相对于Agrostidinae-Brizinae分支，MP和ML/BI树之间不一致。最大似然和贝叶斯分析强烈支持Airinae和Holcinae作为Dactylidinae Loliinae分支的连续姐妹群。
Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single-and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with proteincoding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae-Loliinae clade.