The phylogeny of the BEP clade in grasses revisited: Evidence from the whole-genome sequences of chloroplasts
The phylogeny of the BEP clade in grasses revisited: Evidence from the whole-genome sequences of chloroplasts
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DOI：
10.1016/j.ympev.2011.10.019
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发表时间：
2012-01-01
影响因子：
4.1
通讯作者：
Ge, Song
中科院分区：
文献类型：
--
作者：
Wu, Zhi-Qiang;Ge, Song
尽管重建禾本科植物的系统发育已经付出了相当大的努力，但在BEP分支中竹亚科、早熟禾亚科和Ehrhartoideae亚科之间的关系仍然没有得到解决。本研究对竹亚科（Bambusoideae）和狗牙根亚科（Ehrhartoideae）的3种代表性禾本科植物的叶绿体基因组进行了全序列测定，并从GenBank中获得了另外19种禾本科植物的叶绿体基因组序列。利用来自22种禾本科植物的76个叶绿体蛋白编码基因的序列，我们完全解决了BEP分支的进化。我们的结果强烈支持（B，P）E假说，即，竹亚科与早熟禾亚科的亲缘关系较近。这一结果不受系统误差或抽样误差的影响，也不受系统发育方法或模型规格的影响。分歧时间估计表明，最初的多样化的BEP分支成三个亚科发生在很短的时间内（类似4 MY）。这些短的内部分支的存在可以解释以前的研究无法实现一个有信心的解决的BEP分支。整个叶绿体基因组序列的组合提供了足够的系统发育信息，以充分解决的BEP系统发育。这些结果提供了一个有价值的进化框架，比较和功能基因组研究使用禾本科作为模式系统。(C)2011 Elsevier Inc. All rights reserved.
Despite the considerable efforts to reconstruct the phylogeny of grasses, the relationships among the subfamilies Bambusoideae, Pooideae and Ehrhartoideae in the BEP clade remain unresolved. Here we completely sequenced three chloroplast genomes of representative species from Bambusoideae and Ehrhartoideae and obtained 19 additional chloroplast genome sequences of other grasses from GenBank. Using sequences of 76 chloroplast protein-coding genes from the 22 grass species, we fully resolved the phylogeny of the BEP clade. Our results strongly supported the (B,P)E hypothesis, i.e., Bambusoideae and Pooideae are more closely related than Ehrhartoideae. This result was not biased by systematic or sampling errors and was impervious to phylogenetic methods or model specification. The divergence time estimate suggests that the initial diversification of the BEP clade into three subfamilies happened within a short time period (similar to 4 MY). The presence of these short internal branches may explain the inability of previous studies to achieve a confident resolution of the BEP clade. The combination of the sequences of the entire chloroplast genomes provided sufficient phylogenetic information to resolve the BEP phylogeny fully. These results provide a valuable evolutionary framework for comparative and functional genomic studies using the grass family as a model system. (C) 2011 Elsevier Inc. All rights reserved.