State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
Mol Phylogenet Evol. 2012 Jan;62(1):573-8. doi: 10.1016/j.ympev.2011.10.019. Epub 2011 Nov 10.
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 (≈ 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.
尽管人们为重建禾本科植物的系统发育做出了相当大的努力，但 BEP 分支中竹亚科、禾本科和画眉草亚科之间的关系仍未得到解决。在这里，我们对竹亚科和画眉草亚科的代表物种的三个叶绿体基因组进行了完全测序，并从 GenBank 获得了其他 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 分支的系统发育问题。我们的研究结果强烈支持（B，P）E 假说，即竹亚科和禾本科比画眉草亚科更为密切相关。这一结果不受系统或抽样误差的影响，也不受系统发育方法或模型规范的影响。时间估计表明，BEP 分支最初分为三个亚科的时间很短（约 4 百万年）。这些短的内部分支的存在可能解释了以前的研究无法对 BEP 分支进行自信的分辨率的原因。整个叶绿体基因组序列的结合提供了足够的系统发育信息，可完全解决 BEP 系统发育问题。这些结果为利用禾本科作为模式系统进行比较和功能基因组学研究提供了有价值的进化框架。
