Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
PLoS One. 2013 May 29;8(5):e64642. doi: 10.1371/journal.pone.0064642. Print 2013.
BEP clade of the grass family (Poaceae) is composed of three subfamilies, i.e. Bambusoideae, Ehrhartoideae, and Pooideae. Controversies on the phylogenetic relationships among three subfamilies still persist in spite of great efforts. However, previous evidence was mainly provided from plastid genes with only a few nuclear genes utilized. Given different evolutionary histories recorded by plastid and nuclear genes, it is indispensable to uncover their relationships based on nuclear genes. Here, eleven species with whole-sequenced genome and six species with transcriptomic data were included in this study. A total of 121 one-to-one orthologous groups (OGs) were identified and phylogenetic trees were reconstructed by different tree-building methods. Genes which might have undergone positive selection and played important roles in adaptive evolution were also investigated from 314 and 173 one-to-one OGs in two bamboo species and 14 grass species, respectively. Our results support the ((B, P) E) topology with high supporting values. Besides, our findings also indicate that 24 and nine orthologs with statistically significant evidence of positive selection are mainly involved in abiotic and biotic stress response, reproduction and development, plant metabolism and enzyme etc. from two bamboo species and 14 grass species, respectively. In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the grass family.
BEP 分支的禾本科（Poaceae）由三个亚科组成，即竹亚科、高粱亚科和禾亚科。尽管已经做出了巨大的努力，但三个亚科之间的系统发育关系仍然存在争议。然而，以前的证据主要来自质体基因，只有少数核基因被利用。鉴于质体和核基因记录的不同进化历史，基于核基因揭示它们的关系是必不可少的。本研究共包括 11 个全基因组测序物种和 6 个转录组数据物种。共鉴定出 121 个一对一的直系同源群（OG），并采用不同的建树方法构建了系统发育树。还从两个竹种的 314 个和 173 个一对一 OG 以及 14 个草种中分别研究了可能经历正选择并在适应性进化中发挥重要作用的基因。我们的结果支持（B，P）E 拓扑结构，具有较高的支持值。此外，我们的研究结果还表明，从两个竹种和 14 个草种中分别有 24 个和 9 个直系同源物具有统计学意义上的正选择证据，主要涉及非生物和生物胁迫反应、繁殖和发育、植物代谢和酶等。综上所述，本研究展示了系统发育组学方法在揭示 BEP 分支内进化关系方面的强大功能，并为禾本科的适应性进化提供了有价值的见解。
