Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae

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.

禾本科（Poaceae）的BEP演化支（BEP clade）由3个亚科构成，即竹亚科（Bambusoideae）、稻亚科（Ehrhartoideae）与早熟禾亚科（Pooideae）。尽管已有大量研究尝试解析该类群，但其三个亚科间的系统发育关系仍存在争议。既往研究的证据主要来源于质体基因，仅少数研究使用了核基因。鉴于质体基因与核基因所记录的演化历程存在差异，基于核基因解析三者间的系统发育关系至关必要。本研究纳入11个完成全基因组测序的物种，以及6个具备转录组数据（transcriptomic data）的物种。最终共鉴定得到121个一对一直系同源基因簇（one-to-one orthologous groups，OGs），并通过多种树构建方法重建系统发育树。此外，本研究还分别从2个竹类物种的314个一对一直系同源基因簇，以及14个禾本科物种的173个一对一直系同源基因簇中，筛选出可能经历正选择并在适应性进化中发挥关键作用的基因。研究结果支持((B, P), E)拓扑结构，且该拓扑结构具有较高的支持度。此外，研究发现分别有24个和9个直系同源基因经统计学检验呈现显著正选择信号，前者来自2个竹类物种的数据集，主要参与非生物胁迫响应、生殖发育、植物代谢及酶相关功能；后者来自14个禾本科物种的数据集，主要参与生物胁迫响应、生殖发育及植物代谢等过程。综上，本研究证实系统发育组学方法（phylogenomic approach）可有效解析BEP演化支内的演化关系，同时为禾本科植物的适应性进化研究提供了极具价值的新视角。