Data from: Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos (Poaceae: Bambusoideae)

The temperate woody bamboos (Arundinarieae) are highly diverse in morphology but lack a substantial amount of genetic variation. The taxonomy of this lineage is intractable, and the relationships within the tribe have not been well resolved. Recent studies indicated that this tribe could have a complex evolutionary history. Although phylogenetic studies of the tribe have been carried out, most of these phylogenetic reconstructions were based on plastid data, which provide lower phylogenetic resolution compared to nuclear data. In this study, we intended to identify a set of desirable nuclear genes for resolving the phylogeny of the temperate woody bamboos. Using two different methodologies, we identified 209 and 916 genes, respectively, as putative single copy orthologous genes. A total of 112 genes was successfully amplified and sequenced by next-generation sequencing technologies in five species sampled from the tribe. As most of the genes exhibited intra-individual allele heterozygotes (IIAHs), we investigated phylogenetic utility by reconstructing the phylogeny based on individual genes. Discordance among gene trees was observed and, to resolve the conflict, we performed a range of analyses using BUCKy and HybTree. While caution should be taken when inferring a phylogeny from multiple conflicting genes, our analysis indicated that 74 of the 112 investigated genes are potential markers for resolving the phylogeny of the temperate woody bamboos.

温带木本竹类（Arundinarieae）形态多样性极高，但遗传变异相对匮乏。该族类群的分类学研究极具挑战性，其族内系统发育关系尚未得到充分解析。近期研究显示，该族拥有复杂的演化历史。尽管已有针对该族的系统发育研究，但多数系统发育重建均以质体数据（plastid data）为基础，相较核基因数据，其系统发育分辨率相对较低。本研究旨在筛选出一套适用于解析温带木本竹类系统发育的优质核基因。我们采用两种不同方法，分别筛选出209个与916个推定单拷贝直系同源基因（single copy orthologous genes）。本研究通过二代测序技术（next-generation sequencing technologies），成功对该族5个采样物种的112个基因完成了扩增与测序。由于多数基因存在个体内等位基因杂合性（intra-individual allele heterozygotes, IIAHs），我们通过基于单个基因的系统发育重建来评估其系统发育实用性。研究观察到基因树间存在拓扑冲突，为解决这一冲突，我们采用BUCKy与HybTree开展了一系列分析。尽管基于多个冲突基因推断系统发育时需谨慎行事，但本研究分析结果表明，112个研究基因中的74个可作为解析温带木本竹类系统发育的潜在分子标记。