Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China; Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China; Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
Mol Ecol Resour. 2014 Sep;14(5):988-99. doi: 10.1111/1755-0998.12248. Epub 2014 Apr 2.
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 with 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, 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）在形态上高度多样化，但遗传变异却相对较少。该谱系的分类学难以处理，其族内的关系也尚未得到很好的解决。最近的研究表明，该族可能具有复杂的进化历史。尽管已经对该族进行了系统发育研究，但大多数系统发育重建都是基于质体数据，其提供的系统发育分辨率低于核数据。在这项研究中，我们旨在确定一组理想的核基因，以解决温带木本竹类的系统发育关系。使用两种不同的方法，我们分别鉴定出 209 个和 916 个基因，作为假定的单拷贝直系同源基因。通过对来自该族的 5 个物种的下一代测序技术，共成功扩增和测序了 112 个基因。由于大多数基因表现出个体内等位基因异质性，我们通过基于单个基因重建系统发育来研究其系统发育的有用性。观察到基因树之间的分歧，并为了解决冲突，我们使用 BUCKy 和 HybTree 进行了一系列分析。虽然从多个相互冲突的基因推断系统发育时应谨慎，但我们的分析表明，在所研究的 112 个基因中，有 74 个基因可能是解决温带木本竹类系统发育的潜在标记。
