Data from: Phylogenomic analysis of BAC-end sequence libraries in Oryza (Poaceae)

Analyses of genome scale data sets are beginning to clarify the phylogenetic relationships of species with complex evolutionary histories. Broad sampling across many genes allows for both large concatenated data sets to improve genome-scale phylogenetic resolution and also for independent analysis of gene trees and detection of phylogenetic incongruence. Recent sequencing projects in Oryza sativa and its wild relatives have positioned rice as a model system for such “phylogenomic” studies. We describe the assembly of a phylogenomic data set from 800,000 bacterial artificial chromosome (BAC) end sequences, producing an alignment of 2.4 million nucleotides for 10 diploid species of Oryza. A supermatrix approach confirms the broad outline of previous phylogenetic studies, although the non-phylogenetic signal and high levels of missing data must be handled carefully. Phylogenetic analysis of 12 chromosomes and nearly 2000 genes finds strikingly high levels of incongruence across different genomic scales, a result that is likely to apply to other low-level phylogenies in plants. We conclude that there is great potential for phylogenetic inference using data from next-generation sequencing protocols but that attention to methodological issues arising inevitably in these data sets is critical.

全基因组规模数据集的分析正逐步阐明具有复杂演化历史的物种种系发育关系。对众多基因的广泛取样，既可构建大型串联数据集以提升全基因组规模的系统发育分辨率，也可独立开展基因树分析并检测系统发育冲突。近期在栽培稻（Oryza sativa）及其野生近缘物种中开展的测序项目，已将水稻确立为这类“系统发育基因组学”研究的模式系统。本研究报道了一套基于80万条细菌人工染色体（BAC）末端序列构建的系统发育基因组数据集，为10个二倍体稻属物种生成了总长240万核苷酸的序列联配。超矩阵分析验证了此前系统发育研究的整体框架，但需谨慎处理非系统发育信号与高水平缺失数据。对12条染色体及近2000个基因的系统发育分析发现，不同基因组尺度下存在极高水平的系统发育冲突，这一结论大概率也适用于植物中其他低级分类单元的系统发育研究。本研究得出结论：利用下一代测序技术获取的数据开展系统发育推断具有巨大潜力，但必须高度重视这类数据集不可避免会出现的方法学相关问题。