Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data

Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multi-locus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing 9 of the 11 known major lineages and 10 non-yeast fungal outgroups to generate a 1,233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the 9 major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, 8 of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.阐明酵母菌亚门（Saccharomycotina）各酵母物种间的系统发育关系，是理解其代谢演化与生态生活方式的先决条件。近二十年来，核糖体DNA（rDNA）与多基因座数据集的应用极大推动了我们对酵母系统发育的认知，但诸多深层系统发育关系仍未得到有效支持。与之形成对比的是，过往系统发育基因组学分析所涉及的分类单元与演化支数量相对较少，且在选取时往往未充分考虑覆盖酵母生物多样性的广度。本研究使用了86个公开可用的酵母基因组序列数据，这些基因组涵盖了已知11个主要演化支中的9个，以及10个非酵母真菌外类群，最终构建得到包含1233个基因、96个分类单元的数据集矩阵。本研究采用两种不同方法（串联法与溯祖法）以及两种数据集矩阵（氨基酸序列数据或密码子前两位位点数据）重建物种系统发育，结果显示9个主要演化支间的关系完全一致且支持度极高。除毕赤酵母科（Pichiaceae）所构成的演化支外，其余所有演化支均为单系群。绝大多数酵母物种间的系统发育关系在两种方法与两种数据集矩阵下均表现出稳健性。然而，93个系统发育节间中有8个在不同分析方法或数据集间存在冲突，涉及的类群定位包括：将CUG密码子重新分配为丝氨酸（而非亮氨酸）编码的物种所构成的演化支；由全基因组复制事件定义的演化支；以及淡红瓶囊酵母（Ascoidea rubescens）。本研究的系统发育基因组学分析为未来在分类学、分子遗传学、进化生物学、生态学以及生物技术学等领域开展酵母菌亚门的比较研究提供了坚实的研究框架。为达成这一目标，本研究还搭建了可检索86个酵母菌亚门基因组的BLAST（Basic Local Alignment Search Tool）服务器，访问地址为http://y1000plus.org/blast。