Bern Marshall, Goldberg David, Lyashenko Eugenia
Palo Alto Research Center, 3333 Coyote Hill Road, Palo Alto, CA 94304, USA.
Nucleic Acids Res. 2006;34(16):4342-53. doi: 10.1093/nar/gkl440. Epub 2006 Aug 26.
A synapomorphy is a phylogenetic character that provides evidence of shared descent. Ideally a synapomorphy is ubiquitous within the clade of related organisms and nonexistent outside the clade, implying that it arose after divergence from other extant species and before the last common ancestor of the clade. With the recent proliferation of genetic sequence data, molecular synapomorphies have assumed great importance, yet there is no convenient means to search for them over entire genomes. We have developed a new program called Conserv, which can rapidly assemble orthologous sequences and rank them by various metrics, such as degree of conservation or divergence from out-group orthologs. We have used Conserv to conduct a largescale search for molecular synapomorphies for bacterial clades. The search discovered sequences unique to clades, such as Actinobacteria, Firmicutes and gamma-Proteobacteria, and shed light on several open questions, such as whether Symbiobacterium thermophilum belongs with Actinobacteria or Firmicutes. We conclude that Conserv can quickly marshall evidence relevant to evolutionary questions that would be much harder to assemble with other tools.
共近裔性状是一种系统发育特征，它为共同祖先提供了证据。理想情况下，共近裔性状在相关生物类群中普遍存在，而在该类群之外不存在，这意味着它是在与其他现存物种分化之后、该类群的最后一个共同祖先之前出现的。随着最近基因序列数据的激增，分子共近裔性状变得极为重要，但目前还没有一种便捷的方法能在整个基因组中搜索它们。我们开发了一个名为Conserv的新程序，它可以快速组装直系同源序列，并根据各种指标（如保守程度或与外类群直系同源序列的差异程度）对它们进行排序。我们使用Conserv对细菌类群的分子共近裔性状进行了大规模搜索。该搜索发现了一些类群特有的序列，如放线菌门、厚壁菌门和γ-变形菌纲，并为几个悬而未决的问题提供了线索，比如嗜热共生菌是属于放线菌门还是厚壁菌门。我们得出结论，Conserv可以迅速整理与进化问题相关的证据，而用其他工具来整理这些证据则要困难得多。
