Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in phylogenetic trees of phylogenetic marker genes

BACKGROUND: Most of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new source of data for such studies has arrived: DNA sequence data generated directly from environmental samples. Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early events in the evolution of gene families and of species. METHODOLOGY/PRINCIPAL FINDINGS: We designed and implemented new methods for analyzing metagenomic data and used them to search the Global Ocean Sampling (GOS) Expedition data set for novel lineages in three gene families commonly used in phylogenetic studies of known and unknown organisms: small subunit rRNA and the recA and rpoB superfamilies. Though the methods available could not accurately identify very deeply branched ss-rRNAs (...

研究背景：当前，我们对生物古老演化历程的认知大多源自与特定已知生物相关的数据——即我们可直接开展研究的生物，例如植物、后生动物（metazoans）以及可培养微生物。然而近年来，这类研究迎来了全新的数据来源：直接从环境样本中获取的DNA序列数据。此类宏基因组数据（metagenomic data）在诸多领域均具备巨大应用潜力，正如本文所述，其可用于探究基因家族与物种演化过程中的极早期事件。

研究方法与主要发现：我们设计并实现了用于宏基因组数据分析的全新方法，并利用该方法对全球海洋采样（Global Ocean Sampling, GOS）考察计划的数据集进行检索，以寻找三类常用于已知与未知生物系统发育研究（phylogenetic studies）的基因家族中的新型进化谱系：小亚基核糖体RNA（small subunit rRNA）、recA超家族与rpoB超家族。尽管现有方法无法精准识别深度极深分支的小亚基核糖体RNA（ss-rRNAs）……