Deschamps Philippe, Zivanovic Yvan, Moreira David, Rodriguez-Valera Francisco, López-García Purificación
Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique (CNRS) and Université Paris-Sud, Orsay, France.
Institut de Génétique et Microbiologie, Centre National de la Recherche Scientifique (CNRS) and Université Paris-Sud, Orsay, France.
Genome Biol Evol. 2014 Jun 12;6(7):1549-63. doi: 10.1093/gbe/evu127.
Horizontal gene transfer (HGT) is an important force in evolution, which may lead, among other things, to the adaptation to new environments by the import of new metabolic functions. Recent studies based on phylogenetic analyses of a few genome fragments containing archaeal 16S rRNA genes and fosmid-end sequences from deep-sea metagenomic libraries have suggested that marine planktonic archaea could be affected by high HGT frequency. Likewise, a composite genome of an uncultured marine euryarchaeote showed high levels of gene sequence similarity to bacterial genes. In this work, we ask whether HGT is frequent and widespread in genomes of these marine archaea, and whether HGT is an ancient and/or recurrent phenomenon. To answer these questions, we sequenced 997 fosmid archaeal clones from metagenomic libraries of deep-Mediterranean waters (1,000 and 3,000 m depth) and built comprehensive pangenomes for planktonic Thaumarchaeota (Group I archaea) and Euryarchaeota belonging to the uncultured Groups II and III Euryarchaeota (GII/III-Euryarchaeota). Comparison with available reference genomes of Thaumarchaeota and a composite marine surface euryarchaeote genome allowed us to define sets of core, lineage-specific core, and shell gene ortholog clusters for the two archaeal lineages. Molecular phylogenetic analyses of all gene clusters showed that 23.9% of marine Thaumarchaeota genes and 29.7% of GII/III-Euryarchaeota genes had been horizontally acquired from bacteria. HGT is not only extensive and directional but also ongoing, with high HGT levels in lineage-specific core (ancient transfers) and shell (recent transfers) genes. Many of the acquired genes are related to metabolism and membrane biogenesis, suggesting an adaptive value for life in cold, oligotrophic oceans. We hypothesize that the acquisition of an important amount of foreign genes by the ancestors of these archaeal groups significantly contributed to their divergence and ecological success.
水平基因转移（HGT）是进化中的一种重要力量，除其他影响外，它可能通过导入新的代谢功能导致生物适应新环境。最近基于对一些含有古菌16S rRNA基因的基因组片段以及来自深海宏基因组文库的fosmid末端序列进行系统发育分析的研究表明，海洋浮游古菌可能受到高频率HGT的影响。同样，一种未培养的海洋广古菌的复合基因组显示出与细菌基因有高度的基因序列相似性。在这项研究中，我们探究HGT在这些海洋古菌的基因组中是否频繁且广泛存在，以及HGT是否是一种古老和/或反复出现的现象。为了回答这些问题，我们对来自地中海深海水域（深度为1000米和3000米）宏基因组文库的997个fosmid古菌克隆进行了测序，并为浮游奇古菌（第一组古菌）以及属于未培养的第二和第三广古菌组（GII/III-广古菌）的广古菌构建了全面的泛基因组。与奇古菌的可用参考基因组以及一个复合海洋表层广古菌基因组进行比较，使我们能够为这两个古菌谱系定义核心、谱系特异性核心和外壳基因直系同源簇集。对所有基因簇的分子系统发育分析表明，23.9%的海洋奇古菌基因和29.7%的GII/III-广古菌基因是从细菌中水平获得的。HGT不仅广泛且具有方向性，而且仍在进行中，在谱系特异性核心（古老转移）和外壳（近期转移）基因中具有较高的HGT水平。许多获得的基因与代谢和膜生物合成有关，这表明其对于在寒冷、贫营养海洋中的生存具有适应性价值。我们推测这些古菌群体的祖先获取大量外源基因对它们的分化和生态成功起到了重要作用。
