Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM 1095, AP-HM, IHU - Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, France.
Institut Universitaire de France (IUF), Paris, France.
Genome Biol Evol. 2017 Oct 1;9(10):2635-2639. doi: 10.1093/gbe/evx208.
Genome remodeling and exchange of sequences are widespread in the prokaryotic world and mosaic genomes challenge the classification of prokaryotes, which cannot be properly achieved in terms of a single gene or group of genes. Here, we studied individually the gene collection of the archaic microorganism Lokiarchaeum sp., suggested as an archaeal host close to the emergence of the eukaryotes. The network or rhizome of all Lokiarchaeum sp. genes revealed that the genomic repertoire is mainly composed of genes from archaeal (∼36%) and bacterial origin (∼28%), distantly followed by components of eukaryotic origin (∼2%). Thirty-three percent of genes were unique to this species (ORFans). The mosaicity of archaea was also supported by studying Methanomassiliicoccus luminyensis, an archaea from the gut, in which 67% of the genomic repertoire arised from archaea and 22% from bacteria. Our results illustrate the intricate evolutionary relationships of the archaeal genome repertoire and highlight the rhizome-like processes of evolution in archaea, their mosaicity, and chimeric origin composed of different domains of life, questioning the reality of a tree of life.
基因组重排和序列交换在原核生物世界中广泛存在，镶嵌基因组挑战了原核生物的分类，单凭单个基因或一组基因无法准确实现分类。在这里，我们单独研究了古老微生物 Lokiarchaeum sp. 的基因集合，该微生物被认为是接近真核生物出现的古菌宿主。Lokiarchaeum sp. 所有基因的网络或根茎揭示了基因组的组成主要由来自古菌（约 36%）和细菌（约 28%）的基因组成，其次是远缘的真核生物起源的成分（约 2%）。33%的基因是该物种特有的（ORFans）。通过研究肠道中的古菌 Methanomassiliicoccus luminyensis，也支持了古菌的镶嵌性，其基因组组成的 67%来自古菌，22%来自细菌。我们的结果说明了古菌基因组组成的复杂进化关系，并强调了古菌进化的根茎样过程、其镶嵌性以及由不同生命领域组成的嵌合体起源，这对生命之树的现实提出了质疑。
