Origins of major archaeal clades correspond to gene acquisitions from bacteria

Nelson-Sathi, S.; Sousa, F. L.; Roettger, M.; Lozada-Chavez, N.; Thiergart, T.; Janssen, A.; Bryant, D.; Landan, G.; Schonheit, P.; Siebers, B.; McInerney, J. O.; Martin, W. F.

Abstract

The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms--ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions. To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes. Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample. Here we report that the origins of these 13 groups unexpectedly correspond to 2,264 group-specific gene acquisitions from bacteria. Interdomain gene transfer is highly asymmetric, transfers from bacteria to archaea are more than fivefold more frequent than vice versa. Gene transfers identified at major evolutionary transitions among prokaryotes specifically implicate gene acquisitions for metabolic functions from bacteria as key innovations in the origin of higher archaeal taxa.

Citation

Nelson-Sathi, S., Sousa, F. L., Roettger, M., Lozada-Chavez, N., Thiergart, T., Janssen, A., …Martin, W. F. (2015). Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature, 517(7532), 77-80. https://doi.org/10.1038/nature13805

• Journal Article Type: Article
• Acceptance Date: Aug 28, 2014
• Online Publication Date: Oct 15, 2014
• Publication Date: 2015
• Deposit Date: Jul 15, 2020
• Journal: Nature
• Print ISSN: 0028-0836
• Electronic ISSN: 1476-4687
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 517
• Issue: 7532
• Pages: 77-80
• DOI: https://doi.org/10.1038/nature13805
• Keywords: Archaea; Archaeal Proteins; Evolution, ; Molecular Gene Transfer; Genes, Bacteria; Phylogeny
• Public URL: http://www.ncbi.nlm.nih.gov/pubmed/25317564
• Publisher URL: https://www.nature.com/articles/nature13805