Gene duplication drives genome expansion in a major lineage of Thaumarchaeota

Sheridan, Paul O.; Raguideau, Sebastien; Quince, Christopher; Holden, Jennifer; Zhang, Lihong; Gaze, William H.; Mead, Andrew; Singer, Andrew C. ORCID: https://orcid.org/0000-0003-4705-6063; Wellington, Elizabeth M.H.; Williams, Tom A.; Gubry-Rangin, Cécile. 2020 Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nature Communications, 11, 5494. 12, pp. 10.1038/s41467-020-19132-x

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Official URL: http://dx.doi.org/10.1038/s41467-020-19132-x

Abstract/Summary

Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle, but the mechanisms driving their radiation into diverse ecosystems remain underexplored. Here, existing thaumarchaeotal genomes are complemented with 12 genomes belonging to the previously under-sampled Nitrososphaerales to investigate the impact of lateral gene transfer (LGT), gene duplication and loss across thaumarchaeotal evolution. We reveal a major role for gene duplication in driving genome expansion subsequent to early LGT. In particular, two large LGT events are identified into Nitrososphaerales and the fate of these gene families is highly lineage-specific, being lost in some descendant lineages, but undergoing extensive duplication in others, suggesting niche-specific roles. Notably, some genes involved in carbohydrate transport or coenzyme metabolism were duplicated, likely facilitating niche specialisation in soils and sediments. Overall, our results suggest that LGT followed by gene duplication drives Nitrososphaerales evolution, highlighting a previously under-appreciated mechanism of genome expansion in archaea.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	10.1038/s41467-020-19132-x
UKCEH and CEH Sections/Science Areas:	Pollution (Science Area 2017-)
ISSN:	2041-1723
Additional Information. Not used in RCUK Gateway to Research.:	Open Access paper - full text available via Official URL link.
Additional Keywords:	archaeal genomics, genome evolution, metagenomics, phylogenetics
NORA Subject Terms:	Biology and Microbiology
Date made live:	02 Dec 2020 12:54 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/529075

Item Type:

Publication - Article

Digital Object Identifier (DOI):

10.1038/s41467-020-19132-x

UKCEH and CEH Sections/Science Areas:

Pollution (Science Area 2017-)

ISSN:

2041-1723

Additional Information. Not used in RCUK Gateway to Research.:

Open Access paper - full text available via Official URL link.

Additional Keywords:

archaeal genomics, genome evolution, metagenomics, phylogenetics