Gene duplication drives genome expansion in a major lineage of Thaumarchaeota

Paul O. Sheridan, Sebastien Raguideau, Christopher Quince, Jennifer Holden, Lihong Zhang, Tom A. Williams and Cécile Gubry-Rangin ()
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Paul O. Sheridan: University of Aberdeen
Sebastien Raguideau: University of Warwick
Christopher Quince: University of Warwick
Jennifer Holden: University of Warwick
Lihong Zhang: University of Exeter
Tom A. Williams: University of Bristol
Cécile Gubry-Rangin: University of Aberdeen

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: Abstract 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.

Date: 2020
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DOI: 10.1038/s41467-020-19132-x

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