Gene duplication drives genome expansion in a major lineage of Thaumarchaeota

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-sam...

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Bibliographic Details
Published in:	Nature communications 2020-10, Vol.11 (1), p.5494-12, Article 5494
Main Authors:	Sheridan, Paul O, Raguideau, Sebastien, Quince, Christopher, Holden, Jennifer, Zhang, Lihong, Williams, Tom A, Gubry-Rangin, Cécile
Format:	Article
Language:	eng
Subjects:	Ammonia Archaea Archaea - classification Archaea - genetics Archaea - metabolism Carbohydrate metabolism Carbohydrates Ecosystem Evolution Evolution, Molecular Expansion Gene Duplication Gene families Gene transfer Gene Transfer, Horizontal Genome, Archaeal Genomes Metagenomics Niches Nitrogen cycle Phylogeny Proteome Radiation Reproduction (copying) Sediments Thaumarchaeota
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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.
ISSN:	2041-1723 2041-1723