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Gene duplication drives genome expansion in a major lineage of Thaumarchaeota

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Sheridan, Paul O., Raguideau, Sébastien, Quince, Christopher, Holden, Jennifer, Thames Consortium, , Zhang, Lihong, Gubry-Rangin, Cécile and Williams, Tom A. (2020) Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nature Communications, 11 (1). 5494. doi:10.1038/s41467-020-19132-x

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

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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.

Item Type: Journal Article
Subjects: Q Science > QH Natural history
Q Science > QR Microbiology
Divisions: Faculty of Medicine > Warwick Medical School > Biomedical Sciences
Faculty of Science > Life Sciences (2010- )
Faculty of Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection
Faculty of Medicine > Warwick Medical School
Library of Congress Subject Headings (LCSH): Archaebacteria , Genetic transformation
Journal or Publication Title: Nature Communications
Publisher: Nature Publishing Group
ISSN: 2041-1723
Official Date: 30 October 2020
Dates:
DateEvent
30 October 2020Published
21 September 2020Accepted
Date of first compliant deposit: 16 November 2020
Volume: 11
Number: 1
Article Number: 5494
DOI: 10.1038/s41467-020-19132-x
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
NE/ R001529/1UK Research and Innovationhttp://dx.doi.org/10.13039/100014013
URF150571 Royal Societyhttp://dx.doi.org/10.13039/501100000288
UF140626Royal Societyhttp://dx.doi.org/10.13039/501100000288
MR/M50161X/1[MRC] Medical Research Councilhttp://dx.doi.org/10.13039/501100000265
MR/L015080/1[MRC] Medical Research Councilhttp://dx.doi.org/10.13039/501100000265
BB/R015171/1[BBSRC] Biotechnology and Biological Sciences Research Councilhttp://dx.doi.org/10.13039/501100000268
NE/M011674/1[NERC] Natural Environment Research Councilhttp://dx.doi.org/10.13039/501100000270
NE/M011259/1[NERC] Natural Environment Research Councilhttp://dx.doi.org/10.13039/501100000270
NE/M01133X/1[NERC] Natural Environment Research Councilhttp://dx.doi.org/10.13039/501100000270
UNSPECIFIEDUniversity of Aberdeenhttp://dx.doi.org/10.13039/501100000882
Contributors:
ContributionNameContributor ID
Research GroupThames Consortium, UNSPECIFIED
ResearcherGaze, William H.UNSPECIFIED
ResearcherHolden, JenniferUNSPECIFIED
ResearcherMead, AndrewUNSPECIFIED
ResearcherRaguideau, SébastienUNSPECIFIED
ResearcherQuince, ChristopherUNSPECIFIED
ResearcherSinger, Andrew C.UNSPECIFIED
ResearcherWellington, Elizabeth M. H.35071
ResearcherZhang, LihongUNSPECIFIED

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