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Pervasive tandem duplications and convergent evolution shape coral genomes

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Title: Pervasive tandem duplications and convergent evolution shape coral genomes
Authors: Benjamin Noel, France Denoeud, Alice Rouan, Carol Buitrago-López, Laura Capasso, Julie Poulain, Emilie Boissin, Mélanie Pousse, Corinne Da Silva, Arnaud Couloux, Eric Armstrong, Quentin Carradec, Corinne Cruaud, Karine Labadie, Julie Lê-Hoang, Sylvie Tambutté, Valérie Barbe, Clémentine Moulin, Guillaume Bourdin, Guillaume Iwankow, Sarah Romac, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Eric Douville, J. Michel Flores, Didier Forcioli, Paola Furla, Pierre E. Galand, Fabien Lombard, Stéphane Pesant, Stéphanie Reynaud, Matthew B. Sullivan, Shinichi Sunagawa, Olivier P. Thomas, Romain Troublé, Rebecca Vega Thurber, Denis Allemand, Serge Planes, Eric Gilson, Didier Zoccola, Patrick Wincker, Christian R. Voolstra, Jean-Marc Aury
Source: Genome Biology, Vol 24, Iss 1, Pp 1-38 (2023)
Publisher Information: BMC, 2023.
Publication Year: 2023
Collection: LCC:Biology (General)
LCC:Genetics
Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470
More Details: Abstract Background Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. Results In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. Conclusions At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.
Document Type: article
File Description: electronic resource
Language: English
ISSN: 1474-760X
Relation: https://doaj.org/toc/1474-760X
DOI: 10.1186/s13059-023-02960-7
Access URL: https://doaj.org/article/1fa823a183e44ba3820bb85d0832cc5e
Accession Number: edsdoj.1fa823a183e44ba3820bb85d0832cc5e
Database: Directory of Open Access Journals
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  Data: Abstract Background Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. Results In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. Conclusions At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.
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