Pervasive tandem duplications and convergent evolution shape coral genomes. Noel, B., Denoeud, F., Rouan, A., Buitrago-López, C., Capasso, L., Poulain, J., Boissin, E., Pousse, M., Da Silva, C., Couloux, A., Armstrong, E., Carradec, Q., Cruaud, C., Labadie, K., Lê-Hoang, J., Tambutté, S., Barbe, V., Moulin, C., Bourdin, G., Iwankow, G., Romac, S., Agostini, S., Banaigs, B., Boss, E., Bowler, C., De Vargas, C., Douville, E., Flores, J. M., Forcioli, D., Furla, P., Galand, P. E., Lombard, F., Pesant, S., Reynaud, S., Sullivan, M. B., Sunagawa, S., Thomas, O. P., Troublé, R., Thurber, R. V., Allemand, D., Planes, S., Gilson, E., Zoccola, D., Wincker, P., Voolstra, C. R., & Aury, J. Genome Biology, 24(1):123, June, 2023.
Pervasive tandem duplications and convergent evolution shape coral genomes [link]Paper  doi  abstract   bibtex   2 downloads  
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.
@article{noel_pervasive_2023,
	title = {Pervasive tandem duplications and convergent evolution shape coral genomes},
	volume = {24},
	issn = {1474-760X},
	url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02960-7},
	doi = {10.1186/s13059-023-02960-7},
	abstract = {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.},
	language = {en},
	number = {1},
	urldate = {2023-06-12},
	journal = {Genome Biology},
	author = {Noel, Benjamin and Denoeud, France and Rouan, Alice and Buitrago-López, Carol and Capasso, Laura and Poulain, Julie and Boissin, Emilie and Pousse, Mélanie and Da Silva, Corinne and Couloux, Arnaud and Armstrong, Eric and Carradec, Quentin and Cruaud, Corinne and Labadie, Karine and Lê-Hoang, Julie and Tambutté, Sylvie and Barbe, Valérie and Moulin, Clémentine and Bourdin, Guillaume and Iwankow, Guillaume and Romac, Sarah and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Douville, Eric and Flores, J. Michel and Forcioli, Didier and Furla, Paola and Galand, Pierre E. and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Sullivan, Matthew B. and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Allemand, Denis and Planes, Serge and Gilson, Eric and Zoccola, Didier and Wincker, Patrick and Voolstra, Christian R. and Aury, Jean-Marc},
	month = jun,
	year = {2023},
	pages = {123},
}
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