Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus

dc.contributor.authorCormier, Alexandre
dc.contributor.authorAvia, Komlan
dc.contributor.authorSterck, Lieven
dc.contributor.authorDerrien, Thomas
dc.contributor.authorWucher, Valentin
dc.contributor.authorAndres, Gwendoline
dc.contributor.authorMonsoor, Misharl
dc.contributor.authorGodfroy, Olivier
dc.contributor.authorLipinska, Agnieszka
dc.contributor.authorPerrineau, Marie-Mathilde
dc.contributor.authorVan de Peer, Yves
dc.contributor.authorHitte, Christophe
dc.contributor.authorCorre, Erwan
dc.contributor.authorCoelho, Susana M.
dc.contributor.authorCock, J. Mark
dc.date.accessioned2018-02-08T07:53:39Z
dc.date.issued2017-04
dc.description.abstractThe genome of the filamentous brown alga Ectocarpus was the first to be completely sequenced from within the brown algal group and has served as a key reference genome both for this lineage and for the stramenopiles. We present a complete structural and functional reannotation of the Ectocarpus genome. The large-scale assembly of the Ectocarpus genome was significantly improved and genome-wide gene re-annotation using extensive RNA-seq data improved the structure of 11 108 existing protein-coding genes and added 2030 new loci. A genome-wide analysis of splicing isoforms identified an average of 1.6 transcripts per locus. A large number of previously undescribed noncoding genes were identified and annotated, including 717 loci that produce long noncoding RNAs. Conservation of lncRNAs between Ectocarpus and another brown alga, the kelp Saccharina japonica, suggests that at least a proportion of these loci serve a function. Finally, a large collection of single nucleotide polymorphism-based markers was developed for genetic analyses. These resources are available through an updated and improved genome database. This study significantly improves the utility of the Ectocarpus genome as a high-quality reference for the study of many important aspects of brown algal biology and as a reference for genomic analyses across the stramenopiles.en_ZA
dc.description.departmentGeneticsen_ZA
dc.description.embargo2018-04-30
dc.description.librarianhj2018en_ZA
dc.description.sponsorshipThe Centre National de la Recherche Scientifique, the Agence Nationale de la Recherche (project Bi-cycle ANR-10-BLAN-1727, project Idealg ANR-10-BTBR-04-01 and project Sexseaweed ANR-12-JSV7-0008), the University Pierre et Marie Curie and the European Research Council (grant agreement 638240). A.C. was supported by a grant from the Brittany Region.en_ZA
dc.description.urihttp://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1469-8137en_ZA
dc.identifier.citationCormier, A., Avia, K., Sterck, L., Derrien, T., Wucher, V., Andres, G., Monsoor, M., Godfroy, O., Lipinska, A., Perrineau, M.-M., Van De Peer, Y., Hitte, C., Corre, E., Coelho, S. M. and Cock, J. M. (2017), Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus. New Phytol, 214: 219–232. doi:10.1111/nph.14321.en_ZA
dc.identifier.issn0028-646X (print)
dc.identifier.issn1469-8137 (online)
dc.identifier.other10.1111/nph.14321
dc.identifier.urihttp://hdl.handle.net/2263/63892
dc.language.isoenen_ZA
dc.publisherWileyen_ZA
dc.rights© 2017 New Phytologist Trust. This is the pre-peer reviewed version of the following article : Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus. New Phytol, 214: 219–232, 2017, doi : 10.1111/nph.14321. The definite version is available at : http://onlinelibrary.wiley.comjournal/10.1111/(ISSN)1469-8137.en_ZA
dc.subjectStramenopileen_ZA
dc.subjectSaccharina japonicaen_ZA
dc.subjectLong noncoding RNAsen_ZA
dc.subjectGenome reannotationen_ZA
dc.subjectGenetic markersen_ZA
dc.subjectEctocarpusen_ZA
dc.subjectBrown algaeen_ZA
dc.subjectAlternative splicingen_ZA
dc.titleRe-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpusen_ZA
dc.typePostprint Articleen_ZA

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