title: Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus.
abstract: The 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.
authors.affiliation: Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Cormier
authors.affiliation: Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
authors.forename: Komlan
authors.identifier: http://orcid.org/0000-0001-6212-6774
authors.initials: K
authors.lastname: Avia
authors.affiliation: Department of Plant Systems Biology, VIB, B-9052, Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9000, Ghent, Belgium.|Bioinformatics Institute Ghent, Technologiepark 927, 9052, Ghent, Belgium.
authors.forename: Lieven
authors.initials: L
authors.lastname: Sterck
authors.affiliation: IGDR CNRS-UMR6290 - Université Rennes 1, Rennes, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Derrien
authors.affiliation: IGDR CNRS-UMR6290 - Université Rennes 1, Rennes, France.
authors.forename: Valentin
authors.initials: V
authors.lastname: Wucher
authors.affiliation: Abims Platform, CNRS-UPMC, FR2424, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France.
authors.forename: Gwendoline
authors.initials: G
authors.lastname: Andres
authors.affiliation: Abims Platform, CNRS-UPMC, FR2424, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France.
authors.forename: Misharl
authors.initials: M
authors.lastname: Monsoor
authors.affiliation: Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Godfroy
authors.affiliation: Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Lipinska
authors.affiliation: Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
authors.forename: Marie-Mathilde
authors.initials: MM
authors.lastname: Perrineau
authors.affiliation: Department of Plant Systems Biology, VIB, B-9052, Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9000, Ghent, Belgium.|Bioinformatics Institute Ghent, Technologiepark 927, 9052, Ghent, Belgium.|Department of Genetics, Genomics Research Institute, University of Pretoria, 0028, Pretoria, South Africa.
authors.forename: Yves
authors.initials: Y
authors.lastname: Van De Peer
authors.affiliation: IGDR CNRS-UMR6290 - Université Rennes 1, Rennes, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Hitte
authors.affiliation: Abims Platform, CNRS-UPMC, FR2424, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France.
authors.forename: Erwan
authors.initials: E
authors.lastname: Corre
authors.affiliation: Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
authors.forename: Susana M
authors.initials: SM
authors.lastname: Coelho
authors.affiliation: Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
authors.forename: J Mark
authors.initials: JM
authors.lastname: Cock
mesh_terms: D020418:Algal Proteins / Q000235:genetics / Q000378:metabolism; D017398:Alternative Splicing / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics*; D030541:Databases, Genetic; D056426:Genetic Loci; D016678:Genome; D016679:Genome, Viral; D008954:Models, Biological; D058977:Molecular Sequence Annotation; D000459:Phaeophyceae / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics
chemical_list: D020418:Algal Proteins; D021901:DNA, Intergenic; D062085:RNA, Long Noncoding
keywords: 
  Ectocarpus
  ; 
  Saccharina japonica
  ; alternative splicing; brown algae; genetic markers; genome reannotation; long noncoding RNAs; stramenopile