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

Background: 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, more broadly, for the stramenopiles.

Results: Here we present a complete structural and functional reannotation of the Ectocarpus genome sequence. The large-scale assembly of the Ectocarpus genome was significantly improved based on a high-density, RAD-seq-based genetic map. Genome-wide gene re-annotation improved the structure of 11,108 existing protein-coding genes and added 2,030 new loci. A genome-wide analysis of splicing isoforms identified an average of 1.6 transcripts per locus, comparable with alternative splicing levels in other complex eukaryotes. In addition, a large number of previously undescribed non-coding genes were identified and annotated, including 717 loci that produce long non-coding RNAs (lncRNAs). Conservation of lncRNAs between Ectocarpus and the kelp Saccharina japonica suggests that at least a proportion of these loci serve a function. Finally, a large collection of SNP markers was developed as a genetic resource. These improvements have been made available though an updated and improved genome database.

Conclusion: By both markedly improving existing resources and adding important new information, 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.

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