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New Phytol. 2017 Apr;214(1):219-232. doi: 10.1111/nph.14321. Epub 2016 Nov 21.

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

Author information

1
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.
2
Department of Plant Systems Biology, VIB, B-9052, Ghent, Belgium.
3
Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9000, Ghent, Belgium.
4
Bioinformatics Institute Ghent, Technologiepark 927, 9052, Ghent, Belgium.
5
IGDR CNRS-UMR6290 - Université Rennes 1, Rennes, France.
6
Abims Platform, CNRS-UPMC, FR2424, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France.
7
Department of Genetics, Genomics Research Institute, University of Pretoria, 0028, Pretoria, South Africa.

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.

KEYWORDS:

Ectocarpus ; Saccharina japonica ; alternative splicing; brown algae; genetic markers; genome reannotation; long noncoding RNAs; stramenopile

PMID:
27870061
DOI:
10.1111/nph.14321
[Indexed for MEDLINE]
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