Ghent University Academic Bibliography

Advanced

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

Alexandre Cormier, Komlan Avia, Lieven Sterck UGent, Thomas Derrien, Valentin Wucher, Gwendoline Andres, Misharl Monsoor, Olivier Godfroy, Agnieszka Lipinska, Marie-Mathilde Perrineau, et al. (2017) NEW PHYTOLOGIST. 214(1). p.219-232
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
alternative splicing, brown algae, Ectocarpus, genetic markers, genome reannotation, long noncoding RNAs, Saccharina japonica, stramenopile, SMALL NUCLEOLAR RNAS, COMPLEX MULTICELLULARITY, SEQ DATA, SILICULOSUS, REVEALS, EVOLUTION, QUANTIFICATION, TRANSCRIPTOME, GENERATION, EXPRESSION
journal title
NEW PHYTOLOGIST
New Phytol.
volume
214
issue
1
pages
219 - 232
Web of Science type
Article
Web of Science id
000398130300022
ISSN
0028-646X
DOI
10.1111/nph.14321
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
8523484
handle
http://hdl.handle.net/1854/LU-8523484
date created
2017-06-13 09:23:00
date last changed
2017-09-07 13:36:45
@article{8523484,
  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.},
  author       = {Cormier, Alexandre and Avia, Komlan and Sterck, Lieven and Derrien, Thomas and Wucher, Valentin and Andres, Gwendoline and Monsoor, Misharl and Godfroy, Olivier and Lipinska, Agnieszka and Perrineau, Marie-Mathilde and Van de Peer, Yves and Hitte, Christophe and Corre, Erwan and Coelho, Susana M and Cock, J Mark},
  issn         = {0028-646X},
  journal      = {NEW PHYTOLOGIST},
  keyword      = {alternative splicing,brown algae,Ectocarpus,genetic markers,genome reannotation,long noncoding RNAs,Saccharina japonica,stramenopile,SMALL NUCLEOLAR RNAS,COMPLEX MULTICELLULARITY,SEQ DATA,SILICULOSUS,REVEALS,EVOLUTION,QUANTIFICATION,TRANSCRIPTOME,GENERATION,EXPRESSION},
  language     = {eng},
  number       = {1},
  pages        = {219--232},
  title        = {Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus},
  url          = {http://dx.doi.org/10.1111/nph.14321},
  volume       = {214},
  year         = {2017},
}

Chicago
Cormier, Alexandre, Komlan Avia, Lieven Sterck, Thomas Derrien, Valentin Wucher, Gwendoline Andres, Misharl Monsoor, et al. 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 Phytologist 214 (1): 219–232.
APA
Cormier, A., Avia, K., Sterck, L., Derrien, T., Wucher, V., Andres, G., Monsoor, M., et al. (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 PHYTOLOGIST, 214(1), 219–232.
Vancouver
1.
Cormier A, Avia K, Sterck L, Derrien T, Wucher V, Andres G, et al. Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus. NEW PHYTOLOGIST. 2017;214(1):219–32.
MLA
Cormier, Alexandre, Komlan Avia, Lieven Sterck, et al. “Re-annotation, Improved Large-scale Assembly and Establishment of a Catalogue of Noncoding Loci for the Genome of the Model Brown Alga Ectocarpus.” NEW PHYTOLOGIST 214.1 (2017): 219–232. Print.