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An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies

BACKGROUND: Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O. tauri is the smallest free-living photosynthetic eukaryote known to date, a coccoid g...

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Autores principales: Blanc-Mathieu, Romain, Verhelst, Bram, Derelle, Evelyne, Rombauts, Stephane, Bouget, François-Yves, Carré, Isabelle, Château, Annie, Eyre-Walker, Adam, Grimsley, Nigel, Moreau, Hervé, Piégu, Benoit, Rivals, Eric, Schackwitz, Wendy, Van de Peer, Yves, Piganeau, Gwenaël
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378021/
https://www.ncbi.nlm.nih.gov/pubmed/25494611
http://dx.doi.org/10.1186/1471-2164-15-1103
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author Blanc-Mathieu, Romain
Verhelst, Bram
Derelle, Evelyne
Rombauts, Stephane
Bouget, François-Yves
Carré, Isabelle
Château, Annie
Eyre-Walker, Adam
Grimsley, Nigel
Moreau, Hervé
Piégu, Benoit
Rivals, Eric
Schackwitz, Wendy
Van de Peer, Yves
Piganeau, Gwenaël
author_facet Blanc-Mathieu, Romain
Verhelst, Bram
Derelle, Evelyne
Rombauts, Stephane
Bouget, François-Yves
Carré, Isabelle
Château, Annie
Eyre-Walker, Adam
Grimsley, Nigel
Moreau, Hervé
Piégu, Benoit
Rivals, Eric
Schackwitz, Wendy
Van de Peer, Yves
Piganeau, Gwenaël
author_sort Blanc-Mathieu, Romain
collection PubMed
description BACKGROUND: Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O. tauri is the smallest free-living photosynthetic eukaryote known to date, a coccoid green alga that was first isolated in 1995 in a lagoon by the Mediterranean sea. Its simple features, ease of culture and the sequencing of its 13 Mb haploid nuclear genome have promoted this microalga as a new model organism for cell biology. Here, we investigated the quality of genome assemblies of Illumina GAIIx 75 bp paired-end reads from Ostreococcus tauri, thereby also improving the existing assembly and showing the genome to be stably maintained in culture. RESULTS: The 3 assemblers used, ABySS, CLCBio and Velvet, produced 95% complete genomes in 1402 to 2080 scaffolds with a very low rate of misassembly. Reciprocally, these assemblies improved the original genome assembly by filling in 930 gaps. Combined with additional analysis of raw reads and PCR sequencing effort, 1194 gaps have been solved in total adding up to 460 kb of sequence. Mapping of RNAseq Illumina data on this updated genome led to a twofold reduction in the proportion of multi-exon protein coding genes, representing 19% of the total 7699 protein coding genes. The comparison of the DNA extracted in 2001 and 2009 revealed the fixation of 8 single nucleotide substitutions and 2 deletions during the approximately 6000 generations in the lab. The deletions either knocked out or truncated two predicted transmembrane proteins, including a glutamate-receptor like gene. CONCLUSION: High coverage (>80 fold) paired-end Illumina sequencing enables a high quality 95% complete genome assembly of a compact ~13 Mb haploid eukaryote. This genome sequence has remained stable for 6000 generations of lab culture. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-1103) contains supplementary material, which is available to authorized users.
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spelling pubmed-43780212015-03-31 An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies Blanc-Mathieu, Romain Verhelst, Bram Derelle, Evelyne Rombauts, Stephane Bouget, François-Yves Carré, Isabelle Château, Annie Eyre-Walker, Adam Grimsley, Nigel Moreau, Hervé Piégu, Benoit Rivals, Eric Schackwitz, Wendy Van de Peer, Yves Piganeau, Gwenaël BMC Genomics Research Article BACKGROUND: Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O. tauri is the smallest free-living photosynthetic eukaryote known to date, a coccoid green alga that was first isolated in 1995 in a lagoon by the Mediterranean sea. Its simple features, ease of culture and the sequencing of its 13 Mb haploid nuclear genome have promoted this microalga as a new model organism for cell biology. Here, we investigated the quality of genome assemblies of Illumina GAIIx 75 bp paired-end reads from Ostreococcus tauri, thereby also improving the existing assembly and showing the genome to be stably maintained in culture. RESULTS: The 3 assemblers used, ABySS, CLCBio and Velvet, produced 95% complete genomes in 1402 to 2080 scaffolds with a very low rate of misassembly. Reciprocally, these assemblies improved the original genome assembly by filling in 930 gaps. Combined with additional analysis of raw reads and PCR sequencing effort, 1194 gaps have been solved in total adding up to 460 kb of sequence. Mapping of RNAseq Illumina data on this updated genome led to a twofold reduction in the proportion of multi-exon protein coding genes, representing 19% of the total 7699 protein coding genes. The comparison of the DNA extracted in 2001 and 2009 revealed the fixation of 8 single nucleotide substitutions and 2 deletions during the approximately 6000 generations in the lab. The deletions either knocked out or truncated two predicted transmembrane proteins, including a glutamate-receptor like gene. CONCLUSION: High coverage (>80 fold) paired-end Illumina sequencing enables a high quality 95% complete genome assembly of a compact ~13 Mb haploid eukaryote. This genome sequence has remained stable for 6000 generations of lab culture. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-1103) contains supplementary material, which is available to authorized users. BioMed Central 2014-12-13 /pmc/articles/PMC4378021/ /pubmed/25494611 http://dx.doi.org/10.1186/1471-2164-15-1103 Text en © Blanc-Mathieu et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Blanc-Mathieu, Romain
Verhelst, Bram
Derelle, Evelyne
Rombauts, Stephane
Bouget, François-Yves
Carré, Isabelle
Château, Annie
Eyre-Walker, Adam
Grimsley, Nigel
Moreau, Hervé
Piégu, Benoit
Rivals, Eric
Schackwitz, Wendy
Van de Peer, Yves
Piganeau, Gwenaël
An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies
title An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies
title_full An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies
title_fullStr An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies
title_full_unstemmed An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies
title_short An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies
title_sort improved genome of the model marine alga ostreococcus tauri unfolds by assessing illumina de novo assemblies
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378021/
https://www.ncbi.nlm.nih.gov/pubmed/25494611
http://dx.doi.org/10.1186/1471-2164-15-1103
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