An improved genome of the model marine alga [i]Ostreococcus tauri[/i] unfolds by assessing Illumina [i]de novo[/i] assemblies
2014
Blanc Mathieu, Romain | Verhelst, Bram | Derelle, Evelyne | Rombauts, Stephane | Bouget, Francois-Yves | Carré, Isabelle | Chateau, Annie | Eyre Walker, Adam | Grimsley, Nigel | Moreau, Hervé | Piegu, Benoit | Rivals, Eric | Schackwitz, Wendy | van de Peer, Yves | Piganeau, Gwenaël | Biologie intégrative des organismes marins (BIOM) ; Observatoire océanologique de Banyuls (OOB) ; Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) | Université Paris-Sorbonne (UP4) | Department of Plant Biotechnology and Bioinformatics ; Universiteit Gent = Ghent University = Université de Gand (UGENT) | Department of Plant Systems Biology ; Flanders Institute for Biotechnology | Laboratoire d'Océanographie Microbienne (LOMIC) ; Observatoire océanologique de Banyuls (OOB) ; Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) | University of Warwick [Coventry] | Méthodes et Algorithmes pour la Bioinformatique (MAB) ; Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM) ; Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS) | School of Life Sciences ; University of Sussex | Physiologie de la reproduction et des comportements [Nouzilly] (PRC) ; Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS) | US Department of Energy Joint Genome Institute ; University of California (UC) | Department of Genetics, Genomics Research Institute ; University of Pretoria [South Africa] | Ghent University;Defi MASTODONS SePhHaDe CNRS;LabeX NUMev;Project Investissements d'Avenir France Genomique;Nice-Sophia University;ANR-12-BSV7-0006-01 | ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011) | European Project: 254619,EC:FP7:PEOPLE,FP7-PEOPLE-2009-IEF,PICOPOP(2010)
International audience
Mostrar más [+] Menos [-]Inglés. 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 Ustreococcus touri, 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 II lumina 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.
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