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

Authors
  • Blanc-Mathieu, Romain1, 2
  • Verhelst, Bram3, 4
  • Derelle, Evelyne1, 2
  • Rombauts, Stephane3, 4
  • Bouget, François-Yves5, 2
  • Carré, Isabelle6
  • Château, Annie7
  • Eyre-Walker, Adam8
  • Grimsley, Nigel1, 2
  • Moreau, Hervé1, 2
  • Piégu, Benoit9
  • Rivals, Eric7
  • Schackwitz, Wendy10
  • Van de Peer, Yves3, 4, 11
  • Piganeau, Gwenaël1, 2
  • 1 Observatoire Océanologique, CNRS, UMR 7232, Avenue du Fontaulé, BP44, Banyuls-sur-Mer, 66650, France , Banyuls-sur-Mer (France)
  • 2 Sorbonne Universités, UPMC Univ Paris 06, Observatoire Océanologique, Avenue du Fontaulé, Banyuls-sur-Mer, 66650, France , Banyuls-sur-Mer (France)
  • 3 Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, Ghent, B-9052, Belgium , Ghent (Belgium)
  • 4 VIB, Department of Plant Systems Biology, Technologiepark 927, Ghent, B-9052, Belgium , Ghent (Belgium)
  • 5 Observatoire Océanologique, CNRS, UMR 7621, Avenue du Fontaulé, BP44, Banyuls-sur-Mer, 66650, France , Banyuls-sur-Mer (France)
  • 6 University of Warwick, Coventry, UK , Coventry (United Kingdom)
  • 7 CNRS and Universite Montpellier, LIRMM and Institut de Biologie Computationelle, Montpellier Cedex 5, 34095, France , Montpellier Cedex 5 (France)
  • 8 University of Sussex, School of Life Sciences, Brighton, UK , Brighton (United Kingdom)
  • 9 Centre INRA de Nouzilly, UMR 7247, Nouzilly, France , Nouzilly (France)
  • 10 US department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA , Walnut Creek (United States)
  • 11 University of Pretoria, Department of Genetics, Genomics Research Institute, Pretoria, South Africa , Pretoria (South Africa)
Type
Published Article
Journal
BMC Genomics
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Dec 13, 2014
Volume
15
Issue
1
Identifiers
DOI: 10.1186/1471-2164-15-1103
Source
Springer Nature
Keywords
License
Yellow

Abstract

BackgroundCost 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.ResultsThe 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.ConclusionHigh 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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