title: An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.forename: Romain
authors.initials: R
authors.lastname: Blanc-Mathieu
authors.forename: Bram
authors.initials: B
authors.lastname: Verhelst
authors.forename: Evelyne
authors.initials: E
authors.lastname: Derelle
authors.forename: Stephane
authors.initials: S
authors.lastname: Rombauts
authors.forename: François-Yves
authors.initials: FY
authors.lastname: Bouget
authors.forename: Isabelle
authors.initials: I
authors.lastname: Carré
authors.forename: Annie
authors.initials: A
authors.lastname: Château
authors.forename: Adam
authors.initials: A
authors.lastname: Eyre-Walker
authors.forename: Nigel
authors.initials: N
authors.lastname: Grimsley
authors.forename: Hervé
authors.initials: H
authors.lastname: Moreau
authors.forename: Benoit
authors.initials: B
authors.lastname: Piégu
authors.forename: Eric
authors.initials: E
authors.lastname: Rivals
authors.forename: Wendy
authors.initials: W
authors.lastname: Schackwitz
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.affiliation: CNRS, UMR 7232, Observatoire Océanologique, Avenue du Fontaulé, BP44, 66650 Banyuls-sur-Mer, France. gwenael.piganeau@obs-banyuls.fr.
authors.forename: Gwenaël
authors.initials: G
authors.lastname: Piganeau
mesh_terms: D000460:Chlorophyta / Q000235:genetics*; D019295:Computational Biology; D019143:Evolution, Molecular; D014644:Genetic Variation; D018745:Genome, Plant; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data