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.
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.
