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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1103) contains supplementary material, which is available to authorized users.
Highlights
Cost effective generation sequencing technologies enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity
The culture used for the reference genome sequence came from a natural sample of O. tauri isolated 1995 in the Thau Lagoon [11,12] and maintained by serial subcultures using 50 ml plastic tissue culture flasks in 20 ml K medium at 20°C under 100 μE s−1 m−2 constant light in Organisms (Genome Size Mb)
De novo assemblies of O. tauri’s genome We generated de novo assemblies of the O. tauri genome using 41 million paired-end 76 bp Illumina reads from the OT-2009 strain
Summary
Cost effective generation sequencing technologies enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. Unicellular marine photosynthetic eukaryotic organisms represent much of the untapped genetic diversity reservoir of our planet [1,2] Their ecological importance in the global carbon cycle [3,4] and their biotechnological potential as possible sources of biofuels and dietary «omega-3» lipid food supplements, have fostered several genome projects to gain knowledge into their diversity and metabolic potential [5,6,7,8,9,10]. Ostreococus tauri is the smallest photosynthetic eukaryote known and its genome was the first marine green algal genome to be sequenced It has a simple cellular organization with a single mitochondrion and a single chloroplast [11,12], all orchestrated by a 13 Mb haploid nuclear genome [7]. It has been successfully used to gain knowledge into fundamental cellular processes such as the cell cycle [15,16,17], the circadian clock [18,19,20], lipid [21] and starch synthesis [22], as well as the mechanisms of genome evolution [23,24,25]
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