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

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.

A Viral Immunity Chromosome in the Marine Picoeukaryote, Ostreococcus tauri

“…tauri parent line with single molecule PacBio technology was able to resolve a large inverted repeat region (LIRR) on chromosome 19 totalling ~180 kb (Fig 4) that was predicted to exist from previous work [4]. The assembled PacBio contig was 311,428 bp, in agreement with its expected size from gel mobility (Fig 5).…”

“…tauri since comparison of the re-sequenced O . tauri genome between 2001 and 2009 revealed the fixation of eight single nucleotide substitutions and two deletions during the approximately 6,000 generations in the lab [4]. We thus preferred an alternative hypothesis, that resistance is induced by the biotic challenge of virus infection, for example by epigenetic modifications affecting gene expression patterns.…”

“…Transcriptome read pairs (fragments) were aligned using TopHat2 [91] (alignment parameters: -i 10 -I 4000, -G) to the annotated genome sequence of O . tauri RCC4221 [4]. The counts of fragments aligning to each gene was determined using the htseq-count function of HTSeq [92] with parameters (-t CDS -s no -m intersection-nonempty).…”

“…Their tiny size (1–3 μm), simple cells (one chloroplast, one mitochondrion), ease of laboratory culture and extremely small genomes, several of which have been completely sequenced [4–8], render them attractive as models for marine ecology [9–11], cell biology [12] and evolution in the green lineage [4,13]. Typical features of the highly streamlined genomes of the Mamiellales include a higher GC content (48–64% [7,14], 59% for O .…”

“…Here we aimed to unravel the molecular mechanisms underlying viral resistance using clonal lines of O . tauri RCC4221 [4] and its virus, OtV5. We produced numerous independent OtV5-resistant lines to examine host and viral gene expression in detail with RNA-Seq technology and to test whether altered gene expression could be responsible for the resistance phenotypes.…”