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

BMC Genomics

Gwenaël Piganeau²  Yves Van de Peer⁶  Wendy Schackwitz¹  Eric Rivals⁵  Benoit Piégu³  Hervé Moreau²  Nigel Grimsley²  Adam Eyre-Walker⁴  Annie Château⁵  Isabelle Carré⁷  François-Yves Bouget⁸  Stephane Rombauts⁶  Evelyne Derelle²  Bram Verhelst⁶  Romain Blanc-Mathieu² 

[1] US department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA;Sorbonne Universités, UPMC Univ Paris 06, Observatoire Océanologique, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France;UMR 7247, Centre INRA de Nouzilly, Nouzilly, France;School of Life Sciences, University of Sussex, Brighton, UK;LIRMM and Institut de Biologie Computationelle, CNRS and Universite Montpellier, 34095 Montpellier Cedex 5, France;Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium;University of Warwick, Coventry, UK;CNRS, UMR 7621, Observatoire Océanologique, Avenue du Fontaulé, BP44, 66650 Banyuls-sur-Mer, France

关键词: Picoeukaryote;    Correctness of short reads assembly;    Plant glutamate receptor;    Illumina re-sequencing;    Domestication of microalgae;    Ostreococcus tauri;    Genome evolution;   

Others  :  1127309
DOI  :  10.1186/1471-2164-15-1103

 received in 2014-06-18, accepted in 2014-11-19,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Blanc-Mathieu et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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