Blanc-Mathieu, Romain, Verhelst, Bram, Derelle, Evelyne, Rombauts, Stephane, Bouget, François-Yves , Carré, Isabelle A., Château, Annie, Eyre-Walker, Adam, Grimsley, Nigel, Moreau, Hervé, Piégu, Benoit, Rivals, Eric , Schackwitz, Wendy, Peer, Yves van de and Piganeau, Gwenaël (2014) An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies. BMC Genomics, Volume 15 . pp. 1-11. Article number 1103. doi:10.1186/1471-2164-15-1103 ISSN 1471-2164.

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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.

Item Type:	Journal Article
Subjects:	Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics Q Science > QR Microbiology S Agriculture > SH Aquaculture. Fisheries. Angling
Divisions:	Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH):	Evolution (Biology), Genomes
Journal or Publication Title:	BMC Genomics
Publisher:	BioMed Central Ltd.
ISSN:	1471-2164
Official Date:	13 December 2014
Dates:	Date Event 13 December 2014 Published 19 November 2014 Accepted 18 June 2014 Submitted
Volume:	Volume 15
Number of Pages:	11
Page Range:	pp. 1-11
Article Number:	Article number 1103
DOI:	10.1186/1471-2164-15-1103
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Open Access (Creative Commons)
Date of first compliant deposit:	28 December 2015
Date of first compliant Open Access:	28 December 2015
Funder:	Seventh Framework Programme (European Commission) (FP7)
Grant number:	ANR-12-BSV7-0006-01 (FP7)
Adapted As:
Open Access Version:	Publisher

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