dc.contributor.author |
Blanc-Mathieu, Romain
|
|
dc.contributor.author |
Verhelst, Bram
|
|
dc.contributor.author |
Derelle, Evelyne
|
|
dc.contributor.author |
Rombauts, Stephane
|
|
dc.contributor.author |
Bouget, François-Yves
|
|
dc.contributor.author |
Carré, Isabelle
|
|
dc.contributor.author |
Château, Annie
|
|
dc.contributor.author |
Eyre-Walker, Adam
|
|
dc.contributor.author |
Grimsley, Nigel
|
|
dc.contributor.author |
Moreau, Hervé
|
|
dc.contributor.author |
Piégu, Benoit
|
|
dc.contributor.author |
Rivals, Eric
|
|
dc.contributor.author |
Schackwitz, Wendy
|
|
dc.contributor.author |
Van de Peer, Yves
|
|
dc.contributor.author |
Piganeau, Gwenaël
|
|
dc.date.accessioned |
2015-02-17T06:08:30Z |
|
dc.date.available |
2015-02-17T06:08:30Z |
|
dc.date.issued |
2014-12 |
|
dc.description.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. |
en_ZA |
dc.description.librarian |
hb2015 |
en_ZA |
dc.description.sponsorship |
Part of this work was funded by ANR-12-BSV7-0006-01 "REVIREC" (NG)
and the European Community’s 7th Framework program FP7 under grant
agreement no 254619 (GP and AEW). BV, SR and YVDP would like to acknowledge
the support of Ghent University (Multidisciplinary Research Partnership
‘Bioinformatics: from nucleotides to networks’; http://www.nucleotides2
networks.be). ER and AC acknowledge the support from the Défi MASTODONS
SePhHaDe CNRS, the Labex NUMev, and the Projet Investissements d'Avenir
France Génomique. RBM acknowledge Nice-Sophia University for funding. |
en_ZA |
dc.description.uri |
http://www.biomedcentral.com/bmcgenomics |
en_ZA |
dc.identifier.citation |
Blanc-Mathieu, R, Verhelst, B, Derelle, E, Rombauts, S, Bouget, FY, Carre, I, Chateau, A, Eyre-Walker, A, Grimsley, N, Moreau, H, Piegu, B, Rivals, E, Schackwitz, W, Van de Peer, Y & Piganeau, G 2014, 'An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies', BMC Genomics, vol. 15, art.. 1103, pp. 1-11. |
en_ZA |
dc.identifier.issn |
1471-2164 (print) |
|
dc.identifier.other |
10.1186/1471-2164-15-1103 |
|
dc.identifier.uri |
http://hdl.handle.net/2263/43667 |
|
dc.language.iso |
en |
en_ZA |
dc.publisher |
BioMed Central |
en_ZA |
dc.rights |
© 2014 Blanc-Mathieu et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use,distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
en_ZA |
dc.subject |
Genome evolution |
en_ZA |
dc.subject |
Ostreococcus tauri |
en_ZA |
dc.subject |
Domestication of microalgae |
en_ZA |
dc.subject |
Illumina re-sequencing |
en_ZA |
dc.subject |
Plant glutamate receptor |
en_ZA |
dc.subject |
Correctness of short reads assembly |
en_ZA |
dc.subject |
Picoeukaryote |
en_ZA |
dc.title |
An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies |
en_ZA |
dc.type |
Article |
en_ZA |