Metagenomes of the Picoalga Bathycoccus from the Chile Coastal Upwelling
| Type | Article | ||||||||
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| Date | 2012-06 | ||||||||
| Language | English | ||||||||
| Author(s) | Vaulot Daniel1, 2, Lepere Cecile1, 2, Toulza Eve3, 4, de La Iglesia Rodrigo5, 6, Poulain Julie7, Gaboyer Frederic1, 2, Moreau Herve3, 4, Vandepoele Klaas8, 9, Ulloa Osvaldo5, 6, Gavory Frederick7, Piganeau Gwenael3, 4 | ||||||||
| Affiliation(s) | 1 : Univ Paris 06, UPMC, Roscoff, France. 2 : CNRS, Biol Stn, UMR 7144, Roscoff, France. 3 : CNRS, Banyuls Sur Mer, France. 4 : Univ Paris 06, UPMC, OOB, UMR 7232, Banyuls Sur Mer, France. 5 : Univ Concepcion, Dept Oceanog, Concepcion, Chile. 6 : Univ Concepcion, Ctr Invest Oceanog Pacifico Sur Oriental, Concepcion, Chile. 7 : CEA, Inst Genom, Genoscope, Evry, France. 8 : VIB, Dept Plant Syst Biol, Ghent, Belgium. 9 : Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9000 Ghent, Belgium. |
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| Source | Plos One (1932-6203) (Public Library Science), 2012-06 , Vol. 7 , N. 6 , P. - | ||||||||
| DOI | 10.1371/journal.pone.0039648 | ||||||||
| WOS© Times Cited | 46 | ||||||||
| Abstract | Among small photosynthetic eukaryotes that play a key role in oceanic food webs, picoplanktonic Mamiellophyceae such as Bathycoccus, Micromonas, and Ostreococcus are particularly important in coastal regions. By using a combination of cell sorting by flow cytometry, whole genome amplification (WGA), and 454 pyrosequencing, we obtained metagenomic data for two natural picophytoplankton populations from the coastal upwelling waters off central Chile. About 60% of the reads of each sample could be mapped to the genome of Bathycoccus strain from the Mediterranean Sea (RCC1105), representing a total of 9 Mbp (sample T142) and 13 Mbp (sample T149) of non-redundant Bathycoccus genome sequences. WGA did not amplify all regions uniformly, resulting in unequal coverage along a given chromosome and between chromosomes. The identity at the DNA level between the metagenomes and the cultured genome was very high (96.3% identical bases for the three larger chromosomes over a 360 kbp alignment). At least two to three different genotypes seemed to be present in each natural sample based on read mapping to Bathycoccus RCC1105 genome. | ||||||||
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