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Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling

(2012) PLOS ONE. 7(6).
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Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
PICOPHYTOPLANKTON, SARGASSO SEA METAGENOME, SOUTH EAST PACIFIC, EUKARYOTIC PHYTOPLANKTON, MEDITERRANEAN SEA, GENETIC DIVERSITY, OSTREOCOCCUS CHLOROPHYTA, MARINE PICOEUKARYOTES, PRASINOPHYCEAE, ATLANTIC-OCEAN

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Chicago
Vaulot, Daniel, Cécile Lepere, Eve Toulza, Rodrigo De la Iglesia, Julie Poulain, Frédéric Gaboyer, Hervé Moreau, et al. 2012. “Metagenomes of the Picoalga Bathycoccus from the Chile Coastal Upwelling.” Plos One 7 (6).
APA
Vaulot, D., Lepere, C., Toulza, E., De la Iglesia, R., Poulain, J., Gaboyer, F., Moreau, H., et al. (2012). Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling. PLOS ONE, 7(6).
Vancouver
1.
Vaulot D, Lepere C, Toulza E, De la Iglesia R, Poulain J, Gaboyer F, et al. Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling. PLOS ONE. 2012;7(6).
MLA
Vaulot, Daniel, Cécile Lepere, Eve Toulza, et al. “Metagenomes of the Picoalga Bathycoccus from the Chile Coastal Upwelling.” PLOS ONE 7.6 (2012): n. pag. Print.
@article{2997577,
  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.},
  articleno    = {e39648},
  author       = {Vaulot, Daniel and Lepere, C{\'e}cile and Toulza, Eve and De la Iglesia, Rodrigo and Poulain, Julie and Gaboyer, Fr{\'e}d{\'e}ric and Moreau, Herv{\'e} and Vandepoele, Klaas and Ulloa, Osvaldo and Gavory, Frederick and Piganeau, Gwenael},
  issn         = {1932-6203},
  journal      = {PLOS ONE},
  language     = {eng},
  number       = {6},
  pages        = {13},
  title        = {Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling},
  url          = {http://dx.doi.org/10.1371/journal.pone.0039648},
  volume       = {7},
  year         = {2012},
}

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