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Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling

Daniel Vaulot, Cécile Lepere, Eve Toulza, Rodrigo De la Iglesia, Julie Poulain, Frédéric Gaboyer, Hervé Moreau, Klaas Vandepoele UGent, Osvaldo Ulloa and Frederick Gavory, et al. (2012) PLOS ONE. 7(6).
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
PICOPHYTOPLANKTON, SARGASSO SEA METAGENOME, SOUTH EAST PACIFIC, EUKARYOTIC PHYTOPLANKTON, MEDITERRANEAN SEA, GENETIC DIVERSITY, OSTREOCOCCUS CHLOROPHYTA, MARINE PICOEUKARYOTES, PRASINOPHYCEAE, ATLANTIC-OCEAN
journal title
PLOS ONE
PLoS One
volume
7
issue
6
article_number
e39648
pages
13 pages
Web of Science type
Article
Web of Science id
000305730900092
JCR category
MULTIDISCIPLINARY SCIENCES
JCR impact factor
3.73 (2012)
JCR rank
7/56 (2012)
JCR quartile
1 (2012)
ISSN
1932-6203
DOI
10.1371/journal.pone.0039648
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
2997577
handle
http://hdl.handle.net/1854/LU-2997577
date created
2012-09-21 16:20:32
date last changed
2013-05-06 11:10:34
@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},
  keyword      = {PICOPHYTOPLANKTON,SARGASSO SEA METAGENOME,SOUTH EAST PACIFIC,EUKARYOTIC PHYTOPLANKTON,MEDITERRANEAN SEA,GENETIC DIVERSITY,OSTREOCOCCUS CHLOROPHYTA,MARINE PICOEUKARYOTES,PRASINOPHYCEAE,ATLANTIC-OCEAN},
  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},
}

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.