Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling.

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.
Complete list of metadatas

Cited literature [56 references]  Display  Hide  Download

https://hal.archives-ouvertes.fr/hal-00848707
Contributor : Francoise Rieu <>
Submitted on : Sunday, July 28, 2013 - 8:55:18 AM
Last modification on : Tuesday, May 21, 2019 - 2:48:53 PM
Long-term archiving on : Tuesday, October 29, 2013 - 2:35:13 AM

File

Vaulot2012_Metagenomes.pdf
Publisher files allowed on an open archive

Identifiers

Citation

Daniel Vaulot, Cécile Lepère, Eve Toulza, Rodrigo de La Iglesia, Julie Poulain, et al.. Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling.. PLoS ONE, Public Library of Science, 2012, 7 (6), pp.e39648. ⟨10.1371/journal.pone.0039648⟩. ⟨hal-00848707⟩

Share

Metrics

Record views

1670

Files downloads

482