Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling.
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),...
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2012-01-01
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doaj-c081ee29149d4e0499f6565ff6107de62020-11-25T01:25:06ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0176e3964810.1371/journal.pone.0039648Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling.Daniel VaulotCécile LepèreEve ToulzaRodrigo De la IglesiaJulie PoulainFrédéric GaboyerHervé MoreauKlaas VandepoeleOsvaldo UlloaFrederick GavoryGwenael PiganeauAmong 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.http://europepmc.org/articles/PMC3382182?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Daniel Vaulot Cécile Lepère Eve Toulza Rodrigo De la Iglesia Julie Poulain Frédéric Gaboyer Hervé Moreau Klaas Vandepoele Osvaldo Ulloa Frederick Gavory Gwenael Piganeau |
spellingShingle |
Daniel Vaulot Cécile Lepère Eve Toulza Rodrigo De la Iglesia Julie Poulain Frédéric Gaboyer Hervé Moreau Klaas Vandepoele Osvaldo Ulloa Frederick Gavory Gwenael Piganeau Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling. PLoS ONE |
author_facet |
Daniel Vaulot Cécile Lepère Eve Toulza Rodrigo De la Iglesia Julie Poulain Frédéric Gaboyer Hervé Moreau Klaas Vandepoele Osvaldo Ulloa Frederick Gavory Gwenael Piganeau |
author_sort |
Daniel Vaulot |
title |
Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling. |
title_short |
Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling. |
title_full |
Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling. |
title_fullStr |
Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling. |
title_full_unstemmed |
Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling. |
title_sort |
metagenomes of the picoalga bathycoccus from the chile coastal upwelling. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2012-01-01 |
description |
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. |
url |
http://europepmc.org/articles/PMC3382182?pdf=render |
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