Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel

Jack Gilbert, Folker Meyer, Lynn Schriml, Ian Joint, Martin Muhling, Dawn Field

Abstract


Both metagenomic data and metatranscriptomic data were collected from surface water (0-2m) of the L4 sampling station (50.2518 N, 4.2089 W), which is part of the Western Channel Observatory long-term coastal-marine monitoring station. We previously generated from this area a six-year time series of 16S rRNA V6 data, which demonstrated robust seasonal structure for the bacterial community, with diversity correlated with day length. Here we describe the features of these metagenomes and metatranscriptomes. We generated 8 metagenomes (4.5 million sequences, 1.9 Gbp, average read-length 350 bp) and 7 metatranscriptomes (392,632 putative mRNA-derived sequences, 159 Mbp, average read-length 272 bp) for eight time-points sampled in 2008. These time points represent three seasons (winter, spring, and summer) and include both day and night samples. These data demonstrate the major differences between genetic potential and actuality, whereby genomes follow general seasonal trends yet with surprisingly little change in the functional potential over time; transcripts tended to be far more structured by changes occurring between day and night.

 

doi:10.4056/sigs.1202536


Keywords


Metagenomics; Report; Metatranscriptomics; Western English Channel; L4; Marine; Coastal

Full Text: HTML PDF

Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 License.

This article doi:10.4056/sigs.1202536 has been cited by 4 other articles:

Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics
Eiler et al.
Environ Microbiol () n/a.
10.1111/1462-2920.12301

The State of Standards in Genomic Sciences
Garrity
Stand. Genomic Sci. 5(3) 262.
10.4056/sigs.2515706

Structure, fluctuation and magnitude of a natural grassland soil metagenome
Delmont et al.
ISME J 6(9) 1677.
10.1038/ismej.2011.197

Effective gene collection from the metatranscriptome of marine microorganisms
Ogura et al.
BMC Genomics 12(Suppl 3) S15.
10.1186/1471-2164-12-S3-S15




Announcement

Publication of Standards in Genomic Sciences has been transferred to a new publisher, BioMed Central on behalf of the Genomic Standards Consortium. All submissions to the journal should now be made directly through the BMC website for the journal at: http://www.standardsingenomics.com

Acknowledgements

We would like to gratefully acknowledge the support of many members of the Genomic Standards Consortium, the broader genomic science community, and those who have indicated their willingness to serve as editors, reviewers and contributors.

SIGS was founded with grants from the Office of the Vice President for Research and Graduate Studies at Michigan State University, the Michigan State University Foundation, and the US Department of Energy Biological and Environmental Research DE-FG02-08ER64707. The journal became self-supporting on October 1, 2011.

Standards in Genomic Sciences is indexed in: