Go Back   SEQanswers > Literature Watch

Similar Threads
Thread Thread Starter Forum Replies Last Post
miRNA seq analysis - large numbers of non-aligning reads lbeltrame Bioinformatics 10 05-03-2013 09:30 AM
repeat sequences/large files in galaxy Giles Bioinformatics 2 06-27-2011 12:08 PM
Large RNA sequences ? Does it has any sense ? perencia Bioinformatics 10 07-29-2010 08:05 AM
PubMed: Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep- Newsbot! Literature Watch 0 04-14-2010 03:01 AM
PubMed: Frameshift detection in prokaryotic genomic sequences. Newsbot! Literature Watch 0 07-31-2009 06:00 AM

Thread Tools
Old 08-30-2008, 06:06 AM   #1
RSS Posting Maniac

Join Date: Feb 2008
Posts: 1,443
Default PubMed: Detection of large numbers of novel sequences in the metatranscriptomes of co

Syndicated from PubMed RSS Feeds

Related Articles Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities.

PLoS ONE. 2008;3(8):e3042

Authors: Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I

BACKGROUND: Sequencing the expressed genetic information of an ecosystem (metatranscriptome) can provide information about the response of organisms to varying environmental conditions. Until recently, metatranscriptomics has been limited to microarray technology and random cloning methodologies. The application of high-throughput sequencing technology is now enabling access to both known and previously unknown transcripts in natural communities. METHODOLOGY/PRINCIPAL FINDINGS: We present a study of a complex marine metatranscriptome obtained from random whole-community mRNA using the GS-FLX Pyrosequencing technology. Eight samples, four DNA and four mRNA, were processed from two time points in a controlled coastal ocean mesocosm study (Bergen, Norway) involving an induced phytoplankton bloom producing a total of 323,161,989 base pairs. Our study confirms the finding of the first published metatranscriptomic studies of marine and soil environments that metatranscriptomics targets highly expressed sequences which are frequently novel. Our alternative methodology increases the range of experimental options available for conducting such studies and is characterized by an exceptional enrichment of mRNA (99.92%) versus ribosomal RNA. Analysis of corresponding metagenomes confirms much higher levels of assembly in the metatranscriptomic samples and a far higher yield of large gene families with >100 members, approximately 91% of which were novel. CONCLUSIONS/SIGNIFICANCE: This study provides further evidence that metatranscriptomic studies of natural microbial communities are not only feasible, but when paired with metagenomic data sets, offer an unprecedented opportunity to explore both structure and function of microbial communities--if we can overcome the challenges of elucidating the functions of so many never-seen-before gene families.

PMID: 18725995 [PubMed - in process]

Newsbot! is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 02:43 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO