Dataset Information

Reference-independent comparative metagenomics using cross-assembly: crAss.

ABSTRACT:

Motivation

Metagenomes are often characterized by high levels of unknown sequences. Reads derived from known microorganisms can easily be identified and analyzed using fast homology search algorithms and a suitable reference database, but the unknown sequences are often ignored in further analyses, biasing conclusions. Nevertheless, it is possible to use more data in a comparative metagenomic analysis by creating a cross-assembly of all reads, i.e. a single assembly of reads from different samples. Comparative metagenomics studies the interrelationships between metagenomes from different samples. Using an assembly algorithm is a fast and intuitive way to link (partially) homologous reads without requiring a database of reference sequences.

Results

Here, we introduce crAss, a novel bioinformatic tool that enables fast simple analysis of cross-assembly files, yielding distances between all metagenomic sample pairs and an insightful image displaying the similarities.

SUBMITTER: Dutilh BE

PROVIDER: S-EPMC3519457 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature

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Publications

Reference-independent comparative metagenomics using cross-assembly: crAss.

Dutilh Bas E BE Schmieder Robert R Nulton Jim J Felts Ben B Salamon Peter P Edwards Robert A RA Mokili John L JL

Bioinformatics (Oxford, England) 20121016 24

<h4>Motivation</h4>Metagenomes are often characterized by high levels of unknown sequences. Reads derived from known microorganisms can easily be identified and analyzed using fast homology search algorithms and a suitable reference database, but the unknown sequences are often ignored in further analyses, biasing conclusions. Nevertheless, it is possible to use more data in a comparative metagenomic analysis by creating a cross-assembly of all reads, i.e. a single assembly of reads from differe ...[more]

PMID: 23074261

Similar Datasets

Project description:BACKGROUND: Shotgun sequences of DNA extracts from whole organisms allow a comprehensive assessment of possible symbionts. The current project makes use of four shotgun datasets from three species of the planktonic freshwater crustaceans Daphnia: one dataset from clones of D. pulex and D. pulicaria and two datasets from one clone of D. magna. We analyzed these datasets with three aims: First, we search for bacterial symbionts, which are present in all three species. Second, we search for evidence for Cyanobacteria and plastids, which had been suggested to occur as symbionts in a related Daphnia species. Third, we compare the metacommunities revealed by two different 454 pyrosequencing methods (GS 20 and GS FLX). RESULTS: In all datasets we found evidence for a large number of bacteria belonging to diverse taxa. The vast majority of these were Proteobacteria. Of those, most sequences were assigned to different genera of the Betaproteobacteria family Comamonadaceae. Other taxa represented in all datasets included the genera Flavobacterium, Rhodobacter, Chromobacterium, Methylibium, Bordetella, Burkholderia and Cupriavidus. A few taxa matched sequences only from the D. pulex and the D. pulicaria datasets: Aeromonas, Pseudomonas and Delftia. Taxa with many hits specific to a single dataset were rare. For most of the identified taxa earlier studies reported the finding of related taxa in aquatic environmental samples. We found no clear evidence for the presence of symbiotic Cyanobacteria or plastids. The apparent similarity of the symbiont communities of the three Daphnia species breaks down on a species and strain level. Communities have a similar composition at a higher taxonomic level, but the actual sequences found are divergent. The two Daphnia magna datasets obtained from two different pyrosequencing platforms revealed rather similar results. CONCLUSION: Three clones from three species of the genus Daphnia were found to harbor a rich community of symbionts. These communities are similar at the genus and higher taxonomic level, but are composed of different species. The similarity of these three symbiont communities hints that some of these associations may be stable in the long-term.

Dataset Information

Reference-independent comparative metagenomics using cross-assembly: crAss.

Motivation

Results

Publications

Reference-independent comparative metagenomics using cross-assembly: crAss.

Similar Datasets

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