Phylogenetic classification of short environmental DNA fragments

Krause, Lutz, Diaz, Naryttza N., Goesmann, Alexander, Kelley, Scott, Nattkemper, Tim W., Rohwer, Forest, Edwards, Robert A. and Stoye, Jens (2008) Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Research, 36 7: 2230-2239. doi:10.1093/nar/gkn038


Author Krause, Lutz
Diaz, Naryttza N.
Goesmann, Alexander
Kelley, Scott
Nattkemper, Tim W.
Rohwer, Forest
Edwards, Robert A.
Stoye, Jens
Title Phylogenetic classification of short environmental DNA fragments
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 0305-1048
1362-4962
Publication date 2008-04
Sub-type Article (original research)
DOI 10.1093/nar/gkn038
Open Access Status DOI
Volume 36
Issue 7
Start page 2230
End page 2239
Total pages 10
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Abstract Metagenomics is providing striking insights into the ecology of microbial communities. The recently developed massively parallel 454 pyrosequencing technique gives the opportunity to rapidly obtain metagenomic sequences at a low cost and without cloning bias. However, the phylogenetic analysis of the short reads produced represents a significant computational challenge. The phylogenetic algorithm CARMA for predicting the source organisms of environmental 454 reads is described. The algorithm searches for conserved Pfam domain and protein families in the unassembled reads of a sample. These gene fragments (environmental gene tags, EGTs), are classified into a higher-order taxonomy based on the reconstruction of a phylogenetic tree of each matching Pfam family. The method exhibits high accuracy for a wide range of taxonomic groups, and EGTs as short as 27 amino acids can be phylogenetically classified up to the rank of genus. The algorithm was applied in a comparative study of three aquatic microbial samples obtained by 454 pyrosequencing. Profound differences in the taxonomic composition of these samples could be clearly revealed.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: UQ Diamantina Institute Publications
 
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