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  Application of tetranucleotide frequencies for the assignment of genomic fragments

Teeling, H., Meyerdierks, A., Bauer, M., Amann, R., & Glöckner, F. O. (2004). Application of tetranucleotide frequencies for the assignment of genomic fragments. Environmental Microbiology, 6(9), 938-947.

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 Creators:
Teeling, H.1, Author           
Meyerdierks, A.1, Author           
Bauer, M.2, Author           
Amann, R.1, Author           
Glöckner, F. O.2, Author           
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1Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society, ou_2481696              
2Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society, ou_2481697              

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 Abstract: A basic problem of the metagenomic approach in microbial ecology is the assignment of genomic fragments to a certain species or taxonomic group, when suitable marker genes are absent. Currently, the (G + C)-content together with phylogenetic information and codon adaptation for functional genes is mostly used to assess the relationship of different fragments. These methods, however, can produce ambiguous results. In order to evaluate sequence-based methods for fragment identification, we extensively compared (G + C)-contents and tetranucleotide usage patterns of 9054 fosmid-sized genomic fragments generated in silico from 118 completely sequenced bacterial genomes (40 982 931 fragment pairs were compared in total). The results of this systematic study show that the discriminatory power of correlations of tetranucleotide-derived z-scores is by far superior to that of differences in (G + C)-content and provides reasonable assignment probabilities when applied to metagenome libraries of small diversity. Using six fully sequenced fosmid inserts from a metagenomic analysis of microbial consortia mediating the anaerobic oxidation of methane (AOM), we demonstrate that discrimination based on tetranucleotide-derived z-score correlations was consistent with corresponding data from 16S ribosomal RNA sequence analysis and allowed us to discriminate between fosmid inserts that were indistinguishable with respect to their (G + C)-contents.

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Language(s): eng - English
 Dates: 2004-08-112004-09
 Publication Status: Issued
 Pages: 10
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: eDoc: 220903
ISI: 000223254700008
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Title: Environmental Microbiology
  Other : Environmental Microbiology and Environmental Microbiology Reports
Source Genre: Journal
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Publ. Info: Oxford, England : Blackwell Science
Pages: - Volume / Issue: 6 (9) Sequence Number: - Start / End Page: 938 - 947 Identifier: ISSN: 1462-2912
CoNE: https://pure.mpg.de/cone/journals/resource/959328105031