Antonie van Leeuwenhoek

, 100:471 | Cite as

Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

  • Johan Bengtsson
  • K. Martin Eriksson
  • Martin Hartmann
  • Zheng Wang
  • Belle Damodara Shenoy
  • Gwen-Aëlle Grelet
  • Kessy Abarenkov
  • Anna Petri
  • Magnus Alm Rosenblad
  • R. Henrik Nilsson
Short Communication

Abstract

The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. In addition to being present in the nucleus of eukaryotes and the core genome of prokaryotes, the gene is also found in the mitochondria of eukaryotes and in the chloroplasts of photosynthetic eukaryotes. These three sets of genes are conceptually paralogous and should in most situations not be aligned and analyzed jointly. To identify the origin of SSU sequences in complex sequence datasets has hitherto been a time-consuming and largely manual undertaking. However, the present study introduces Metaxa (http://microbiology.se/software/metaxa/), an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacterial, nuclear eukaryote, mitochondrial, or chloroplast origin. Using data from reference databases and from full-length organelle and organism genomes, we show that Metaxa detects and scores SSU sequences for origin with very low proportions of false positives and negatives. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.

Keywords

Metagenomics Microbial communities rRNA libraries Phylogenetic assignment 

Supplementary material

10482_2011_9598_MOESM1_ESM.zip (13.6 mb)
Supplementary material 1 (ZIP 13957 kb)
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Supplementary material 2 (ZIP 1122 kb)
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Supplementary material 3 (ZIP 279 kb)
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Supplementary material 4 (ZIP 4 kb)
10482_2011_9598_MOESM5_ESM.pdf (47 kb)
Supplementary material 5 (PDF 47 kb)

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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Johan Bengtsson
    • 1
    • 2
  • K. Martin Eriksson
    • 1
  • Martin Hartmann
    • 3
  • Zheng Wang
    • 4
  • Belle Damodara Shenoy
    • 5
  • Gwen-Aëlle Grelet
    • 6
  • Kessy Abarenkov
    • 7
  • Anna Petri
    • 1
  • Magnus Alm Rosenblad
    • 2
  • R. Henrik Nilsson
    • 1
    • 7
  1. 1.Department of Plant and Environmental SciencesUniversity of GothenburgGöteborgSweden
  2. 2.Department of Cell and Molecular BiologyUniversity of GothenburgGöteborgSweden
  3. 3.Department of Microbiology and Immunology, Life Sciences CentreUniversity of British ColumbiaVancouver, BCCanada
  4. 4.Department of Ecology and Evolutionary BiologyYale UniversityNew HavenUSA
  5. 5.Microbial Type Culture Collection and Gene Bank, Institute of Microbial Technology (CSIR-IMTECH)ChandigarhIndia
  6. 6.Landcare ResearchLincolnNew Zealand
  7. 7.Department of BotanyInstitute of Ecology and Earth Sciences, University of TartuTartuEstonia

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