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

Bengtsson-Palme, Johan,1985Gothenburg University,Göteborgs universitet,Institutionen för neurovetenskap och fysiologi, sektionen för fysiologi,Institutionen för cell- och molekylärbiologi,Institutionen för växt- och miljövetenskaper,Institute of Neuroscience and Physiology, Department of Physiology,Department of Cell and Molecular Biology,Department of Plant and Environmental Sciences,University of Gothenburg (author)

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.

Eriksson, Martin,1970Gothenburg University,Göteborgs universitet,Institutionen för växt- och miljövetenskaper,Department of Plant and Environmental Sciences,University of Gothenburg(Swepub:gu)xemarp (author)
Hartmann, Martin,1977 (author)
Zheng, Wang (author)
Shenoy, Belle Damodara (author)
Grelet, Gwen-Aëlle (author)
Abarenkov, Kessy (author)
Petri, Anna,1980Gothenburg University,Göteborgs universitet,Institutionen för växt- och miljövetenskaper,Department of Plant and Environmental Sciences,University of Gothenburg(Swepub:gu)xpetra (author)
Alm Rosenblad, Magnus,1957Gothenburg University,Göteborgs universitet,Institutionen för cell- och molekylärbiologi,Department of Cell and Molecular Biology,University of Gothenburg(Swepub:gu)xalmma (author)
Nilsson, R. Henrik,1976Gothenburg University,Göteborgs universitet,Institutionen för växt- och miljövetenskaper,Department of Plant and Environmental Sciences,University of Gothenburg(Swepub:gu)xnihen (author)
Göteborgs universitetInstitutionen för neurovetenskap och fysiologi, sektionen för fysiologi (creator_code:org_t)

In:Antonie van Leeuwenhoek: international journal of general and molecular microbiology: Springer Science and Business Media LLC100:3, s. 471-4750003-60721572-9699
In:Antonie van Leeuwenhoek: Springer Science and Business Media LLC100:3, s. 471-4751572-9699

By the author/editor: Bengtsson-Palme, ...; Eriksson, Martin ...; Hartmann, Martin ...; Zheng, Wang; Shenoy, Belle Da ...; Grelet, Gwen-Aël ...; show more...; Abarenkov, Kessy; Petri, Anna, 198 ...; Alm Rosenblad, M ...; Nilsson, R. Henr ...; show less...

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Bioinformatics a ...

MEDICAL AND HEALTH SCIENCES: MEDICAL AND HEAL ...; and Basic Medicine; and Microbiology in ...

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Microbiology

By the university: University of Gothenburg; Chalmers University of Technology

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