title: 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.
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.
authors.affiliation: Department of Plant and Environmental Sciences, University of Gothenburg, Göteborg, Sweden. johan@microbiology.se
authors.forename: Johan
authors.initials: J
authors.lastname: Bengtsson
authors.forename: K Martin
authors.initials: KM
authors.lastname: Eriksson
authors.forename: Martin
authors.initials: M
authors.lastname: Hartmann
authors.forename: Zheng
authors.initials: Z
authors.lastname: Wang
authors.forename: Belle Damodara
authors.initials: BD
authors.lastname: Shenoy
authors.forename: Gwen-Aëlle
authors.initials: GA
authors.lastname: Grelet
authors.forename: Kessy
authors.initials: K
authors.lastname: Abarenkov
authors.forename: Anna
authors.initials: A
authors.lastname: Petri
authors.forename: Magnus Alm
authors.initials: MA
authors.lastname: Rosenblad
authors.forename: R Henrik
authors.initials: RH
authors.lastname: Nilsson
mesh_terms: D001105:Archaea / Q000235:genetics* / Q000302:isolation & purification; D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification; D002736:Chloroplasts / Q000235:genetics*; D030561:Databases, Nucleic Acid; D056890:Eukaryota / Q000235:genetics* / Q000302:isolation & purification; D054892:Metagenome; D056186:Metagenomics / Q000295:instrumentation / Q000379:methods*; D008928:Mitochondria / Q000235:genetics*; D010802:Phylogeny; D054679:Ribosome Subunits, Small / Q000235:genetics*; D016415:Sequence Alignment; D012984:Software