Reference databases for taxonomic assignment in metagenomics

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Abstract

Metagenomics is providing an unprecedented access to the environmental microbial diversity. The amplicon-basedmetagenomics approach involves the PCR-targeted sequencing of a genetic locus fitting different features. Namely,it must be ubiquitous in the taxonomic range of interest, variable enough to discriminate between different speciesbut flanked by highly conserved sequences, and of suitable size to be sequenced through next-generation platforms.The internal transcribed spacers 1 and 2 (ITS1 and ITS2) of the ribosomal DNA operon and one or morehyper-variable regions of 16S ribosomal RNA gene are typically used to identify fungal and bacterial species, respectively.In this context, reliable reference databases and taxonomies are crucial to assign amplicon sequence reads tothe correct phylogenetic ranks. Several resources provide consistent phylogenetic classification of publicly available16S ribosomal DNA sequences, whereas the state of ribosomal internal transcribed spacers reference databases isnotably less advanced. In this review, we aim to give an overview of existing reference resources for both types ofmarkers, highlighting strengths and possible shortcomings of their use for metagenomics purposes. Moreover, wepresent a new database, ITSoneDB, of well annotated and phylogenetically classified ITS1 sequences to be used asa reference collection in metagenomic studies of environmental fungal communities. ITSoneDB is available for downloadand browsing at http://itsonedb.ba.itb.cnr.it/.

Autore Pugliese

Tutti gli autori

  • M. Santamaria ; B. Fosso ; A. Consiglio ; G. De Caro ; G. Grillo ; F. Licciulli ; S. Liuni ; M. Marzano ; D. Alonso-Alemany ; G. Valiente; G. Pesole

Titolo volume/Rivista

Briefings in bioinformatics

Anno di pubblicazione

2012

ISSN

1467-5463

ISBN

Non Disponibile

Numero di citazioni Wos

Nessuna citazione

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Numero di citazioni Scopus

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Settori ERC

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Codici ASJC

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