Abstract
BackgroundThe correct taxonomic assignment of bacterial genomes is a primary and challenging task. With the availability of whole genome sequences, the gene content based approaches appear promising in inferring the bacterial taxonomy. The complete genome sequencing of a bacterial genome often reveals a substantial number of unique genes present only in that genome which can be used for its taxonomic classification.ResultsIn this study, we have proposed a comprehensive method which uses the taxon-specific genes for the correct taxonomic assignment of existing and new bacterial genomes. The taxon-specific genes identified at each taxonomic rank have been successfully used for the taxonomic classification of 2,342 genomes present in the NCBI genomes, 36 newly sequenced genomes, and 17 genomes for which the complete taxonomy is not yet known. This approach has been implemented for the development of a tool ‘Microtaxi’ which can be used for the taxonomic assignment of complete bacterial genomes.ConclusionThe taxon-specific gene based approach provides an alternate valuable methodology to carry out the taxonomic classification of newly sequenced or existing bacterial genomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1542-0) contains supplementary material, which is available to authorized users.
Highlights
The correct taxonomic assignment of bacterial genomes is a primary and challenging task
Among the several available methods, DNA-DNA hybridization (DDH) and 16S rRNA gene based classification have been the key methods for the identification and taxonomic assignments of bacterial species [2]
In order to compare the gene content of different species, a unique gene symbol or id is required for each functional gene since there is enormous diversity in gene functions and ambiguity in the gene annotations
Summary
The correct taxonomic assignment of bacterial genomes is a primary and challenging task. The phylogeny based classification is commonly carried out by the comparison of a highly conserved 16S rRNA gene which is a part of the Commonly, a species is defined as a set of strains with approximately 70% or greater DNA-DNA relatedness or 97% 16S rRNA identity [2]. These two methods are still the keystones of the present-day bacterial taxonomic classification, they have their own limitations. Multi-locus sequence analysis (MLSA) of housekeeping genes is another molecular method which has recently become popular for investigating taxonomic
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