A genome sequence-based approach to taxonomy of the genus Nocardia
| Autor: | Toru Gonoi, Ken-ichiro Suzuki, Nobuyuki Fujita, Syoko Oji, Tetsuhiro Matsuzawa, Moriyuki Hamada, Tomohiko Tamura, Atsushi Yamazoe, Natsuko Ichikawa, Akira Hosoyama, Hiroshi Katsumata |
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| Rok vydání: | 2012 |
| Předmět: |
Sequence analysis
In silico Biology Microbiology Genome Nocardia medicine Humans Molecular Biology Gene Phylogeny Whole genome sequencing Genetics Phylogenetic tree Nocardiosis Computational Biology Genetic Variation General Medicine medicine.disease biology.organism_classification Classification Evolutionary biology bacteria Genome Bacterial Multilocus Sequence Typing |
| Zdroj: | Antonie van Leeuwenhoek. 102(3) |
| ISSN: | 1572-9699 |
| Popis: | The genus Nocardia includes both pathogens and producers of useful secondary metabolites. Although 16S rRNA analysis is required to accurately discriminate among phylogenetic relationships of the Nocardia species, most branches of 16S rRNA-based phylogenetic trees are not reliable. In this study, we performed in silico analyses of the genome sequences of Nocardia species in order to understand their diversity and classification for their identification and applications. Draft genome sequences of 26 Nocardia strains were determined. Phylogenetic trees were prepared on the basis of multilocus sequence analysis of the concatenated sequences of 12 genes (atpD-dnaJ-groL1-groL2-gyrB-recA-rpoA-secA-secY-sodA-trpB-ychF) and a bidirectional best hit. To elucidate the evolutionary relationships of these genes, the genome-to-genome distance was investigated on the basis of the average nucleotide identity, DNA maximal unique matches index, and genome-to-genome distance calculator. The topologies of all phylogenetic trees were found to be essentially similar to each other. Furthermore, whole genome-derived and multiple gene-derived relationships were found to be suitable for extensive intra-genus assessment of the genus Nocardia. |
| Databáze: | OpenAIRE |
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