title: A genome sequence-based approach to taxonomy of the genus Nocardia.
abstract: 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.
authors: NITE Biological Resource Center, National Institute of Technology and Evaluation, Kazusakamatari, Kisarazu, Chiba, Japan. tamura-tomohiko@nite.go.jp
authors: Tomohiko
authors: T
authors: Tamura
authors: Tetsuhiro
authors: T
authors: Matsuzawa
authors: Syoko
authors: S
authors: Oji
authors: Natsuko
authors: N
authors: Ichikawa
authors: Akira
authors: A
authors: Hosoyama
authors: Hiroshi
authors: H
authors: Katsumata
authors: Atsushi
authors: A
authors: Yamazoe
authors: Moriyuki
authors: M
authors: Hamada
authors: Ken-ichiro
authors: K
authors: Suzuki
authors: Toru
authors: T
authors: Gonoi
authors: Nobuyuki
authors: N
authors: Fujita
mesh_terms: D002965:Classification / Q000379:methods*; D019295:Computational Biology / Q000379:methods; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D058885:Multilocus Sequence Typing; D009615:Nocardia / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny