title: Analysis of the complete genome sequence of Nocardia seriolae UTF1, the causative agent of fish nocardiosis: The first reference genome sequence of the fish pathogenic Nocardia species.
abstract: Nocardiosis caused by Nocardia seriolae is one of the major threats in the aquaculture of Seriola species (yellowtail; S. quinqueradiata, amberjack; S. dumerili and kingfish; S. lalandi) in Japan. Here, we report the complete nucleotide genome sequence of N. seriolae UTF1, isolated from a cultured yellowtail. The genome is a circular chromosome of 8,121,733 bp with a G+C content of 68.1% that encodes 7,697 predicted proteins. In the N. seriolae UTF1 predicted genes, we found orthologs of virulence factors of pathogenic mycobacteria and human clinical Nocardia isolates involved in host cell invasion, modulation of phagocyte function and survival inside the macrophages. The virulence factor candidates provide an essential basis for understanding their pathogenic mechanisms at the molecular level by the fish nocardiosis research community in future studies. We also found many potential antibiotic resistance genes on the N. seriolae UTF1 chromosome. Comparative analysis with the four existing complete genomes, N. farcinica IFM 10152, N. brasiliensis HUJEG-1 and N. cyriacigeorgica GUH-2 and N. nova SH22a, revealed that 2,745 orthologous genes were present in all five Nocardia genomes (core genes) and 1,982 genes were unique to N. seriolae UTF1. In particular, the N. seriolae UTF1 genome contains a greater number of mobile elements and genes of unknown function that comprise the differences in structure and gene content from the other Nocardia genomes. In addition, a lot of the N. seriolae UTF1-specific genes were assigned to the ABC transport system. Because of limited resources in ocean environments, these N. seriolae UTF1 specific ABC transporters might facilitate adaptation strategies essential for marine environment survival. Thus, the availability of the complete N. seriolae UTF1 genome sequence will provide a valuable resource for comparative genomic studies of N. seriolae isolates, as well as provide new insights into the ecological and functional diversity of the genus Nocardia.
authors.affiliation: Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan.
authors.forename: Motoshige
authors.initials: M
authors.lastname: Yasuike
authors.affiliation: Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan.
authors.forename: Issei
authors.initials: I
authors.lastname: Nishiki
authors.affiliation: Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Iwasaki
authors.affiliation: Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan.
authors.forename: Yoji
authors.initials: Y
authors.lastname: Nakamura
authors.affiliation: Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan.
authors.forename: Atushi
authors.initials: A
authors.lastname: Fujiwara
authors.affiliation: Research Center of Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Saiki, Oita, Japan.
authors.forename: Yoshiko
authors.initials: Y
authors.lastname: Shimahara
authors.affiliation: Fisheries Agency, Ministry of Agriculture, Forestry and Fisheries, Chiyoda-ku, Tokyo, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Kamaishi
authors.affiliation: Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.
authors.forename: Terutoyo
authors.initials: T
authors.lastname: Yoshida
authors.affiliation: Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Nagai
authors.affiliation: Headquarters, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan.
authors.forename: Takanori
authors.initials: T
authors.lastname: Kobayashi
authors.affiliation: Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan.
authors.forename: Masaya
authors.initials: M
authors.lastname: Katoh
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D005393:Fish Diseases / Q000235:genetics / Q000382:microbiology*; D005399:Fishes / Q000382:microbiology; D016678:Genome; D007564:Japan; D058977:Molecular Sequence Annotation; D009615:Nocardia / Q000235:genetics* / Q000472:pathogenicity; D009617:Nocardia Infections / Q000235:genetics* / Q000382:microbiology; D010802:Phylogeny