title: Extremely Low Genomic Diversity of Rickettsia japonica Distributed in Japan.
abstract: Rickettsiae are obligate intracellular bacteria that have small genomes as a result of reductive evolution. Many Rickettsia species of the spotted fever group (SFG) cause tick-borne diseases known as "spotted fevers". The life cycle of SFG rickettsiae is closely associated with that of the tick, which is generally thought to act as a bacterial vector and reservoir that maintains the bacterium through transstadial and transovarial transmission. Each SFG member is thought to have adapted to a specific tick species, thus restricting the bacterial distribution to a relatively limited geographic region. These unique features of SFG rickettsiae allow investigation of how the genomes of such biologically and ecologically specialized bacteria evolve after genome reduction and the types of population structures that are generated. Here, we performed a nationwide, high-resolution phylogenetic analysis of Rickettsia japonica, an etiological agent of Japanese spotted fever that is distributed in Japan and Korea. The comparison of complete or nearly complete sequences obtained from 31 R. japonica strains isolated from various sources in Japan over the past 30 years demonstrated an extremely low level of genomic diversity. In particular, only 34 single nucleotide polymorphisms were identified among the 27 strains of the major lineage containing all clinical isolates and tick isolates from the three tick species. Our data provide novel insights into the biology and genome evolution of R. japonica, including the possibilities of recent clonal expansion and a long generation time in nature due to the long dormant phase associated with tick life cycles.
authors.affiliation: Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
authors.forename: Arzuba
authors.initials: A
authors.lastname: Akter
authors.affiliation: Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
authors.forename: Tadasuke
authors.initials: T
authors.lastname: Ooka
authors.affiliation: Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan.
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Gotoh
authors.affiliation: Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan.
authors.forename: Seigo
authors.initials: S
authors.lastname: Yamamoto
authors.affiliation: Mahara Institute of Medical Acarology, Tokushima, Japan.
authors.forename: Hiromi
authors.initials: H
authors.lastname: Fujita
authors.affiliation: Wakayama Prefectural Research Center of Environment and Public Health, Wakayama, Japan.
authors.forename: Fumio
authors.initials: F
authors.lastname: Terasoma
authors.affiliation: Okayama Prefectural Institute for Environmental Science and Public Health, Okayama, Japan.
authors.forename: Kouji
authors.initials: K
authors.lastname: Kida
authors.affiliation: Chiba Prefectural Institute of Public Health, Chiba, Japan.
authors.forename: Masakatsu
authors.initials: M
authors.lastname: Taira
authors.affiliation: Kagoshima Prefectural Institute for Environmental Research and Public Health, Kagoshima, Japan.
authors.forename: Fumiko
authors.initials: F
authors.lastname: Nakadouzono
authors.affiliation: Kagoshima Prefectural Institute for Environmental Research and Public Health, Kagoshima, Japan.
authors.forename: Mutsuyo
authors.initials: M
authors.lastname: Gokuden
authors.affiliation: Seihi Public Health Center of Nagasaki Prefecture, Nagasaki, Japan.
authors.forename: Manabu
authors.initials: M
authors.lastname: Hirano
authors.affiliation: Fukuoka City Institute for Health and Environment, Fukuoka, Japan.
authors.forename: Mamoru
authors.initials: M
authors.lastname: Miyashiro
authors.affiliation: Mahara Institute of Medical Acarology, Tokushima, Japan.
authors.forename: Kouichi
authors.initials: K
authors.lastname: Inari
authors.affiliation: Hiroshima Prefectural Technology Research Institute, Public Health and Environment Center, Hiroshima, Japan.
authors.forename: Yukie
authors.initials: Y
authors.lastname: Shimazu
authors.affiliation: Department of Health and Welfare, Shimane Prefectural Government, Shimane, Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Tabara
authors.affiliation: Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.affiliation: School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
authors.forename: Dai
authors.initials: D
authors.lastname: Yoshimura
authors.affiliation: School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
authors.forename: Takehiko
authors.initials: T
authors.lastname: Itoh
authors.affiliation: Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
authors.forename: Tomokazu
authors.initials: T
authors.lastname: Kitano
authors.affiliation: Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan.
authors.forename: Mitsuhiko P
authors.initials: MP
authors.lastname: Sato
authors.affiliation: Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Katsura
authors.affiliation: Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
authors.forename: Shakhinur Islam
authors.initials: SI
authors.lastname: Mondal
authors.affiliation: Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan.
authors.forename: Yoshitoshi
authors.initials: Y
authors.lastname: Ogura
authors.affiliation: Department of Virology-1, National Institute of Infectious Diseases, Tokyo, Japan.
authors.forename: Shuji
authors.initials: S
authors.lastname: Ando
authors.affiliation: Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Hayashi
mesh_terms: D020869:Gene Expression Profiling; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D007564:Japan; D010802:Phylogeny; D012281:Rickettsia / Q000145:classification / Q000235:genetics*; D012282:Rickettsia Infections / Q000235:genetics / Q000382:microbiology*; D017422:Sequence Analysis, DNA
keywords: generation time; genome evolution; intra-species genomic diversity; intracellular bacteria; rickettsia