The whole-genome sequencing of the obligate intracellular bacterium orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution

Keisuke Nakayama, Atsushi Yamashita, Ken Kurokawa, Takuya Morimoto, Michihiro Ogawa, Masahiro Fukuhara, Hiroshi Urakami, Makoto Ohnishi, Ikuo Uchiyama, Yoshitoshi Ogura, Tadasuke Ooka, Kenshiro Oshima, Akira Tamura, Masahira Hattori, Tetsuya Hayashi

Research output: Contribution to journalArticle

94 Citations (Scopus)

Abstract

Scrub typhus ('Tsutsugamushi' disease in Japanese) is a mite-borne infectious disease. The causative agent is Orientia tsutsugamushi, an obligate intracellular bacterium belonging to the family Richettsiaceae of the subdivision alpha-Proteobacteria. In this study, we determined the complete genome sequence of O. tsutsugamushi strain lkeda, which comprises a single chromosome of 2 008 987 bp and contains 1967 protein coding sequences (CDSs). The chromosome is much larger than those of other members of Rickettsiaceae, and 46.7% of the sequence was occupied by repetitive sequences derived from an integrative and conjugative element, 10 types of transposable elements, and seven types of short repeats of unknown origins. The massive amplification and degradation of these elements have generated a huge number of repeated genes (1196 CDSs, categorized into 85 families), many of which are pseudogenes (766 CDSs), and also induced intensive genome shuffling. By comparing the gene content with those of other family members of Rickettsiacea, we identified the core gene set of the family Rickettsiaceae and found that, while much more extensive gene loss has taken place among the housekeeping genes of Orientia than those of Rickettsia, O. tsutsugamushi has acquired a large number of foreign genes. The O. tsutsugamushi genome sequence is thus a prominent example of the high plasticity of bacterial genomes, and provides the genetic basis for a better understanding of the biology of O. tsutsugamushi and the pathogenesis of 'Tsutsugamushi' disease.

Original languageEnglish
Pages (from-to)185-199
Number of pages15
JournalDNA Research
Volume15
Issue number4
DOIs
Publication statusPublished - 2008
Externally publishedYes

Fingerprint

Orientia tsutsugamushi
Gene Amplification
Scrub Typhus
Rickettsiaceae
Genome
Bacteria
Genes
Alphaproteobacteria
Bacterial Genomes
Pseudogenes
DNA Transposable Elements
Chromosomes, Human, Pair 2
Nucleic Acid Repetitive Sequences
Mites
Essential Genes
Communicable Diseases
Chromosomes
Proteins

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Medicine(all)

Cite this

The whole-genome sequencing of the obligate intracellular bacterium orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution. / Nakayama, Keisuke; Yamashita, Atsushi; Kurokawa, Ken; Morimoto, Takuya; Ogawa, Michihiro; Fukuhara, Masahiro; Urakami, Hiroshi; Ohnishi, Makoto; Uchiyama, Ikuo; Ogura, Yoshitoshi; Ooka, Tadasuke; Oshima, Kenshiro; Tamura, Akira; Hattori, Masahira; Hayashi, Tetsuya.

In: DNA Research, Vol. 15, No. 4, 2008, p. 185-199.

Research output: Contribution to journalArticle

Nakayama, K, Yamashita, A, Kurokawa, K, Morimoto, T, Ogawa, M, Fukuhara, M, Urakami, H, Ohnishi, M, Uchiyama, I, Ogura, Y, Ooka, T, Oshima, K, Tamura, A, Hattori, M & Hayashi, T 2008, 'The whole-genome sequencing of the obligate intracellular bacterium orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution', DNA Research, vol. 15, no. 4, pp. 185-199. https://doi.org/10.1093/dnares/dsn011
Nakayama, Keisuke ; Yamashita, Atsushi ; Kurokawa, Ken ; Morimoto, Takuya ; Ogawa, Michihiro ; Fukuhara, Masahiro ; Urakami, Hiroshi ; Ohnishi, Makoto ; Uchiyama, Ikuo ; Ogura, Yoshitoshi ; Ooka, Tadasuke ; Oshima, Kenshiro ; Tamura, Akira ; Hattori, Masahira ; Hayashi, Tetsuya. / The whole-genome sequencing of the obligate intracellular bacterium orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution. In: DNA Research. 2008 ; Vol. 15, No. 4. pp. 185-199.
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AU - Morimoto, Takuya

AU - Ogawa, Michihiro

AU - Fukuhara, Masahiro

AU - Urakami, Hiroshi

AU - Ohnishi, Makoto

AU - Uchiyama, Ikuo

AU - Ogura, Yoshitoshi

AU - Ooka, Tadasuke

AU - Oshima, Kenshiro

AU - Tamura, Akira

AU - Hattori, Masahira

AU - Hayashi, Tetsuya

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