Genomic Features of Rickettsia heilongjiangensis Revealed by Intraspecies Comparison and Detailed Comparison With Rickettsia japonica
is the causative agent of Far-Eastern spotted fever (FESF). In Japan, a human case of FESF was identified in Sendai in Miyagi Prefecture in 2008, and bacteria were isolated from ticks collected in the suspected geographical area of infection. Although the intraspecies genome diversity of Rickettsia...
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Published in | Frontiers in microbiology Vol. 10; p. 2787 |
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Main Authors | , , , , , , , |
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Language | English |
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Abstract | is the causative agent of Far-Eastern spotted fever (FESF). In Japan, a human case of FESF was identified in Sendai in Miyagi Prefecture in 2008, and
bacteria were isolated from
ticks collected in the suspected geographical area of infection. Although the intraspecies genome diversity of Rickettsia has been poorly investigated, our recent analysis revealed extremely low genomic diversity of
, the agent of Japanese spotted fever, which is a close relative of
. In this study, to investigate the genomic diversity of
and understand the genetic relationship between Japanese and Chinese isolates, we sequenced three isolates from
ticks collected in Sendai and one isolate from a
tick collected in Inner Mongolia, China, and performed genomic comparisons between these isolates and strain 054, the type strain isolated from a
tick in Heilongjiang Province, China. Although the three Japanese strains were isolated in 2008, 2009, and 2012, their genome sequences were identical, indicating that
ticks carrying a single
clone have been distributed in Sendai, Japan. Among the five
isolates, only 81 SNPs and 13 insertion/deletion sites were identified, despite the significant differences in these isolates both geographically and temporally. A significant portion of the 81 SNPs (16/81) were found to be recombinogenic. These results indicate low genomic diversity of
, as observed in
. We further performed a detailed genomic comparison of
and
to accurately define conserved and species-specific genes. This analysis revealed that although notable variations were found in the genomic loci encoding RelA/SpoT family proteins and tandem repeats in major surface proteins, there was only a small difference in the gene repertoire between the two species, suggesting that SNPs and small InDels are responsible for the functional or physiological differences between the two species, if present. Through this analysis, several species-specific genomic regions that can serve as ideal PCR targets for distinguishing
and
were also identified. |
---|---|
AbstractList | Rickettsia heilongjiangensis
is the causative agent of Far-Eastern spotted fever (FESF). In Japan, a human case of FESF was identified in Sendai in Miyagi Prefecture in 2008, and
R. heilongjiangensis
bacteria were isolated from
Haemaphysalis concinna
ticks collected in the suspected geographical area of infection. Although the intraspecies genome diversity of Rickettsia has been poorly investigated, our recent analysis revealed extremely low genomic diversity of
R. japonica
, the agent of Japanese spotted fever, which is a close relative of
R. heilongjiangensis
. In this study, to investigate the genomic diversity of
R. heilongjiangensis
and understand the genetic relationship between Japanese and Chinese isolates, we sequenced three isolates from
H. concinna
ticks collected in Sendai and one isolate from a
H. concinna
tick collected in Inner Mongolia, China, and performed genomic comparisons between these isolates and strain 054, the type strain isolated from a
Dermacentor silvarum
tick in Heilongjiang Province, China. Although the three Japanese strains were isolated in 2008, 2009, and 2012, their genome sequences were identical, indicating that
H. concinna
ticks carrying a single
R. heilongjiangensis
clone have been distributed in Sendai, Japan. Among the five
R. heilongjiangensis
isolates, only 81 SNPs and 13 insertion/deletion sites were identified, despite the significant differences in these isolates both geographically and temporally. A significant portion of the 81 SNPs (16/81) were found to be recombinogenic. These results indicate low genomic diversity of
R. heilongjiangensis
, as observed in
R. japonica
. We further performed a detailed genomic comparison of
R. heilongjiangensis
and
R. japonica
to accurately define conserved and species-specific genes. This analysis revealed that although notable variations were found in the genomic loci encoding RelA/SpoT family proteins and tandem repeats in major surface proteins, there was only a small difference in the gene repertoire between the two species, suggesting that SNPs and small InDels are responsible for the functional or physiological differences between the two species, if present. Through this analysis, several species-specific genomic regions that can serve as ideal PCR targets for distinguishing
R. heilongjiangensis
and
R. japonica
were also identified. is the causative agent of Far-Eastern spotted fever (FESF). In Japan, a human case of FESF was identified in Sendai in Miyagi Prefecture in 2008, and bacteria were isolated from ticks collected in the suspected geographical area of infection. Although the intraspecies genome diversity of Rickettsia has been poorly investigated, our recent analysis revealed extremely low genomic diversity of , the agent of Japanese spotted fever, which is a close relative of . In this study, to investigate the genomic diversity of and understand the genetic relationship between Japanese and Chinese isolates, we sequenced three isolates from ticks collected in Sendai and one isolate from a tick collected in Inner Mongolia, China, and performed genomic comparisons between these isolates and strain 054, the type strain isolated from a tick in Heilongjiang Province, China. Although the three Japanese strains were isolated in 2008, 2009, and 2012, their genome sequences were identical, indicating that ticks carrying a single clone have been distributed in Sendai, Japan. Among the five isolates, only 81 SNPs and 13 insertion/deletion sites were identified, despite the significant differences in these isolates both geographically and temporally. A significant portion of the 81 SNPs (16/81) were found to be recombinogenic. These results indicate low genomic diversity of , as observed in . We further performed a detailed genomic comparison of and to accurately define conserved and species-specific genes. This analysis revealed that although notable variations were found in the genomic loci encoding RelA/SpoT family proteins and tandem repeats in major surface proteins, there was only a small difference in the gene repertoire between the two species, suggesting that SNPs and small InDels are responsible for the functional or physiological differences between the two species, if present. Through this analysis, several species-specific genomic regions that can serve as ideal PCR targets for distinguishing and were also identified. Rickettsia heilongjiangensis is the causative agent of Far-Eastern spotted fever (FESF). In Japan, a human case of FESF was identified in Sendai in Miyagi Prefecture in 2008, and R. heilongjiangensis bacteria were isolated from Haemaphysalis concinna ticks collected in the suspected geographical area of infection. Although the intraspecies genome diversity of Rickettsia has been poorly investigated, our recent analysis revealed extremely low genomic diversity of R. japonica, the agent of Japanese spotted fever, which is a close relative of R. heilongjiangensis. In this study, to investigate the genomic diversity of R. heilongjiangensis and understand the genetic relationship between Japanese and Chinese isolates, we sequenced three isolates from H. concinna ticks collected in Sendai and one isolate from a H. concinna tick collected in Inner Mongolia, China, and performed genomic comparisons between these isolates and strain 054, the type strain isolated from a Dermacentor silvarum tick in Heilongjiang Province, China. Although the three Japanese strains were isolated in 2008, 2009, and 2012, their genome sequences were identical, indicating that H. concinna ticks carrying a single R. heilongjiangensis clone have been distributed in Sendai, Japan. Among the five R. heilongjiangensis isolates, only 81 SNPs and 13 insertion/deletion sites were identified, despite the significant differences in these isolates both geographically and temporally. A significant portion of the 81 SNPs (16/81) were found to be recombinogenic. These results indicate low genomic diversity of R. heilongjiangensis, as observed in R. japonica. We further performed a detailed genomic comparison of R. heilongjiangensis and R. japonica to accurately define conserved and species-specific genes. This analysis revealed that although notable variations were found in the genomic loci encoding RelA/SpoT family proteins and tandem repeats in major surface proteins, there was only a small difference in the gene repertoire between the two species, suggesting that SNPs and small InDels are responsible for the functional or physiological differences between the two species, if present. Through this analysis, several species-specific genomic regions that can serve as ideal PCR targets for distinguishing R. heilongjiangensis and R. japonica were also identified. |
Author | Fujita, Hiromi Yamamoto, Seigo Gotoh, Yasuhiro Ooka, Tadasuke Kasama, Kentaro Ogura, Yoshitoshi Hayashi, Tetsuya Ando, Shuji |
AuthorAffiliation | 2 Mahara Institute of Medical Acarology , Tokushima , Japan 1 Department of Bacteriology, Faculty of Medical Sciences, Kyushu University , Fukuoka , Japan 5 Department of Virology-I, National Institute of Infectious Diseases , Tokyo , Japan 4 Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University , Kagoshima , Japan 3 Frontier Science Research Center, University of Miyazaki , Miyazaki , Japan |
AuthorAffiliation_xml | – name: 4 Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University , Kagoshima , Japan – name: 1 Department of Bacteriology, Faculty of Medical Sciences, Kyushu University , Fukuoka , Japan – name: 2 Mahara Institute of Medical Acarology , Tokushima , Japan – name: 3 Frontier Science Research Center, University of Miyazaki , Miyazaki , Japan – name: 5 Department of Virology-I, National Institute of Infectious Diseases , Tokyo , Japan |
Author_xml | – sequence: 1 givenname: Kentaro surname: Kasama fullname: Kasama, Kentaro organization: Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan – sequence: 2 givenname: Hiromi surname: Fujita fullname: Fujita, Hiromi organization: Mahara Institute of Medical Acarology, Tokushima, Japan – sequence: 3 givenname: Seigo surname: Yamamoto fullname: Yamamoto, Seigo organization: Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan – sequence: 4 givenname: Tadasuke surname: Ooka fullname: Ooka, Tadasuke organization: Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan – sequence: 5 givenname: Yasuhiro surname: Gotoh fullname: Gotoh, Yasuhiro organization: Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan – sequence: 6 givenname: Yoshitoshi surname: Ogura fullname: Ogura, Yoshitoshi organization: Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan – sequence: 7 givenname: Shuji surname: Ando fullname: Ando, Shuji organization: Department of Virology-I, National Institute of Infectious Diseases, Tokyo, Japan – sequence: 8 givenname: Tetsuya surname: Hayashi fullname: Hayashi, Tetsuya organization: Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31866968$$D View this record in MEDLINE/PubMed |
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Cites_doi | 10.1093/nar/27.2.573 10.1128/JCM.38.9.3498-3501.2000 10.1002/bmb.20244.DNA 10.1051/vetres/2009017 10.1111/j.1462-5822.2012.01815.x 10.1128/CMR.00032-13 10.1371/journal.pone.0000266 10.1016/j.ttbdis.2018.11.007 10.1073/pnas.0906412106 10.1111/1574-6976.12084 10.3201/eid1608.100049 10.1093/bioinformatics/btp352 10.1073/pnas.1307235110 10.1101/gr.215087.116.Freely 10.1146/annurev.micro.62.081307.162903 10.1128/JB.05852-11 10.1016/j.meegid.2014.05.028 10.4161/fly.19695 10.1128/CMR.00045-16 10.1038/ncb2109 10.1128/IAI.00100-10 10.1093/bioinformatics/btp698 10.1186/s13071-016-1764-2 10.1007/s11856-015-1234-0 10.1093/gbe/evw304 10.1371/journal.pone.0023479 10.1093/nar/27.11.2369 10.1016/j.ttbdis.2018.07.015 10.1186/1471-2105-9-376 10.1016/j.pt.2015.03.008 10.1101/gr.170720.113 10.1128/IAI.01165-09 10.1093/nar/30.11.2478 10.1093/bioinformatics/btu153 10.1128/iai.00048-11 |
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Copyright | Copyright © 2019 Kasama, Fujita, Yamamoto, Ooka, Gotoh, Ogura, Ando and Hayashi. Copyright © 2019 Kasama, Fujita, Yamamoto, Ooka, Gotoh, Ogura, Ando and Hayashi. 2019 Kasama, Fujita, Yamamoto, Ooka, Gotoh, Ogura, Ando and Hayashi |
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Keywords | intraspecies genomic diversity genome sequence spotted fever group rickettsia Rickettsia heilongjiangensis Rickettsia japonica |
Language | English |
License | Copyright © 2019 Kasama, Fujita, Yamamoto, Ooka, Gotoh, Ogura, Ando and Hayashi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
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Snippet | is the causative agent of Far-Eastern spotted fever (FESF). In Japan, a human case of FESF was identified in Sendai in Miyagi Prefecture in 2008, and
bacteria... Rickettsia heilongjiangensis is the causative agent of Far-Eastern spotted fever (FESF). In Japan, a human case of FESF was identified in Sendai in Miyagi... Rickettsia heilongjiangensis is the causative agent of Far-Eastern spotted fever (FESF). In Japan, a human case of FESF was identified in Sendai in Miyagi... |
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SubjectTerms | genome sequence intraspecies genomic diversity Microbiology Rickettsia heilongjiangensis Rickettsia japonica spotted fever group rickettsia |
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Title | Genomic Features of Rickettsia heilongjiangensis Revealed by Intraspecies Comparison and Detailed Comparison With Rickettsia japonica |
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