title: Genomic and comparative genomic analyses of Rickettsia heilongjiangensis provide insight into its evolution and pathogenesis.
abstract: Rickettsia heilongjiangensis, the causative agent of far eastern spotted fever, is an obligate intracellular gram-negative bacterium that belongs to the spotted fever group rickettsiae. To understand the evolution and pathogenesis of R. heilongjiangensis, we analyzed its genome and compared it with other rickettsial genomes available in GenBank. The R. heilongjiangensis chromosome contains 1333 genes, including 1297 protein coding genes and 36 RNA coding genes. The genome also contains 121 pseudogenes, 54 insertion sequences, and 39 tandem repeats. Sixteen genes encoding the major components of the type IV secretion systems were identified in the R. heilongjiangensis genome. In total, 37 β-barrel outer membrane proteins were predicted in the genome, eight of which have been previously confirmed to be outer membrane proteins. In addition, 266 potential virulence factor genes, seven partially deleted antibiotic resistance genes, and a genomic island were identified in the genome. The codon usage in the genome is compatible with its low GC content, and the amino acid usage shows apparent bias. A comparative genomic analysis showed that R. heilongjiangensis and R. japonica share one unique fragment that may be a target sequence for a diagnostic assay. The orthologs of 37 genes of R. heilongjiangensis were found in pathogenic R. rickettsii str. Sheila Smith but not in non-pathogenic R. rickettsii str. Iowa, which may explain why R. heilongjiangensis is pathogenic. Pan-genome analysis showed that R. heilongjiangensis and 42 other rickettsiae strains share 693 core genes with a pan-genome size of 4837 genes. The pan-genome-based phylogeny showed that R. heilongjiangensis was closely related to R. japonica.
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China. Electronic address: xysage@163.com.
authors.forename: Changsong
authors.initials: C
authors.lastname: Duan
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China. Electronic address: xiongxiaolu624@sohu.com.
authors.forename: Xiaolu
authors.initials: X
authors.lastname: Xiong
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China. Electronic address: qslark@qmail.com.
authors.forename: Yong
authors.initials: Y
authors.lastname: Qi
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China. Electronic address: gwp891015@whu.edu.cn.
authors.forename: Wenping
authors.initials: W
authors.lastname: Gong
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China. Electronic address: jiaojun51920@sina.com.
authors.forename: Jun
authors.initials: J
authors.lastname: Jiao
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China. Electronic address: bohaiwen@sohu.com.
authors.forename: Bohai
authors.initials: B
authors.lastname: Wen
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D058947:Bacterial Secretion Systems / Q000235:genetics; D003062:Codon; D024881:Drug Resistance, Bacterial / Q000235:genetics; D019143:Evolution, Molecular; D023061:Gene Order; D016680:Genome, Bacterial; D044404:Genomic Islands; D023281:Genomics; D006801:Humans; D016254:Mutagenesis, Insertional; D016366:Open Reading Frames; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid; D012281:Rickettsia / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000472:pathogenicity; D012282:Rickettsia Infections / Q000382:microbiology*; D037521:Virulence Factors / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D058947:Bacterial Secretion Systems; D003062:Codon; D037521:Virulence Factors
keywords: Comparative genomics; Far eastern spotted fever; Pan-genome; Pathogenesis; Rickettsia heilongjiangensis