user

Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme

被引：12
|
作者：
Li, Yanjun [1 ,2 ]
Cui, Yujun [1 ]
Cui, Baizhong [3 ]
Yan, Yanfeng [1 ]
Yang, Xianwei [1 ]
Wang, Haidong [2 ]
Qi, Zhizhen [3 ]
Zhang, Qingwen [3 ]
Xiao, Xiao [1 ]
Guo, Zhaobiao [1 ]
Ma, Cong [2 ]
Wang, Jing [4 ]
Song, Yajun [1 ]
Yang, Ruifu [1 ]
机构：
[1] Beijing Inst Microbiol & Epidemiol, State Key Lab Pathogen & Biosecur, Beijing, Peoples R China
[2] Navy Gen Hosp, Dept Lab, Beijing, Peoples R China
[3] Qinghai Inst Endem Dis Prevent & Control, Xining, Peoples R China
[4] Chinese Acad Inspect & Quarantine, Inst Hlth Quarantine, Beijing, Peoples R China
来源：
PLOS ONE | 2013年 / 8卷 / 06期
基金：
中国国家自然科学基金;
关键词：
COMPLETE GENOME SEQUENCE; PHYLOGENETIC ANALYSIS; POPULATION-STRUCTURE; BACILLUS-ANTHRACIS; PLAGUE; DNA; MICROEVOLUTION; STRAINS; IDENTIFICATION; DIVERSITY;
D O I：
10.1371/journal.pone.0066567
中图分类号：
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号：
07 ; 0710 ; 09 ;
摘要：
Background: Variable number of tandem repeats (VNTRs) that are widely distributed in the genome of Yersinia pestis proved to be useful markers for the genotyping and source-tracing of this notorious pathogen. In this study, we probed into the features of VNTRs in the Y. pestis genome and developed a simple hierarchical genotyping system based on optimized VNTR loci. Methodology/Principal Findings: Capillary electrophoresis was used in this study for multi-locus VNTR analysis (MLVA) in 956 Y. pestis strains. The general features and genetic diversities of 88 VNTR loci in Y. pestis were analyzed with BioNumerics, and a "14+12" loci-based hierarchical genotyping system, which is compatible with single nucleotide polymorphism-based phylogenic analysis, was established. Conclusions/Significance: Appropriate selection of target loci reduces the impact of homoplasies caused by the rapid mutation rates of VNTR loci. The optimized "14+12" loci are highly discriminative in genotyping and source-tracing Y. pestis for molecular epidemiological or microbial forensic investigations with less time and lower cost. An MLVA genotyping datasets of representative strains will improve future research on the source-tracing and microevolution of Y. pestis.
引用
收藏
页数：10
相关论文
共 50 条
  • [31] Variable Number Tandem Repeats in the Mitochondrial DNA of Lentinula edodes
    Kim, Sinil
    Song, Yelin
    Ha, Byeongsuk
    Moon, Yoon Jung
    Kim, Minseek
    Ryu, Hojin
    Ro, Hyeon-Su
    [J]. GENES, 2019, 10 (07):
  • [32] Automatically predicting possible loci of variable number of tandem repeats
    Chang, CH
    Chuang, HY
    Chiang, YH
    Chiou, CS
    Lu, HI
    Kao, CY
    [J]. BIBE 2004: FOURTH IEEE SYMPOSIUM ON BIOINFORMATICS AND BIOENGINEERING, PROCEEDINGS, 2004, : 475 - 482
  • [33] Variable-number tandem repeats that are useful in genotyping isolates of Salmonella enterica subsp enterica serovars Typhimurium and Newport
    Witonski, D.
    Stefanova, R.
    Ranganathan, A.
    Schutze, G. E.
    Eisenach, K. D.
    Cave, M. D.
    [J]. JOURNAL OF CLINICAL MICROBIOLOGY, 2006, 44 (11) : 3849 - 3854
  • [34] Use of Multilocus Variable Number of Tandem Repeats Analysis Genotyping to Determine the Role of Asymptomatic Carriers in Clostridium difficile Transmission
    Curry, Scott R.
    Muto, Carlene A.
    Schlackman, Jessica L.
    Pasculle, A. William
    Shutt, Kathleen A.
    Marsh, Jane W.
    Harrison, Lee H.
    [J]. CLINICAL INFECTIOUS DISEASES, 2013, 57 (08) : 1094 - 1102
  • [35] DEVELOPMENT OF A NEW NOMENCLATURE FOR SALMONELLA TYPHIMURIUM MULTILOCUS VARIABLE NUMBER OF TANDEM REPEATS ANALYSIS (MLVA)
    Larsson, J. T.
    Torpdahl, M.
    Petersen, R. F.
    Sorensen, G.
    Lindstedt, B. A.
    Nielsen, E. M.
    [J]. EUROSURVEILLANCE, 2009, 14 (15): : 6 - 10
  • [36] Transcriptional effects of the insulin variable number of tandem repeats (VNTR) polymorphism
    Ounissi-Benkalha, H
    Polychronakos, C
    [J]. DIABETES, 2005, 54 : S162 - S162
  • [37] In Silico Analysis of Variable Number of Tandem Repeats in Erwinia amylovora Genome
    Dreo, T.
    Ravnikar, M.
    Frey, J. E.
    Smits, T. H. M.
    Duffy, B.
    [J]. XII INTERNATIONAL WORKSHOP ON FIRE BLIGHT, 2011, 896 : 115 - 118
  • [38] Genotypic and phenotypic complexity at the insulin variable number of tandem repeats locus
    Bougneres, Pierre
    [J]. JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM, 2006, 91 (11): : 4246 - 4249
  • [39] Identification of possible loci of variable number of tandem repeats in Mycobacterium tuberculosis
    Smittipat, N
    Palittapongarnpim, P
    [J]. TUBERCLE AND LUNG DISEASE, 2000, 80 (02): : 69 - 74
  • [40] Epidemiological study of Vibrio cholerae using variable number of tandem repeats
    Ghosh, Raikamal
    Nair, G. Balakrish
    Tang, Li
    Morris, J. Glenn
    Sharma, Naresh C.
    Ballal, Mamatha
    Garg, Pallavi
    Ramamurthy, Thandavarayan
    Stine, O. Colin
    [J]. FEMS MICROBIOLOGY LETTERS, 2008, 288 (02) : 196 - 201
12345