Identification and characterization of variable-number tandem repeats in the Yersinia pestis genome

Citation
Am. Klevytska et al., Identification and characterization of variable-number tandem repeats in the Yersinia pestis genome, J CLIN MICR, 39(9), 2001, pp. 3179-3185
Citations number
25
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Clinical Immunolgy & Infectious Disease",Microbiology
Journal title
JOURNAL OF CLINICAL MICROBIOLOGY
ISSN journal
0095-1137 → ACNP
Volume
39
Issue
9
Year of publication
2001
Pages
3179 - 3185
Database
ISI
SICI code
0095-1137(200109)39:9<3179:IACOVT>2.0.ZU;2-A
Abstract
Yersinia pestis, the infamous plague-causing pathogen, appears to have emer ged in relatively recent history. Evidence of this fact comes from several studies that document a lack of nucleotide diversity in the Y. pestis genom e. In contrasts we report that variable-number tandem repeat (VNTR) sequenc es are common in the Y. pestis genome and occur frequently in gene coding r egions. Larger tandem repeat arrays, most useful for phylogenetic analysis, are present at an average of 2.18 arrays per 10 kbp and are distributed ev enly throughout the genome and the two virulence plasmids, pCD1 and pMT1. W e examined allelic diversity at 42 chromosomal VNTR loci in 24 selected iso lates (12 globally distributed and 12 from Siskiyou County, Calif.). Vast d ifferences in diversity were observed among the 42 VNTR loci, ranging from 2 to 11 alleles. We found that the maximum copy number of repeats in an arr ay was highly correlated with diversity (R=.0.86). VNTR-based phylogenetic analysis of the 24 strains successfully grouped isolates from biovar orient alis and most of the antiqua and mediaevalis strains. Hence, multiple-locus VNTR analysis (MLVA) appears capable of both distinguishing closely relate d strains and successfully classifying more distant relationships. Harnessi ng the power of MLVA to establish standardized databases will enable resear chers to better understand plague ecology and evolution around the world.