Article Figures & Data
Figures
- Fig. 1.
Number of tandem repeat sequence arrays in theY. pestis chromosome. Log of array numbers with repeat lengths from 1 to 21 bp detected by Genequest (black bars) and repeat lengths from 1 to 10 bp detected by the SSR program (gray bars) are presented. Larger repeat lengths of 22, 30, 36, 41, 45, 49, 115, 122, 123, 141, and 145 bp were observed but are not presented, as each was observed only once (except the 123-bp repeat length, which was observed three times).
- Fig. 2.
Tandem repeat array distribution in the Y. pestis chromosome. Array distribution observed per 10-kbp interval (black bars) versus the expected Poisson distribution (μ = 2.14 arrays per 10-kbp interval) (gray bars).
- Fig. 3.
VNTR locus diversity. The 42 VNTR loci examined in this study are displayed based on the total number of alleles present in the 24 strains exampled.
- Fig. 4.
Maximum repeat copy number predicts the number of alleles. Correlation between copy number and allele number observed in 42 polymorphic loci. This is presented for 12 Siskiyou County isolates (open circles and line with short dashes), 12 globally dispersed isolates (open triangles and solid line), and all 24 isolates combined (filled circle and line with long dashes).
- Fig. 5.
Phylogenetic analysis using VNTR loci. Neighbor-joining analysis with midpoint rooting using 42 markers identified genetically similar and dissimilar strains. Biovar identities are indicated in parentheses following the strain names. O, orientalis; M, mediaevalis; A, antiqua. Bootstrap values based upon 1,000 simulations for individual branches are indicated. Branches with no numbers had values of less than 50.
Tables
- Table 1.
Y. pestis strains
Straina Geographical origin Biovarb Angola∗ Angola A Antiqua∗ Democratic Republic of Congo A Pestoides F∗ Former Soviet Union A Harbin 35∗ Manchuria M Kim 10 Variant∗ Kurdistan M Nicholisk 41∗ Manchuria M Pestoides A∗ Former Soviet Union M Pestoides Ba∗ Former Soviet Union M 195/P∗ India O Java 9∗ Indonesia O La Paz∗ Bolivia O CO92∗ Colorado O 83A-5257† California O 85A-4160† California O 86A-3503† California O 86A-3654† California O 89A-7521† California O 89A-7544† California O 89A-7545† California O 90A-415† California O 90A-598† California O 90A-4021† California O 90A-6072† California O 90A-7215† California O - Table 2.
Y. pestis VNTR loci and primers used for their amplificationa
Locus CO92 array No. of alleles DIb Forward primer (5′ to 3′) Reverse primer (5′ to 3′) M02 1 by 11 5 0.76 GCCTTGGCGCTGACTCCATTGTGC ∗Hex-GGCCTATTTATCTTAACCACGACTGAACCTC M06 2 by 6 2 0.17 ∗Fam-GATAGATCTCCGAAGGCAGATCGCAATAGGTC GGGCGATAGGATAGCTTGATGCGTTGTTTTAC M09 3 by 6 4 0.51 ∗Fam-GACCTCGATCTGCTTAGAACCTTTGTAGCTGTTGC GTTGCATTTGTTGGCTAACTGCTGACTGAGTTC M12c 4 by 10 7 0.82 GAAGCGGCAACAATTTACCGTTATTTATGCT ∗Ned-TTTATTCGCCTCCCCTTCGAACTTGAA M15 5 by 2 4 0.57 GTCACCTCTCAGGCGGGAATCATCTCTC GCATAACGTCTTCAGTGCGTTGTGGC M18 6 by 6 9 0.82 GGGGTGTTAATTGTGAGGCGTGTTGTC ∗Hex-CCCTACCCGCCACTCTCTTGGTAGC M2 7 by 5 3 0.49 ∗Ned-GATTTATGAATGGCTACAACGTCGTCGCA GTAGTGATACAGGCAAATCCAAGAGCGCA M22 7 by 12 9 0.82 ∗Fam-GCGTGATACCAAAGGCTGGCTCACC GGCACTTTGGGTACGGAACGTCATCAC M23 7 by 6.5 9 0.83 ∗Hex-GTTAAAACTTAATTAACCAACTTAAGAGTCGCCATATC GTTATCAGATTTCGCTTGAAGTAGGTTTAACGATGAC M25 7 by 20 10 0.83 ∗Hex-GTTTAGCTGTAAATAGATTTAGAAGCCTCGTCTTTTGAC GATATAAATGAGTTGATTCAGGTGTTCATATTTAACGAAAC M26 8 by 2 2 0.49 GCTATTTTTTGCGGTTAGTCACATTTGATATTTG GTCCCTTTCCTCACTGGTTCGACTTGTAAG M27 8 by 6 10 0.84 ∗Fam-GTCTAACTGGCGCGGCATTCTTGC GGGTGTTCTTATGTCATCCGCCAACAAAC M28 8 by 7 7 0.75 GTTTGGCGGTTGGGCGTACCTTGGTA ∗Ned-AGCGCCCGTAGACGCTTTCGAAATAGC M29 8 by 8 7 0.83 ∗Ned-GAGCGGCGGGTTCTCATGCTGAT GTTTAAGCAGTAGATCTAAAGCGTTATGAATATTGGTGTTA M31 8 by 8 7 0.78 ∗Fam-GGTTTGCAGGTTTTTGTTGTGGATTATGGACTTAGAT GGCGGGATGGCGTATCGGTTGC M33 9 by 22 7 0.76 ∗Hex-AGCAACCTGTGCCGCCTCGATATAAG GAGACGGGCGAAATTGAAGCACAGTTAT M34 9 by 6 11 0.81 ∗Fam-GAATCGCGGGTTGACGCTGTTGAGC GCTGAACAGCCCCATAAAACCGGAGC M36 10 by 1 2 0.38 GTTAGACAAAACGTTTCTCGATGATTTGTAAGC GACAAACAATAAAAATTCACGATTTATACCCGTC M37 10 by 6 5 0.72 GCCACAGGAAGAGGACATTTCAGAGAAAAC GTTGCTAAAACGATACCGCTACGATCAGC M41 12 by 2 3 0.15 GCAGGGGACACCGAGCAGATTTATGC GCTTTCGCTTTAGGCCTGACCTGTTCTGC M42 12 by 3 2 0.18 GCCGGTAGAGGCGTTGTCTTTGGTTTTTTC GTTTTGGGGTTCAGTGCACGCTTGTGAC M43 12 by 5 4 0.69 GAGTGCGCGACGGTATGGTGC GCCGCGCATTTATTGATGGTGTC M49 14 by 3 2 0.44 GTAATACTTACGCCTTGGCAGCAGTGTTCACGAC GTGGGGTGTTCTACGGTGGATTGTTTTTAGGC M51 15 by 3 2 0.49 GCAACCCGCTGAAGTTGTAAAAACCGAC GCGTTGATCTTCGCGGCCTTCAC M52 15 by 4 2 0.49 GTGGCCTAACCCGTTTTACCGGTGTAGC GCGGTTTTGTCAATCACGAATCAGGACTC M54 16 by 3 3 0.57 GTATGCTTAGCGCCAGTGATAACGAGTC GATCGCGTCATCGGGGTTTGTC M55 16 by 2 3 0.40 GTCATGGGTGATGCTGTTGCTCTCATTTTATAGTTGTAGTGA GCCTTAATGGTTGAATGCGCGAATGAGTCAGATAAC M56 17 by 2 3 0.40 GTGCCAGTGTTTCGAGCATAGCCAATGAAATAC GTACCGCAGCCCAGACTCCTTACTGGAAAC M58 17 by 7.5 6 0.78 ∗Hex-GCGATAACCCACATTATCACAATAACCAACAC GCTGATGGAACCGGTATGCTGAATTTGC M59 17 by 8 4 0.68 ∗Ned-GCTTAGCCGCCAGAAAAGGTGAGTTGGC GATAATGGCGGTAGCCGGAATCTGATAATCATC M61 18 by 5 3 0.60 GCGCCACAATTAGGGCAACTGC GCCGCTTTAATGGTTTGTGAAATGAC M65 19 by 2.5 3 0.29 GTTGTATGTGCGTTGGTTAGGGAAGGC GTCATTTACTCCGGTAGTTTATTGGGTATTGAAC M66 20 by 2 3 0.50 GAGATGGATTAACCAGATGTCTTAAAAACTATCGTAAC GCGAATCGGCGGCCCAAAC M68 20 by 3 3 0.49 GATAAAGCGCAATGGCAAGAGAAAGC GCCTGGCAATTGTTCAGCGAATC M69 21 by 2 2 0.00 GCGGTGCTGTTGTTAATGATTAGGTGTTCAC GCCCTCATCACAAAATACCTAAAATAGTCAATAGC M71 21 by 2 2 0.15 GCGTTGCCAGCCGCAGCGATAC GCACCCCTGCTCTGGGTCACGC M72 22 by 2 2 0.38 GCGACACGCCCTTTCAATGAGATACAC GTAGATCACCGCTAAATGCGAAGGTCCAC M73 30 by 2 2 0.28 GCTTTCTGGCAATGCGATAGTTAGGCATCTC GTTAATTTAACTCAATATTGTCGCTATGGT M74 36 by 2 2 0.28 GATAGAATAGCGCTTCTTTTATTATTGAGATGATGAC GTGCTTGTGGCAGGTGGGTATGAC M76 41 by 2 2 0.49 GCGGCCTGATAAGGGATATTGGAAGC GGCGAAATTCATTAAAGAGGATCCTGACAC M77 45 by 4 2 0.15 GAGTATTGCGAAGGGGTGATAAATGAAGC GTGCCAGAGTCCTTGGTTAAACAAATAGAAGAAC M79 8 by 10 10 0.86 ∗Fam-GCCCTTATCTACTGGGCCAAGCTAACGC GCCATGGCGGGATGTAATGGCAC
