TABLE 5.
Description of various MTC species-, lineage-, and strain-specific LSPs
| Locus | MTC species | MTC strain or no. examined (if more than 1) | Locationa of deletion | ORF(s) affectedb | Nucleotide sequence at the junctionc |
|---|---|---|---|---|---|
| RD7tb | “Ancestral” PGG1b M. tuberculosis | CA-74 | 2214.298-2217.261 [2,964 bp] | Rv1970 to Rv1973 | GCAGCTGCCGGATGTCAACAACATCCAGCCGAACTCGCGGGTGCGGGTTGCCGCGACGCCGCGGTTGCCCGTGCGGAATCCGTGCGGGCCGCGACCGACG |
| RD236a | “Ancestral” PGG1b M. tuberculosis | Percy211 | 4056.946-4058.397 [1,452 bp] | ephA (Rv3617) | GTCATTATCTCCGATCATGTTTGATAAGGCGACGAAAACCGACGATGGAACTACATCGGCGAGTTCACCCGCACCGGTTTCACCGGCGGCCTGAACTGGT |
| N-RD25tbA | “Modern” PGG1b M. tuberculosis | 8 of 13d | 4189.258-4190.367 [1,110 bp] | Rv3737 to PPE67 (Rv3739c) | CCGACGACGGCCGACGACGTGGACGCCGGCTATCGCGGCGATTGGCCCGCCGCAGTGAGCTCTTGGGCTGCCGAAGCATACTCCGCACTCAGCGATGTCC |
| N-RD25tbB | “Modern” PGG1b M. tuberculosis | 2 of 13e | 4189.234-4190.191 [951 bp] | Rv3737 to PPE66 (Rv3738c) | AGCGTCGCGCTGGAGCCGACGACGGCCGACGACGTGGACGCCGGCTATCGTCGGCATCGCCGCCAGCGCGCTGGCATATGCCGTGGTCATAACCTCATGC |
| RD1tbB | “Modern” PGG1b M. tuberculosis | 3 of 13f | 4368.662-4368.718 [57 bp] | Rv3879c | AACGCGCGCCCGCTCCCACGGCGGTACCGCTCGGCGCGGCGGCCGCCGCCGCATGGGCAGGCCCCGACTGCGTCCCCCCGCCCGCATGCTGGCCCGGCAC |
| MiD3g | M. pinnipedii | 7 of 7 | 3741.143-3755.779 [14,636 bp] | PE-PGRS50 (Rv3345c) to IS1561′ (Rv3349c) | GTGGGCGCGGTGCCGTTCGCCCCGGCCGAACCGTTCAGGGCCGGGTTCGCCCTCAGCCGCTAAACACGCCGACCAAGATCAACGAGCTACCTGCCCGGTC |
a
Relative to the M. tuberculosis strain H37Rv genome sequence (accession no. AL123456 [10]); given in kb.
b
ORF, open reading frame; affected by truncation or deletion.
c
Sequences in boldface indicate the 5′ (left-hand) portion of the junction sequence.
d
M. tuberculosis strains 97-742, 97-803, 97-818, 97-1177, 97-1289, 97-1438, Percy7, and Percy91.
e
M. tuberculosis strains 13876 and Percy209.
f
M. tuberculosis strains 97-803, 97-1177, and 97-1438.
g
Identical to the M. microti MiD3 LSP (n = 10).