Table 3.
RGPs identified comparing ST239 and non-ST239-closed genomes using the chromosome of the Brazilian strain BMB9393 as reference.
| Length | Best hit (% query coverage, % subject coverage, | |||||
|---|---|---|---|---|---|---|
| Regions | Coordinates | (kbp) | GC% | Features | % identity, e-value)∗ | |
| RGP1 | 34139 | 105446 | 73.0 | 33.1 | S.b., dGC%, Tnp, Rec, tRNA, GI SCCmec | S. aureus DNA, SCCmercury, SCCmec type III.1.1 (IIIA), complete sequence, strain OC3 (GenBank AB983237.1) (55%, 64%, 99%, 0.0) |
| RGP2 | 398966 | 413781 | 14.8 | 35.3 | S.b., dGC%, Tnp | S. aureus NCTC13435 chromosome 1 (GenBank: LN831036.1) (100%, 0.6%, 99%, 0.0) |
| RGP3 | 451997 | 509822 | 57.8 | 33.3 | S.b., dGC%, Int., Tnp, ICE, GI νSAβ | S. aureus subsp. aureus T0131, complete genome (GenBank: CP002643.1) (100%, 0.95%, 99%, 0.0). |
| RGP4 | 925027 | 939643 | 14.6 | 29.9 | Ss.b., dGC%, Int, SaPI | S. aureus pathogenicity island SaPI Tokyo11212 (GenBank: AB860416.1) (84%, 72%, 98%, 0.0). |
| RGP5 | 1165376 | 1213829 | 48.5 | 33.6 | S.b., dGC%, Rec, phage similar to YMC09 | Staphylococcus phage phiSauS-IPLA35, complete genome (GenBank: EU861005.1) (61%, 65%, 97%, 0.0). |
| RGP6 | 1424422 | 1438004 | 13.5 | 28.1 | S.b., dGC%, Tnp | S. aureus subsp. aureus Z172, complete genome (GenBank: CP006838.1) (100%, 0.2%, 100%, 0.0). |
| RGP7 | 1632358 | 1684127 | 51.8 | 34.6 | S.b., dGC%, Int., phage similar to phiMR11 | Staphylococcus phage 55, complete genome (GenBank: AY954963.1) (61%, 59% 98%, 0.0). |
| RGP8 | 2013514 | 2044432 | 30.9 | 28.9 | S.b., dGC%, Tnp, tRNA, GI □SA□ | S. aureus XN108, complete genome (GenBank: CP007447.1) (100%, 1.0%, 99%, 0.0). |
| RGP9 | 2149470 | 2222679 | 73.2 | 31.7 | S.b., dGC%, Rec., phage similar to phiNM3, Tnp | S. aureus subsp. aureus ST72 strain TMUS2134, complete genome (59%, 1.4%, 99%, 0.0). |
| RGP10 | 2263898 | 2269345 | 5.4 | 31.1 | S.b., dGC%, Tnp, tRNA | S. aureus BK16691, transposon Tn4001 (GenBank: GU235985.1) (83%, 12%, 99%, 0.0). |
| RGP11 | 2353104 | 2378952 | 25.8 | 32.9 | S.b., Tnp, Res, tRNA | S. aureus subsp. aureus TW20, complete genome (GenBank: FN433596.1) (100%, 0.8%, 99%, 0.0). |
| RGP12 | 2811924 | 2832078 | 20.2 | 29.6 | S.b., dGC%, Tnp, ICE | S. aureus HDG2, integrating conjugative element ICE6013 (GenBank: FJ231270.1) (100%, 98%, 99, 0.0). |
∗BLASTN performed against the “nr” database at the NCBI website; ICE, integrative and conjugative element; SaPI, S. aureus Pathogenicity Island; Int., integrase; Rec., recombinase; Tnp, tranposase; Res, resolvase; dGC%, deviation from mean chromosomal GC content; s.b., synteny break from at least one other compared S. aureus; phage, probable bacteriophage region; tRNA, presence of flanking transfer RNAs; transposases, presence of transposase-related sequences. The complete sequence of each RGP identified in the reference genome BMB9393 was used as a query in the BLASTN against the NCBI. Query coverage corresponds to the sequence of each RGP in reference BMB9393. Subject coverage is the NCBI best hit sequence listed in the last column.