“…The assembled genomes were annotated and mapped to the reference genomes (CT18) as previously described ( Ho et al, 2012 ; Yap et al, 2012a ). The tRNA and tmRNA were predicted using Aragorn ( Laslett and Canback, 2004 ) whereas the rRNA was predicted with rRNAMMer ( Lagesen et al, 2007 ), and manually validated as described earlier ( Osama et al, 2012 ; Suhaimi et al, 2014 ). To compare, we have included three reference genomes and six of our own published sequenced genomes (described earlier), representing ST1 (Ty2, P-stx-12, Ty21a, BL196, CR0044) and ST2 populations (CT18, CR0063, UJ308A, UJ816A, ST0208).…”