Table 1.
Mapping statistics.
Table 2.
Regions of MAH104 genome predicted to be absent in MAA TMC724.
Figure 1.
Functional classes of genes with the highest transcription.
Bars show the levels of over- or underrepresentation of each functional category among 450 genes with the highest expression. Functional categories significantly over- or underrepresented in this list of genes are indicated with asterisks.
Figure 2.
Transcriptional start points and cis-ncRNAs.
Genomic loci and transcriptional profiles were visualized in the Artemis genome browser. Transcription from the forward or reverse strand of the genome is shown in red or green lines, respectively. Genes are expressed as blue boxes, with arrowheads pointing toward the right or left for genes encoded by the forward or reverse strand, respectively. (A) Genome locus comprising genes MAV_0130–MAV_0137. Identified TSPs for genes MAV_0130, MAV_0135, and MAV_0136 are indicated by arrows. (B) asMAV_0554. This antisense RNA to the gene lysS is transcribed at a level lower than lysS. (C) asMAV_3303. The level of transcription of this antisense RNA is much higher than that of acnA. (D) asMAV_1569–1571. This antisense RNA is transcribed at a relatively high level and spans 3 genes. Transcription of the genes antisense to asMAV_1569–1571 is negligible.
Table 3.
Predicted riboswitches.
Table 4.
Trans-ncRNAs.
Figure 3.
Intergenic sRNA igMAV_2868–2869 and its predicted homologs in M. ulcerans and M. tuberculosis.
(A) Alignment of the intergenic region, MAV_2868–MAV_2869, coding for sRNA with its homologs in M. ulcerans (MUL_3032–3033) and M. tuberculosis (rv1846c–1847). Only regions coding for sRNA and their promoters are shown. Alignment of DNA sequences was performed with UGENE software [52]. The promoter regions containing –35 and –10 sequences and the coding regions are conserved among the 3 species. Alignment of sRNAs and their consensus secondary structures was performed with the WAR webserver [45] and is shown below the alignment. Nucleotides that are conserved among the 3 species and form duplex structures are highlighted in green. (B) Predicted consensus secondary structure of igMAV_2868–2869. Extensive complementary regions form the secondary structure with very low free energy.
Figure 4.
Expression of igMAV_0468–0469 and igMAV_0469–0470 in M. avium isolated from cultures or the lungs of resistant and susceptible mouse strains.
The quantities of intergenic sRNAs relative to 16S rRNA are shown on a logarithmic scale. The relative quantities of intergenic sRNAs, as well as their confidence intervals, are summarized in the table below the figure. The CFU/lung values for I/St and B6 mice are also shown.