Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens
Figure 7
Genomic organization of the scaffold associated with the VHv1 locus conferring high virulence of pathotype 2 isolate ND90Pr to barley cv. Bowman compared to the corresponding region in pathotype 0, isolate ND93-1.
A. Mauve alignment [44] of ND93-1 scaffolds to ND90Pr. Colored blocks [Locally Collinear Blocks (LCB)] indicate matches between the two genomes, and vertical block shading corresponds with % similarity. Note very few colored blocks at right end of top row. The ∼133 kb VHv1 locus, which maps to distal end of scaffold 5 (2.18 Mb), is unique to isolate ND90Pr, as indicated by absence of colored blocks at right end of the top row and the second row which is the same region at higher resolution. Below this Mauve alignment segment of the VHv1 region on scaffold 5 (from position 2,044,422 to 2,177,878) is the JGI browser view of the same region, displaying gene models and repeats. There are forty-three predicted genes (blue) in this region, only a fraction of which have KOG or GO descriptions (Table S7). Two NRPSs (ID # 115356 and 140513, shown in red) map to this region and are unique to the ND90Pr isolate and also not found in any of the genomes examined in this manuscript (Figure 3, Figure 5, Table 8). E-AG/M-CG-121 is one of two AFLP markers (the other is E-AG/M-CA-207 on scaffold 40) are linked to the virulence locus, VHv1 (Figure S3). B. Quantitative real-time PCR analysis of five NPS genes (protein ID 49884, 350779, 130053, 115356, 140513) during infection of barley cv. Bowman. Gene expression was normalized based on the expression of the β-Actin gene, and the values are the relative expression levels in comparison with M96, a mixture of mycelia harvested, at 96 hours after culture set up, from different media including PDA, MM, V8PDA, and water agar. B6, B12, B24, B48, B72, and B96 are samples collected at 6, 12, 24, 48, 72, and 96 hours after inoculation. Primers are shown in Table S9. The error bars indicate the minimum and maximum values of relative expression of the gene. C. Inoculation of barley cv. Bowman with wild type (ND90Pr) and a mutant lacking the gene corresponding to protein ID 115356. Images taken 7 days after inoculation. Virulence on Bowman is significantly reduced compared to that of plants inoculated with the wild-type strain (Figure S7).