Analysis of perA integrity within nonhybrid Epichloë species.

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Analysis of perA integrity within nonhybrid Epichloë species. Analysis of perA integrity within nonhybrid Epichloë species. PCR-based size polymorphism analysis of perA from genomic DNA. The PCR products were produced using primers designed to the conserved sequence in or near each of the major perA domains and the two flanking genes mfsA and qcrA (see Table S3 in the supplemental material). Gray shading indicates the regions amplified. The dashed lines indicate the region that will amplify with primers perA-mid2-F2/perA_17bp_R only from isolates containing perA-ΔR* (Fig. 3). The regions encoding the adenylation (A), thiolation (T), condensation (C), methylation (M), and reductase* (R*) domains are shown within the perA gene map, with numbers indicating whether they are located in the first or second module. Isolates for which perA was subsequently sequenced or for which the perA sequence was already available (16, 33, 42) are shown in boldface. Low-intensity PCR products indicate the presence of SNPs in the primer target binding sequence. A host species labeled “NA” indicates the endophyte strain is the result of a controlled sexual cross. Festuca rubra subsp. commutata is abbreviated Festuca rubra ssp. comm. nt, not tested. Known peramine chemotypes are indicated as Per+ (peramine producer) or per− (peramine nonproducer) (5, 6, 16, 29, 43, 44). Peramine production was predicted for isolates with unknown peramine chemotypes based on the presence of the expected PCR products amplified from all perA domains and is indicated by + or −. Although not apparent in this screen, a perA remnant retaining the R* domain remains in E184 (39). Daniel Berry et al. Appl. Environ. Microbiol. 2015;81:2797-2807