Isolates sequenced using RNA-seq and GBS.

a Two sets of analyses were performed, one maximizing the number of SNPs, resulting in the exclusion of isolates with low sequencing depth (filtering priority = max SNPs) and the other retaining isolates at the sacrifice of SNPs (filtering priority = max isolates). I = included in both analyses; S = excluded from the ‘max SNPs’ run but included in the ‘max isolates’ run); E = excluded from both sets of analyses due to missing data; NS = not sequenced. Isolates sequenced using RNA-seq and GBS.