Fig. S1 Local genetic maps anchored onto the genome sequence v1.1.

Fig. S2 Detailed alignment of the two versions of the Populus genome assembly (v1.1 and v2.0) of the region encompassing the super cluster of resistance genes.

Fig. S3 Alignment between the two haplotypical physical maps.

Table S1 Sequences of markers derived from the bulk segregant analysis (BSA) approach

Table S2 Primer pairs developed for genetic and physical marker development

Table S3 Bacterial artificial chromosome (BAC) insert sizes and location of BAC end sequences (BES) on the genome sequence v2.0

Table S4 Bacterial artificial chromosome (BAC) end sequences in the genomic target region of physical maps

Table S5 Bacterial artificial chromosome (BAC) end sequence analysis

Table S6 Repetitive and transposable element composition of bacterial artificial chromosome (BAC) end sequences (BES) (GenBank: HN280500–HN291979) and BES integrated to the physical maps

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