Figure S1. Graphic view of the C. hystrix genetic map developed using the WI7001 × WI7002 F2 mapping population.

Figure S2. Examples of comparative pachytene FISH among cucumber, C. hystrix and melon.

Figure S3. Sequence alignment between Gy14 cucumber and DHL92 melon draft genomes revealed syntenic blocks of melon chromosome V with three regions in cucumber chromosomes C2, C4 and C6.

Figure S4. Comparative analysis in an 8 Mb region in the long arm of cucumber chromosome C7 and its syntenic blocks in melon (13 Mbp) and watermelon (8.4 Mbp).

Figure S5. Reconstruction of karyotype evolution history of seven wild (CSH) or cultivated (CSS) cucumber chromosomes (C1–C7) from 12 ancestral chromosomes (AK1–AK12).


Table S1. Alignment of the 40 largest C. hystrix scaffolds with the Gy14 cucumber and DHL92 melon draft genome scaffolds.

Table S2. Summary statistics of the C. hystrix genetic map with 416 SSR marker loci.

Table S3. Physical locations in the DHL92 melon draft genome assembly of molecular markers placed on the C. hystrix genetic map.

Table S4. Information on cucumber fosmid clones used for FISH in this study.

Table S5. Syntenic relationships of C. hystrix and cucumber genomes revealed by genome alignment, and comparative genetic and FISH mapping.

Table S6. Syntenic blocks (>500 kb) between melon and cucumber genomes based on whole-genome sequence alignment.

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