SUPPLEMENTAL DATA
The following materials are available in the online version of this article.
Supplementary tables
Table S1. Alignment of 40 largest C. hystrix scaffolds with Gy14 cucumber and DHL92 melon
draft genome scaffolds
Table S2. Summary statistics of C. hystrix genetic map with 416 SSR marker loci.
Table S3. Physical locations in DHL92 melon draft genome assembly of molecular markers
placed on the C. hystrix genetic map.
Table S4. Information of cucumber fosmid clones used in fluorescence in situ hybridization
(FISH) of 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 (>500kb) between melon and cucumber genomes based on whole
genome sequence alignment.
Supplementary figures
Figure S1. Graphic view of C. hystrix genetic map developed with the WI7001 × WI7002 F2
mapping population. Numbers on top of the map are linkage groups (LG) (H01 through
H12) which also correspond to chromosomes numbers. Cumulative map distance (cM) is
shown to the left of each linkage group and marker designation is on the right.
Figure S2. Examples of comparative pachytene FISH among cucumber, C. hystrix and melon. In
3A, fosmid clones in cucumber chromosome C5 were hybridized to pachytene
chromosomes of the three species. The identity of each probe is given next to its
representative FISH signal. White triangles point to putative centromere locations. Bars =10
µm. 3B and 3C are comparative physical maps showing locations of fosmid loci to reveal
syntenic relationships among the three species.
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 8Mb region in the long arm of cucumber chromosome C7
and its syntenic blocks in melon (13 Mbp) and watermelon (8.4 Mbp). For each species,
sequence alignment is shown at the bottom, and a density map with numbers of genes (blue
dots), DNA transposons (orange dots) and retrotransposons (red dots) within 100kb
windows is shown at the top.
Figure S5. Reconstruction of karyotype evolution history of seven wild (CSH) or cultivated
(CSS) cucumber chromosomes (C1 to C7) from 12 ancestral chromosomes (AK1 to AK12),
which are assumed to have the same syntenic block organization as C. hystrix. The meaning
of each symbol is presented at end of the figure.