The genus Cucumis (family Cucurbitaceae) includes two economically important vegetable crop species that are cultivated worldwide: cucumber (C. sativus L., 2n = 2 × = 14) and melon (C. melo L., 2n = 2 × = 24). The genetic, phylogenetic, and evolutionary relationships of cucumber and melon have been the subject of much research. The genus Cucumis initially contained 32 species that was divided into two subgenera, Melo and Cucumis . While the subgenus Melo is centered in Africa with 30 species including melon (all of which have 2n = 24 chromosomes), the subgenus Cucumis is of Asian origin and includes the cultivated cucumber C. sativus and its wild relative C. hystrix Char. (2n = 2 × = 24). Although C. melo is considered the most morphologically diverse species in Cucumis [1, 2], two inter-fertile botanical varieties (2n = 2 × = 14), the cultivated C. sativus var. sativus L. and the wild C. sativus var. hardwickii (Royle) Alef., comprise the primary gene pool of cucumber. This gene pool has a rather narrow genetic base as evidenced in various genetic diversity studies [3–6]. No interspecific hybrids between melon and cucumber have been reported due to their sexual incompatibility .
The genus Cucumis has undergone considerable revision in recent years. For instance, molecular phylogenetic studies indicated that the genera such as Cucumella, Mukia, Dicaelospermum, Myrmecosicyos, and Oreosyce possess genetic affinities with Cucumis species resulting in their inclusion in Cucumis in more recent taxonomic treatments [8–10]. The genus Cucumis in the newest treatment contains 52 species, which are grouped into two subgenera: Humifructus (two species, C. humifructus and C. hirsutus) and Cucumis (consisting of the remaining 50 species) [9, 11]. In addition, both melon and cucumber are believed to be of Asian origin, which were derived from a common ancestor approximately nine million years ago .
The genome size of melon (12 chromosome pairs) is estimated to be 454 Mb, and cucumber (7 chromosome pairs) has a genome size of 367 Mbp . The evolutionary relationship between melon and cucumber can be investigated through chromosome analysis. In Kirkbride's taxonomic assessment of Cucumis , subgenus Cucumis is considered primitive and subgenus Melo was hypothesized to have been derived from it through chromosomal fragmentation [14–16]. In contrast, cytological investigations have also suggested that ancestral species of subgenus Melo gave rise to subgenus Cucumis species via chromosome fusion or non-homologous translocation [17, 18]. However, Ramachandran and Seshadri  argued that the two subgenera are not closely related given differences in geographical distribution and chromosome number, size, organization, and behavior. More recent molecular-based phylogenetic analyses of Cucumis support the hypothesis that the base chromosome number of x = 7 was achieved by chromosome reduction from x = 12 progenitor species [8, 10, 12].
Despite their distinct phylogenetic relationships [20, 21], the genomes of melon and cucumber seem to be highly conserved. Cross-species similarities based on molecular marker transferability among cucurbit crops are well documented. Neuhausen  first reported affinities among cucurbit species by identifying molecular cross-hybridizations (i.e., signals) using RFLP probes. More recently, Katzir et al.  and Danin-Poleg et al.  defined specific genomic regions using SSR primer products to reveal considerable sequence homologies between cucumber and melon. Danin-Poleg et al.  identified nine SSR markers shared between melon and cucumber and proposed that their cucumber Linkage Group B and melon Linkage Groups E and 2 were syntenic. Since 2000, molecular markers (primarily SSRs) developed from melon have been used routinely in cucumber genetic mapping studies or vice versa [24–37]. The high degree of synteny and conservation between the melon and cucumber genomes has also been demonstrated at the DNA sequence level (micro-synteny). Park et al.  and Meyer et al.  compared genomic DNA flanking the zucchini yellow mosaic virus resistance locus (zym) in melon and cucumber and detected considerable marker colinearity between those species. Alignment of melon BAC-end and BAC clone (6.7 Mbp) sequences of melon against a cucumber draft genome assembly (line Gy 14) revealed 90% homology between the compared sequences [40, 41]. Although transposition activity was found to be low in cucumber, it is comparatively high in melon . Thus, it has been postulated that the genomic size differences between melon and cucumber is due mainly to the expansion of inter-genic regions and proliferation of transposable elements in the melon genome .
Recently, whole genome sequencing in cucumber  and the availability of large numbers of molecular markers  has made it possible to define more clearly the syntenic relationships between cucumber and melon. By alignment of 348 marker sequences mapped in the melon genome onto the 9930 cucumber draft genome, Huang et al.  found that there was no substantial rearrangement between cucumber Chromosome 7 and melon Chromosome I. In addition, the majority of cucumber Chromosome 4 corresponded to melon Chromosome VII, and each of the remaining five cucumber chromosomes was collinear to two melon chromosomes . The correspondance between melon and cucumber chromosomes was also observed in a comparative mapping study by Fukino et al. , who placed 70 cucumber SSR markers on a melon linkage map.
Comparative genetic mapping is useful for revealing syntenic relationships among closely related planted species [45, 46]. An understanding of syntenic relationships among species facilitates the investigation of genome evolution and dynamics [47, 48], and allows for the use of genetic information among related species in gene isolation and molecular tagging experiments [49–51]. Comparative mapping has been used successfully to define syntenic relationships among closely related plant species in the Solanaceae (pepper, tomato, and potato) [52–55], Gramineae grasses [56, 57], Fabaceae legumes [47, 58–62], Brassicaceae , and Rosaceae (Prunun spp) [64, 65].
When compared to other crop species, genetic and genomic resources in cucurbit crops have historically been limited. However, this situation is changing rapidly. For instance, the draft genomes of two cucumber inbred lines (North China fresh market type 9930 and North American pickling type Gy14) have been released [42, 66] (also Weng et al., unpublished data). A high resolution linkage map and several SSR-based genetic maps have been developed for this species [43, 67–69]. In melon, many linkage maps as well as a BAC-based physical map have been constructed [24, 27–29, 33–37]. In addition, comparative fluorescence in situ hybridization (FISH) mapping in cucumber and melon  suggested that centromere repositioning occurred during the evolution of cucumber chromosomes. Several cucumber chromosomes have been anchored using fosmid clones, and karyotypes of cucumber and melon genomes have been developed [71–75].
Previous studies [38–44] have shown that genomic synteny and co-linearity exists between cucumber and melon. This information is, nevertheless, fragmented and incomplete. Thus experiments were designed herein for large-scale comparative genetic mapping of melon and cucumber to identify syntenic blocks using microsatellite markers. To accomplish this objective, two extended linkage maps in melon were constructed using an F2 and a RIL population, which were subsequently merged to form a consensus map. Then the scaffolds of the Gy14 and 9930 cucumber draft genomes were associated to markers on both the melon consensus map and a high-resolution cucumber genetic map  to define species chromosomes and allow for the detection of syntenic blocks.