BACKGROUND
the genus cucumis  includes two economically important vegetable crop species that are cultivated worldwide: cucumber  and melon .
the genetic, phylogenetic, and evolutionary relationships of cucumber and melon have been the subject of much research.
the genus cucumis initially contained  <dig> species that was divided into two subgenera, melo and cucumis  <cit> .
while the subgenus melo is centered in africa with  <dig> species including melon , the subgenus cucumis is of asian origin and includes the cultivated cucumber c. sativus and its wild relative c. hystrix char.
.
although c. melo is considered the most morphologically diverse species in cucumis  <cit> , two inter-fertile botanical varieties , the cultivated c. sativus var.
sativus l. and the wild c. sativus var.
hardwickii  alef., comprise the primary gene pool of cucumber.
this gene pool has a rather narrow genetic base as evidenced in various genetic diversity studies  <cit> .
no interspecific hybrids between melon and cucumber have been reported due to their sexual incompatibility  <cit> .
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  <cit> .
the genus cucumis in the newest treatment contains  <dig> species, which are grouped into two subgenera: humifructus  and cucumis   <cit> .
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  <cit> .
the genome size of melon  is estimated to be  <dig> mb, and cucumber  has a genome size of  <dig> mbp  <cit> .
the evolutionary relationship between melon and cucumber can be investigated through chromosome analysis.
in kirkbride's taxonomic assessment of cucumis  <cit> , subgenus cucumis is considered primitive and subgenus melo was hypothesized to have been derived from it through chromosomal fragmentation  <cit> .
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  <cit> .
however, ramachandran and seshadri  <cit>  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 =  <dig> was achieved by chromosome reduction from x =  <dig> progenitor species  <cit> .
despite their distinct phylogenetic relationships  <cit> , 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  <cit>  first reported affinities among cucurbit species by identifying molecular cross-hybridizations  using rflp probes.
more recently, katzir et al.
<cit>  and danin-poleg et al.
<cit>  defined specific genomic regions using ssr primer products to reveal considerable sequence homologies between cucumber and melon.
danin-poleg et al.
<cit>  identified nine ssr markers shared between melon and cucumber and proposed that their cucumber linkage group b and melon linkage groups e and  <dig> were syntenic.
since  <dig>  molecular markers  developed from melon have been used routinely in cucumber genetic mapping studies or vice versa  <cit> .
the high degree of synteny and conservation between the melon and cucumber genomes has also been demonstrated at the dna sequence level .
park et al.
<cit>  and meyer et al.
<cit>  compared genomic dna flanking the zucchini yellow mosaic virus resistance locus  in melon and cucumber and detected considerable marker colinearity between those species.
alignment of melon bac-end and bac clone  sequences of melon against a cucumber draft genome assembly  revealed 90% homology between the compared sequences  <cit> .
although transposition activity was found to be low in cucumber, it is comparatively high in melon  <cit> .
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  <cit> .
recently, whole genome sequencing in cucumber  <cit>  and the availability of large numbers of molecular markers  <cit>  has made it possible to define more clearly the syntenic relationships between cucumber and melon.
by alignment of  <dig> marker sequences mapped in the melon genome onto the  <dig> cucumber draft genome, huang et al.
<cit>  found that there was no substantial rearrangement between cucumber chromosome  <dig> and melon chromosome i. in addition, the majority of cucumber chromosome  <dig> corresponded to melon chromosome vii, and each of the remaining five cucumber chromosomes was collinear to two melon chromosomes  <cit> .
the correspondance between melon and cucumber chromosomes was also observed in a comparative mapping study by fukino et al.
<cit> , who placed  <dig> cucumber ssr markers on a melon linkage map.
comparative genetic mapping is useful for revealing syntenic relationships among closely related planted species  <cit> .
an understanding of syntenic relationships among species facilitates the investigation of genome evolution and dynamics  <cit> , and allows for the use of genetic information among related species in gene isolation and molecular tagging experiments  <cit> .
comparative mapping has been used successfully to define syntenic relationships among closely related plant species in the solanaceae   <cit> , gramineae grasses  <cit> , fabaceae legumes  <cit> , brassicaceae  <cit> , and rosaceae   <cit> .
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  have been released  <cit>  .
a high resolution linkage map and several ssr-based genetic maps have been developed for this species  <cit> .
in melon, many linkage maps as well as a bac-based physical map have been constructed  <cit> .
in addition, comparative fluorescence in situ hybridization  mapping in cucumber and melon  <cit>  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  <cit> .
previous studies  <cit>  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 f <dig> and a ril population, which were subsequently merged to form a consensus map.
then the scaffolds of the gy <dig> and  <dig> cucumber draft genomes were associated to markers on both the melon consensus map and a high-resolution cucumber genetic map  <cit>  to define species chromosomes and allow for the detection of syntenic blocks.
RESULTS
<dig>  development of an f2-based extended melon linkage map using cucumber ssrs
in total,  <dig>  ssr markers were used to screen for polymorphisms between the two parental lines, q3-2- <dig> and top mark of the f <dig> mapping population.
of these,  <dig>  were genomic ssrs developed from cucumber,  <dig> from watermelon,  <dig> from melon  <cit> , and  <dig> were est-ssrs from other species  <cit> .
of the  <dig>  cucumber ssrs,  <dig>   produced amplicons in melon after pcr, from which  <dig>  were polymorphic between top mark and q3-2- <dig>  the success in marker transferability for all cucumber ssrs tested was  <dig> % .
of the  <dig> watermelon genomic ssrs that produced amplicons in cucumber , seven  produced amplicons in melon, and two were polymorphic .
in total,  <dig> non-melon polymorphic markers were identified  and  <dig> of them were finally placed on the f <dig> genetic map .
using this f <dig> mapping population, cuevas et al.
<cit>  mapped  <dig> co-dominant markers  in  <dig> linkage groups .
genotypic data from the  <dig> additional cucumber or watermelon markers developed herein were combined with the previously mapped  <dig> markers for linkage analysis.
all  <dig> codominant markers  were placed onto this f2-based melon genetic map in  <dig> lg.
information on lg and map positions is presented in table s <dig> , and their associated statistics are presented in table  <dig>  segregation distortion was rare, where only four markers, cu <dig>  gcm <dig>  ssr <dig>  and uw <dig> significantly deviated from expected 1:2: <dig> segregation ratio .
except for chromosome iv, each lg could be assigned to corresponding chromosomes as defined by liu et al.
<cit> .
in our analysis, chromosome iv was split into two linkage groups   due to an insufficient number of markers.
the f2-based map consisted of  <dig> lg spanning  <dig>  cm, with a mean marker interval of  <dig>  cm, where the largest gap resided in chromosome iv associated with lg 4a and lg 4b.
a lg = linkage group.
chr = chromosome
b # cs markers = number of markers from cucumber that were mapped in each linkage group.
c relative length = length of individual chromosome/total length of all  <dig> chromosomes ×  <dig>  <cit>
<dig>  development of a ril-based extended melon linkage map with cucumber ssrs
the molecular markers employed for f <dig> mapping were also used to identify polymorphisms between top mark and wi 846- <dig> of the ril population.
of the  <dig>  cucumber ssrs tested,  <dig> %  produced amplicons in melon, where  <dig> %  of the ssrs detected polymorphisms between top mark and wi 846- <dig> .
of the  <dig> polymorphic markers identified herein ,  <dig> were placed on the ril map.
using the same melon ril population, cuevas et al.
<cit>  mapped  <dig> marker loci .
the two sets of marker data were pooled for linkage analysis using  <dig> rils.
ten of these markers could not be assigned to any lg.
the resulting linkage map possessed  <dig> marker loci including  <dig> codominant  and  <dig> dominant markers  in  <dig> lg with cumulative genetic distances of  <dig>  cm.
the mapping data are presented in table s <dig>  and associated map statistics are shown in table  <dig>  based on ssr markers shared in common with previously published melon maps  <cit> , it was possible to relegate the lgs constructed herein to  <dig> linkage groups .
<dig>  development of a consensus melon genetic map through map merging
the f <dig> and ril maps developed herein shared  <dig> markers in common , and were merged to produce a consensus map using the joinmap  <dig>  program.
the  <dig> dominant aflp and rapd markers resident on the ril map were excluded from map integration because they were deemed ineffective for defining cucumber-melon synteny.
these markers tended to clustered on the linkage map, and a number of them showed segregation distortion .
in contrast to the ril map, the  <dig> markers on the f <dig> map were co-dominant and their order was used as the reference during map merging.
the resulting consensus linkage map is presented in figure  <dig> and summarized in table  <dig>  shared loci  between the f <dig> and ril maps are given in table s <dig> .
the consensus melon genetic map consisted of  <dig> co-dominant marker loci positioned in  <dig> lgs spanning  <dig> .
<dig> cm with an average marker interval of  <dig>  cm.
among the  <dig> lgs, lg <dig>  had the longest map length  followed by lg <dig>  and lg <dig> .
in contrast, the length of lg  <dig>  was the shortest .
predictably lg <dig> possessed the most loci mapped  and lg <dig>  the least markers .
since marker order of the f <dig> map was used as the reference during map merging, all loci on the consensus map were co-linear with those on the f <dig> map.
moreover, inconsistencies in marker order were rare resulting in substantial colinearity between the ril map  and the consensus map .
<dig>  identification of syntenic blocks between melon and cucumber chromosomes
among the  <dig> markers present on the consensus melon map,  <dig> were ssr or caps markers developed from cucumber, one from the watermelon, and the remaining  <dig> were derived from melon.
the cucumber gy <dig> and  <dig> draft genome scaffold locations of these  <dig> markers were predicted by in silico pcr or blast searches of the cucumber draft genome sequences.
seventy-four of the  <dig> markers on the consensus melon map had no in silico pcr products or blast hits suggesting that they may be specific to the melon genome.
three markers  were located in sequences that were annotated as repeated sequences  <cit> , and, therefore, their cucumber scaffold locations were difficult to determine.
the remaining  <dig> markers could be assigned to the gy <dig> and  <dig> cucumber scaffolds.
the scaffold names and physical positions of these markers are presented in table s <dig> .
once the association of these markers on the melon consensus map with cucumber scaffolds was established, the locations of these cucumber scaffolds in the seven chromosomes of cucumber were deduced from published cucumber genetic maps  <cit>  .
among the  <dig> markers placed on the melon consensus map,  <dig> have been mapped in previous cucumber mapping studies  <cit> .
therefore, their locations on cucumber genetic maps could be assigned directly.
for markers with associated cucumber scaffold, their map locations in the cucumber genome was inferred by other markers derived from the same scaffold, which had been previously placed on cucumber maps .
however, three markers  were located in cucumber scaffolds from which no marker has been mapped.
therefore, their locations in the cucumber genome were unknown.
with molecular markers shared between the melon and cucumber genetic maps or linked by cucumber draft genome scaffolds, syntenic relationships between cucumber and melon chromosomes could be directly inferred.
figure  <dig> depicts a view of the  <dig> melon chromosomes consisting of cucumber syntenic blocks .
inspection of figure  <dig> and table s <dig> indicated that melon chromosome i was syntenic to cucumber chromosome  <dig>  likewise, chromosomes ii and xii were syntenic with cucumber chromosome 1; chromosomes iv and vi were syntenic with cucumber chromosome 3; and chromosomes ix and x were syntenic with cucumber chromosome  <dig>  similarly, the three melon chromosomes iii, viii, and xi contained blocks that were syntenic to two cucumber chromosomes, 2+ <dig>  4+ <dig>  and 2+ <dig>  respectively.
these melon-cucumber syntenic relationships are summarized in table  <dig>
it has been previously hypothesized that cucumber chromosomes evolved from a progenitor species with 2n =  <dig> × =  <dig> chromosomes through chromosome fusion .
thus, a melon syntenic block view of cucumber chromosomes was developed which is shown in figure  <dig>  in this view, the scaffolds in each cucumber chromosome were arranged in the same order as were marker loci on cucumber genetic maps.
in most cases, the high resolution genetic map developed by ren et al.
<cit>  was used as a reference for ordering those scaffolds.
in rare instances, however, marker locations did not coincide with those of ren et al.
<cit>  and, thus, other more recent cucumber genetic maps  <cit>  were consulted to infer marker map locations .
the arrangement of melon syntenic blocks across the seven cucumber chromosomes indicates that cucumber chromosome evolution is more complex than simple chromosome fusion .
for instance, cucumber chromosome  <dig> was homoeologous to melon chromosome i along its entire length.
cucumber chromosomes  <dig> and  <dig> each contained three syntenic blocks detected in melon chromosomes v+xi+iii, and iii+xi+xiii, respectively, and the remaining four cucumber chromosomes  were syntenic with two melon chromosomes but differed in patterns of arrangement of melon syntenic blocks.
cucumber chromosome  <dig> was syntenic to melon chromosome ii and xii, whereas cucumber chromosome  <dig> was syntenic to melon chromosome ix and x. in both cases, the syntenic blocks from the two melon chromosomes were arranged alternatively along each cucumber chromosome.
in contrast, the syntenic blocks residing in melon chromosomes vi and iv were in a side-by-side alignment in cucumber chromosome  <dig>  lastly, cucumber chromosome  <dig> housed syntenic blocks of melon chromosome vii and viii, but the syntenic block of melon chromosome viii was found to be incorporated into the syntenic block of melon chromosome vii.
taken collectively, these syntenic patterns were suggestive of a complex history of chromosomal structure changes during cucumber evolution.
<dig>  verification of melon-cucumber syntenic relationships
in this study, in silico pcr and blast sequence alignment proved useful for inferring the cucumber scaffold location of markers on the melon consensus map .
to verify the syntenic relationships between cucumber and melon chromosomes detected from comparative mapping conducted herein, a similar strategy was used with molecular markers from a melon linkage map developed by deleu et al.
<cit> .
this gene-based melon linkage map consists of  <dig> marker loci, of which nearly  <dig> were snps developed from melon est sequences, and all these markers were derived exclusively from the melon genome.
the details of this map are shown in table s <dig> .
the genomic or est sequences from which these markers were developed were used in blast analysis against the cucumber draft genome assemblies.
of the  <dig> markers, only  <dig>  did not yield either in silico pcr products or blast hits in the cucumber draft genomes examined.
this contrasted with markers on the consensus melon map , where  <dig>  of  <dig>  did not produce hits in either gy <dig> or  <dig> genome assembly.
this suggests that the est sequences examined are highly conserved between these genomes.
the syntenic relationships between melon and cucumber chromosomes inferred from this gene-based melon genetic map are shown in table s <dig> .
although there were no cucumber source markers on this map, melon-cucumber syntenic relationships revealed from the present study  were confirmed by this independent study  <cit> .
discussion
cross-species transferability and polymorphisms of cucumber ssrs in the melon genome
nearly  <dig>  randomly sampled cucumber genomic ssrs were tested herein for their ability to detect polymorphisms among three melon parental lines used in map construction.
the polymorphism level of cross-species transferable cucumber ssrs was  <dig> % between top mark and wi 846- <dig>  and  <dig> % between top mark and line q3-2- <dig>  which would be reduced to  <dig>  and  <dig> %, respectively if all cucumber ssrs tested were considered.
this level was appreciably lower than that reported in other studies  <cit>  using melon ssrs.
for example, of  <dig> melon ssrs evaluated for map construction by cuevas et al.
<cit> , 32% were polymorphic between two melon lines q3-2- <dig> and top mark.
likewise, the level of polymorphism of melon ssrs between the two melon lines pi  <dig> and dulce used by harel-beja et al.
<cit>  was comparatively high .
such differences in polymorphism level may be attributable to the sources of markers , the melon lines used, or the relative genetic distance among the germplasm being evaluated.
two additional factors may also contribute to the low polymorphism level detected by cucumber ssrs.
firstly, unlike melon, which is considered genetically diverse  <cit> , cucumber has a narrow genetic base  <cit> , and the degree of polymorphism at the whole genome level for randomly chosen ssrs between any two cultivated cucumber genotypes is in general less than 20%  <cit> .
in the present study, about 45% of cucumber ssrs examined exhibited cross-species amplification in the melon genome after pcr.
this amplification level is similar to that detected by ritschel et al.
<cit>  who found that ~50% of the melon ssr markers evaluated produced amplicons when cucumber dnas were used as templates.
gonzález et al.
<cit>  found 54% of the melon bac-end sequences under investigation could be aligned to the cucumber genome.
it is likely that the melon genomic regions that were amplified by cucumber ssrs represent conserved portions between the cucumber and melon genomes.
the genomes of gy <dig> and  <dig> cucumber lines have been sequenced using the "next generation" sequencing technologies   <cit> , and, therefore, most of the assembled genome sequences may originate from the gene-rich low or single copy dna fraction in the genome, which are more conserved between closely related species such as melon and cucumber than repetitive dna sequences  <cit> .
therefore, using ssrs developed from highly conserved gene-rich genomic dna regions of a genome with limited genetic diversity may be an important contributor to the low polymorphism of cucumber ssrs in the melon genome.
the second factor, as discussed in cavagnaro et al.
<cit> , is that melon ssrs used in previous mapping studies  may over-estimate the polymorphism in the genome due to biases created during ssr selection, because of the reiterative selection for longer repeats during development of microsatellite markers.
that is, library screening methods for ssr isolation are designed to yield a higher proportion of long ssrs, which are preferentially used for designing primers, which are then typically pre-screened for their relative polymorphism level in potential parental lines.
thus, the most polymorphic loci are selected for further utilization .
in this study, the polymorphism level detected between q3-2- <dig> and top mark  or top mark and wi 846- <dig> , although very low, may reflect the true global polymorphism of cucumber ssrs at the whole melon genome level.
the melon consensus linkage map with cucumber ssrs
the consensus map developed herein added a considerable number of ssr markers  towards map saturation in melon .
we added  <dig> and  <dig> new markers to the previously developed melon f <dig>  and ril  maps  <cit> , respectively.
marker order on the new  and the historic f <dig> maps were almost identical.
the ril map was improved over the historic map  <cit>  , but was still relatively fragmented , which was likely due to the large number of dominant markers incorporated into the ril-based map.
it is known that dominant markers such as rapds or aflps tend to be clustered on the linkage maps  <cit> , and for this reason, dominant markers were excluded in map merging for development of the consensus map.
even though more than the predicted numbers of lgs were present on the f <dig> and ril maps, the large number of shared marker loci enabled integration of the two maps to produce a consensus melon genetic map with the expected  <dig> lgs .
this consensus map contained  <dig> co-dominant markers including  <dig> derived from cucumber, and is the first melon map containing such a high number of cucumber-derived markers.
the map length of this consensus map was  <dig>  cm, which is within the predicted size range of the melon genome   <cit> .
the reliability  of this map can be measured by its colinearity and its relationship with available cucumber scaffolds.
although there were minor discrepancies in marker orders  between markers on the consensus and the ril-based maps, these maps were largely collinear .
the disparities detected between these maps may be, in part, due to varying recombination rates between mapping population , relatively small mapping populations  used, and/or genome structural variations  between populations.
with few exceptions, closely linked markers on these melon maps were located in the same cucumber draft genome scaffolds .
synteny between melon and cucumber chromosomes
comparative mapping, in silico pcr, and blast sequence alignment allowed a comprehensive assessment of syntenic relationships between the cucumber and melon chromosomes .
among the  <dig> markers positioned on the melon consensus map,  <dig> provided no in silico pcr products or blast hits in the cucumber genome sequences examined .
most of these  <dig> markers were derived from melon genomic dna sequences , indicating their uniqueness to the melon genome.
the genomic distribution of these "no-hit" markers also appears to be non-random on the melon consensus map, and in many cases , these markers were located at telomeric ends, implying the possibility of rapid evolutionary divergence .
such information may allow design of experiments to investigate the nature of these regions in cucumis chromosome evolution.
phylogenetic analyses  <cit>  in cucumis support an early hypothesis that the base chromosome number x =  <dig> in cucumber is derived from a progenitor species with x =  <dig>  <cit> .
six of the seven cucumber chromosomes may be originated from chromosome fusion of such a progenitor species  <cit> .
we provide herein additional information regarding the syntenic relationships between cucumber and melon chromosomes indicating that the evolutionary dynamics of cucumber evolution is complex .
although we confirmed the early finding  <cit>  that cucumber chromosome  <dig> was syntenic with melon chromosome i, we found that the co-linearity of marker loci in the two chromosomes has been broken  suggesting that chromosome  <dig> of cultivated cucumber may have undergone certain structural changes since its divergence from an ancestral species .
the other six chromosomes of cucumber appear to have more complicated evolutionary histories.
for instance, both chromosomes  <dig> and  <dig> possess genomic regions that are syntenic to genetic blocks from at least three melon chromosomes , suggesting they are derived from more than simple chromosome fusion.
although chromosomes  <dig>   <dig>   <dig>  and  <dig> each possessed genomic blocks syntenic with those from two melon chromosomes, the arrangements of these blocks differed among chromosomes .
since cucumber chromosome  <dig>   <cit>  appears to be comparatively simple in its syntenic block organization, it is tempting to hypothesize that it originated from simple fusion of melon chromosomes iv and vi.
however, close inspection of marker order in cucumber chromosome  <dig> and melon chromosomes iv and vi  reveals non-colinearity, which suggests that additional structural changes may have occurred after a hypothetical chromosome fusion event.
data presented herein provides a rather complicated description of cucumis species chromosome evolution, making a comprehensive statement regarding chromosome evolution in melon and cucumber difficult at this time.
it is apparent that additional information is required regarding the genomic nature of melon, and cucumber, as well as potential 'bridge" species [ <cit> , e.g., c. hystrix) to elucidate more clear evolutionary relationships in this genus.
to better understand these relationships a more saturated cucumber genetic map is needed to increase the resolution of cucumber scaffolds for comparative mapping.
the cucumber map used herein was developed with  <dig> rils from an inter-subspecific cross between cultivated cucumber  line gy <dig> and the wild c. sativus var.
hardwickii line pi  <dig>  <cit> .
there were, however, strong recombination suppressions detected during map construction resulting in clustering of molecular markers in several regions of cucumber chromosomes  <dig>   <dig>  and  <dig>  such recombination suppression may, in part, be due to structural differences in chromosomes between cultivated and wild cucumbers , which, in turn, may have reduced the power of ordering markers and scaffolds.
meanwhile, the whole genome sequencing of melon is near completion .
this will provide a powerful tool to understand the synteny between the melon and cucumber chromosomes at dna sequence level.
a wild relative of cucumber, c. hystrix , may play the key role in understanding the process of cucumber chromosome evolution.
extensive phylogenetic analyses in cucumis have indicated that c. hystrix is so far the closest wild relative of cucumber  <cit> .
the lack of genetic affinity between c. hystrix and c. melo, and african species, lends support to the hypothesis that c. hystrix is a progenitor species of c. sativus, or that they at least share a common ancestral lineage  <cit> .
c. hystrix has the same number of chromosomes as melon, and is sparingly cross-compatible with cucumber, but not melon  <cit> .
a fertile amphidiploid, c. hystivus  between cucumber and c. hystrix, as well as alien addition lines have also been successfully created  <cit> .
the seven meiotic chromosomes of c. sativus are larger than the  <dig> chromosomes of c. hystrix  <cit> .
fluorescence in situ hybridization of 45s rdna and cscent <dig> repetitve dna probes to cucumber pachytene chromosomes also suggested that cucumber chromosomes  <dig> and  <dig> may have evolved from fusions of an ancestral karyotype with 2n =  <dig>  <cit> .
these findings make c. hystrix the primary resource for testing genetic hypotheses for further characterizing the evolution of modern cucumber.
CONCLUSIONS
this is the first broad-based comparative analysis of synteny between melon and cucumber.
the consensus melon linkage map derived herein from two historic maps possesses the largest number of cross-species cucumber molecular markers currently mapped in the melon genome and provides a greater understanding of genomic relationships between these two important cucumis species.
data support the hypothesis that cucumber chromosomes originate from fusions of chromosomes of an x =  <dig> ancestral progenitor.
however, many structural changes may have occurred in the evolution of the seven cucumber chromosomes.
in depth cytogenetic and molecular investigations of x =  <dig> cucumis species  will likely provide further evidence of chromosome evolution in cucumber, melon and related taxons.

 the genus cucumis includes two economically important vegetable crop species that are cultivated worldwide: cucumber and melon. the genetic, phylogenetic, and evolutionary relationships of cucumber and melon have been the subject of much research. the genus cucumis initially contained species that was divided into two subgenera, melo and cucumis. while the subgenus melo is centered in africa with species including melon, the subgenus cucumis is of asian origin and includes the cultivated cucumber c. sativus and its wild relative c. hystrix char.. although c. melo is considered the most morphologically diverse species in cucumis, two inter-fertile botanical varieties, the cultivated c. sativus var. sativus l. and the wild c. sativus var. hardwickii alef., comprise the primary gene pool of cucumber. this gene pool has a rather narrow genetic base as evidenced in various genetic diversity studies. 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. the genus cucumis in the newest treatment contains species, which are grouped into two subgenera: humifructus and cucumis. 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 is estimated to be mb, and cucumber has a genome size of 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. 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. 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 = was achieved by chromosome reduction from x = progenitor species. despite their distinct phylogenetic relationships, 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 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 were syntenic. since molecular markers developed from melon have been used routinely in cucumber genetic mapping studies or vice versa. the high degree of synteny and conservation between the melon and cucumber genomes has also been demonstrated at the dna sequence level. park et al. and meyer et al. compared genomic dna flanking the zucchini yellow mosaic virus resistance locus in melon and cucumber and detected considerable marker colinearity between those species. alignment of melon bac-end and bac clone sequences of melon against a cucumber draft genome assembly revealed 90% homology between the compared sequences. 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 marker sequences mapped in the melon genome onto the cucumber draft genome, huang et al. found that there was no substantial rearrangement between cucumber chromosome and melon chromosome i. in addition, the majority of cucumber chromosome 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 cucumber ssr markers on a melon linkage map. comparative genetic mapping is useful for revealing syntenic relationships among closely related planted species. an understanding of syntenic relationships among species facilitates the investigation of genome evolution and dynamics, and allows for the use of genetic information among related species in gene isolation and molecular tagging experiments. comparative mapping has been used successfully to define syntenic relationships among closely related plant species in the solanaceae, gramineae grasses, fabaceae legumes, brassicaceae, and rosaceae. 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 have been released. a high resolution linkage map and several ssr-based genetic maps have been developed for this species. in melon, many linkage maps as well as a bac-based physical map have been constructed. in addition, comparative fluorescence in situ hybridization 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. previous studies 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 f and a ril population, which were subsequently merged to form a consensus map. then the scaffolds of the gy and 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.  development of an f2-based extended melon linkage map using cucumber ssrs in total, ssr markers were used to screen for polymorphisms between the two parental lines, q3-2- and top mark of the f mapping population. of these, were genomic ssrs developed from cucumber, from watermelon, from melon, and were est-ssrs from other species. of the cucumber ssrs, produced amplicons in melon after pcr, from which were polymorphic between top mark and q3-2- the success in marker transferability for all cucumber ssrs tested was %. of the watermelon genomic ssrs that produced amplicons in cucumber, seven produced amplicons in melon, and two were polymorphic. in total, non-melon polymorphic markers were identified and of them were finally placed on the f genetic map. using this f mapping population, cuevas et al. mapped co-dominant markers in linkage groups. genotypic data from the additional cucumber or watermelon markers developed herein were combined with the previously mapped markers for linkage analysis. all codominant markers were placed onto this f2-based melon genetic map in lg. information on lg and map positions is presented in table s, and their associated statistics are presented in table segregation distortion was rare, where only four markers, cu gcm ssr and uw significantly deviated from expected 1:2: segregation ratio. except for chromosome iv, each lg could be assigned to corresponding chromosomes as defined by liu et al.. in our analysis, chromosome iv was split into two linkage groups due to an insufficient number of markers. the f2-based map consisted of lg spanning cm, with a mean marker interval of cm, where the largest gap resided in chromosome iv associated with lg 4a and lg 4b. a lg = linkage group. chr = chromosome b # cs markers = number of markers from cucumber that were mapped in each linkage group. c relative length = length of individual chromosome/total length of all chromosomes × development of a ril-based extended melon linkage map with cucumber ssrs the molecular markers employed for f mapping were also used to identify polymorphisms between top mark and wi 846- of the ril population. of the cucumber ssrs tested, % produced amplicons in melon, where % of the ssrs detected polymorphisms between top mark and wi 846-. of the polymorphic markers identified herein, were placed on the ril map. using the same melon ril population, cuevas et al. mapped marker loci. the two sets of marker data were pooled for linkage analysis using rils. ten of these markers could not be assigned to any lg. the resulting linkage map possessed marker loci including codominant and dominant markers in lg with cumulative genetic distances of cm. the mapping data are presented in table s and associated map statistics are shown in table based on ssr markers shared in common with previously published melon maps, it was possible to relegate the lgs constructed herein to linkage groups. development of a consensus melon genetic map through map merging the f and ril maps developed herein shared markers in common, and were merged to produce a consensus map using the joinmap program. the dominant aflp and rapd markers resident on the ril map were excluded from map integration because they were deemed ineffective for defining cucumber-melon synteny. these markers tended to clustered on the linkage map, and a number of them showed segregation distortion. in contrast to the ril map, the markers on the f map were co-dominant and their order was used as the reference during map merging. the resulting consensus linkage map is presented in figure and summarized in table shared loci between the f and ril maps are given in table s. the consensus melon genetic map consisted of co-dominant marker loci positioned in lgs spanning. cm with an average marker interval of cm. among the lgs, lg had the longest map length followed by lg and lg. in contrast, the length of lg was the shortest. predictably lg possessed the most loci mapped and lg the least markers. since marker order of the f map was used as the reference during map merging, all loci on the consensus map were co-linear with those on the f map. moreover, inconsistencies in marker order were rare resulting in substantial colinearity between the ril map and the consensus map. identification of syntenic blocks between melon and cucumber chromosomes among the markers present on the consensus melon map, were ssr or caps markers developed from cucumber, one from the watermelon, and the remaining were derived from melon. the cucumber gy and draft genome scaffold locations of these markers were predicted by in silico pcr or blast searches of the cucumber draft genome sequences. seventy-four of the markers on the consensus melon map had no in silico pcr products or blast hits suggesting that they may be specific to the melon genome. three markers were located in sequences that were annotated as repeated sequences, and, therefore, their cucumber scaffold locations were difficult to determine. the remaining markers could be assigned to the gy and cucumber scaffolds. the scaffold names and physical positions of these markers are presented in table s. once the association of these markers on the melon consensus map with cucumber scaffolds was established, the locations of these cucumber scaffolds in the seven chromosomes of cucumber were deduced from published cucumber genetic maps. among the markers placed on the melon consensus map, have been mapped in previous cucumber mapping studies. therefore, their locations on cucumber genetic maps could be assigned directly. for markers with associated cucumber scaffold, their map locations in the cucumber genome was inferred by other markers derived from the same scaffold, which had been previously placed on cucumber maps. however, three markers were located in cucumber scaffolds from which no marker has been mapped. therefore, their locations in the cucumber genome were unknown. with molecular markers shared between the melon and cucumber genetic maps or linked by cucumber draft genome scaffolds, syntenic relationships between cucumber and melon chromosomes could be directly inferred. figure depicts a view of the melon chromosomes consisting of cucumber syntenic blocks. inspection of figure and table s indicated that melon chromosome i was syntenic to cucumber chromosome likewise, chromosomes ii and xii were syntenic with cucumber chromosome 1; chromosomes iv and vi were syntenic with cucumber chromosome 3; and chromosomes ix and x were syntenic with cucumber chromosome similarly, the three melon chromosomes iii, viii, and xi contained blocks that were syntenic to two cucumber chromosomes, 2+ 4+ and 2+ respectively. these melon-cucumber syntenic relationships are summarized in table it has been previously hypothesized that cucumber chromosomes evolved from a progenitor species with 2n = × = chromosomes through chromosome fusion. thus, a melon syntenic block view of cucumber chromosomes was developed which is shown in figure in this view, the scaffolds in each cucumber chromosome were arranged in the same order as were marker loci on cucumber genetic maps. in most cases, the high resolution genetic map developed by ren et al. was used as a reference for ordering those scaffolds. in rare instances, however, marker locations did not coincide with those of ren et al. and, thus, other more recent cucumber genetic maps were consulted to infer marker map locations. the arrangement of melon syntenic blocks across the seven cucumber chromosomes indicates that cucumber chromosome evolution is more complex than simple chromosome fusion. for instance, cucumber chromosome was homoeologous to melon chromosome i along its entire length. cucumber chromosomes and each contained three syntenic blocks detected in melon chromosomes v+xi+iii, and iii+xi+xiii, respectively, and the remaining four cucumber chromosomes were syntenic with two melon chromosomes but differed in patterns of arrangement of melon syntenic blocks. cucumber chromosome was syntenic to melon chromosome ii and xii, whereas cucumber chromosome was syntenic to melon chromosome ix and x. in both cases, the syntenic blocks from the two melon chromosomes were arranged alternatively along each cucumber chromosome. in contrast, the syntenic blocks residing in melon chromosomes vi and iv were in a side-by-side alignment in cucumber chromosome lastly, cucumber chromosome housed syntenic blocks of melon chromosome vii and viii, but the syntenic block of melon chromosome viii was found to be incorporated into the syntenic block of melon chromosome vii. taken collectively, these syntenic patterns were suggestive of a complex history of chromosomal structure changes during cucumber evolution. verification of melon-cucumber syntenic relationships in this study, in silico pcr and blast sequence alignment proved useful for inferring the cucumber scaffold location of markers on the melon consensus map. to verify the syntenic relationships between cucumber and melon chromosomes detected from comparative mapping conducted herein, a similar strategy was used with molecular markers from a melon linkage map developed by deleu et al.. this gene-based melon linkage map consists of marker loci, of which nearly were snps developed from melon est sequences, and all these markers were derived exclusively from the melon genome. the details of this map are shown in table s. the genomic or est sequences from which these markers were developed were used in blast analysis against the cucumber draft genome assemblies. of the markers, only did not yield either in silico pcr products or blast hits in the cucumber draft genomes examined. this contrasted with markers on the consensus melon map, where of did not produce hits in either gy or genome assembly. this suggests that the est sequences examined are highly conserved between these genomes. the syntenic relationships between melon and cucumber chromosomes inferred from this gene-based melon genetic map are shown in table s. although there were no cucumber source markers on this map, melon-cucumber syntenic relationships revealed from the present study were confirmed by this independent study. discussion cross-species transferability and polymorphisms of cucumber ssrs in the melon genome nearly randomly sampled cucumber genomic ssrs were tested herein for their ability to detect polymorphisms among three melon parental lines used in map construction. the polymorphism level of cross-species transferable cucumber ssrs was % between top mark and wi 846- and % between top mark and line q3-2- which would be reduced to and %, respectively if all cucumber ssrs tested were considered. this level was appreciably lower than that reported in other studies using melon ssrs. for example, of melon ssrs evaluated for map construction by cuevas et al., 32% were polymorphic between two melon lines q3-2- and top mark. likewise, the level of polymorphism of melon ssrs between the two melon lines pi and dulce used by harel-beja et al. was comparatively high. such differences in polymorphism level may be attributable to the sources of markers, the melon lines used, or the relative genetic distance among the germplasm being evaluated. two additional factors may also contribute to the low polymorphism level detected by cucumber ssrs. firstly, unlike melon, which is considered genetically diverse, cucumber has a narrow genetic base, and the degree of polymorphism at the whole genome level for randomly chosen ssrs between any two cultivated cucumber genotypes is in general less than 20%. in the present study, about 45% of cucumber ssrs examined exhibited cross-species amplification in the melon genome after pcr. this amplification level is similar to that detected by ritschel et al. who found that ~50% of the melon ssr markers evaluated produced amplicons when cucumber dnas were used as templates. gonzález et al. found 54% of the melon bac-end sequences under investigation could be aligned to the cucumber genome. it is likely that the melon genomic regions that were amplified by cucumber ssrs represent conserved portions between the cucumber and melon genomes. the genomes of gy and cucumber lines have been sequenced using the "next generation" sequencing technologies, and, therefore, most of the assembled genome sequences may originate from the gene-rich low or single copy dna fraction in the genome, which are more conserved between closely related species such as melon and cucumber than repetitive dna sequences. therefore, using ssrs developed from highly conserved gene-rich genomic dna regions of a genome with limited genetic diversity may be an important contributor to the low polymorphism of cucumber ssrs in the melon genome. the second factor, as discussed in cavagnaro et al., is that melon ssrs used in previous mapping studies may over-estimate the polymorphism in the genome due to biases created during ssr selection, because of the reiterative selection for longer repeats during development of microsatellite markers. that is, library screening methods for ssr isolation are designed to yield a higher proportion of long ssrs, which are preferentially used for designing primers, which are then typically pre-screened for their relative polymorphism level in potential parental lines. thus, the most polymorphic loci are selected for further utilization. in this study, the polymorphism level detected between q3-2- and top mark or top mark and wi 846-, although very low, may reflect the true global polymorphism of cucumber ssrs at the whole melon genome level. the melon consensus linkage map with cucumber ssrs the consensus map developed herein added a considerable number of ssr markers towards map saturation in melon. we added and new markers to the previously developed melon f and ril maps, respectively. marker order on the new and the historic f maps were almost identical. the ril map was improved over the historic map, but was still relatively fragmented, which was likely due to the large number of dominant markers incorporated into the ril-based map. it is known that dominant markers such as rapds or aflps tend to be clustered on the linkage maps, and for this reason, dominant markers were excluded in map merging for development of the consensus map. even though more than the predicted numbers of lgs were present on the f and ril maps, the large number of shared marker loci enabled integration of the two maps to produce a consensus melon genetic map with the expected lgs. this consensus map contained co-dominant markers including derived from cucumber, and is the first melon map containing such a high number of cucumber-derived markers. the map length of this consensus map was cm, which is within the predicted size range of the melon genome. the reliability of this map can be measured by its colinearity and its relationship with available cucumber scaffolds. although there were minor discrepancies in marker orders between markers on the consensus and the ril-based maps, these maps were largely collinear. the disparities detected between these maps may be, in part, due to varying recombination rates between mapping population, relatively small mapping populations used, and/or genome structural variations between populations. with few exceptions, closely linked markers on these melon maps were located in the same cucumber draft genome scaffolds. synteny between melon and cucumber chromosomes comparative mapping, in silico pcr, and blast sequence alignment allowed a comprehensive assessment of syntenic relationships between the cucumber and melon chromosomes. among the markers positioned on the melon consensus map, provided no in silico pcr products or blast hits in the cucumber genome sequences examined. most of these markers were derived from melon genomic dna sequences, indicating their uniqueness to the melon genome. the genomic distribution of these "no-hit" markers also appears to be non-random on the melon consensus map, and in many cases, these markers were located at telomeric ends, implying the possibility of rapid evolutionary divergence. such information may allow design of experiments to investigate the nature of these regions in cucumis chromosome evolution. phylogenetic analyses in cucumis support an early hypothesis that the base chromosome number x = in cucumber is derived from a progenitor species with x =. six of the seven cucumber chromosomes may be originated from chromosome fusion of such a progenitor species. we provide herein additional information regarding the syntenic relationships between cucumber and melon chromosomes indicating that the evolutionary dynamics of cucumber evolution is complex. although we confirmed the early finding that cucumber chromosome was syntenic with melon chromosome i, we found that the co-linearity of marker loci in the two chromosomes has been broken suggesting that chromosome of cultivated cucumber may have undergone certain structural changes since its divergence from an ancestral species. the other six chromosomes of cucumber appear to have more complicated evolutionary histories. for instance, both chromosomes and possess genomic regions that are syntenic to genetic blocks from at least three melon chromosomes, suggesting they are derived from more than simple chromosome fusion. although chromosomes and each possessed genomic blocks syntenic with those from two melon chromosomes, the arrangements of these blocks differed among chromosomes. since cucumber chromosome appears to be comparatively simple in its syntenic block organization, it is tempting to hypothesize that it originated from simple fusion of melon chromosomes iv and vi. however, close inspection of marker order in cucumber chromosome and melon chromosomes iv and vi reveals non-colinearity, which suggests that additional structural changes may have occurred after a hypothetical chromosome fusion event. data presented herein provides a rather complicated description of cucumis species chromosome evolution, making a comprehensive statement regarding chromosome evolution in melon and cucumber difficult at this time. it is apparent that additional information is required regarding the genomic nature of melon, and cucumber, as well as potential'bridge" species [, e.g., c. hystrix) to elucidate more clear evolutionary relationships in this genus. to better understand these relationships a more saturated cucumber genetic map is needed to increase the resolution of cucumber scaffolds for comparative mapping. the cucumber map used herein was developed with rils from an inter-subspecific cross between cultivated cucumber line gy and the wild c. sativus var. hardwickii line pi. there were, however, strong recombination suppressions detected during map construction resulting in clustering of molecular markers in several regions of cucumber chromosomes and such recombination suppression may, in part, be due to structural differences in chromosomes between cultivated and wild cucumbers, which, in turn, may have reduced the power of ordering markers and scaffolds. meanwhile, the whole genome sequencing of melon is near completion. this will provide a powerful tool to understand the synteny between the melon and cucumber chromosomes at dna sequence level. a wild relative of cucumber, c. hystrix, may play the key role in understanding the process of cucumber chromosome evolution. extensive phylogenetic analyses in cucumis have indicated that c. hystrix is so far the closest wild relative of cucumber. the lack of genetic affinity between c. hystrix and c. melo, and african species, lends support to the hypothesis that c. hystrix is a progenitor species of c. sativus, or that they at least share a common ancestral lineage. c. hystrix has the same number of chromosomes as melon, and is sparingly cross-compatible with cucumber, but not melon. a fertile amphidiploid, c. hystivus between cucumber and c. hystrix, as well as alien addition lines have also been successfully created. the seven meiotic chromosomes of c. sativus are larger than the chromosomes of c. hystrix. fluorescence in situ hybridization of 45s rdna and cscent repetitve dna probes to cucumber pachytene chromosomes also suggested that cucumber chromosomes and may have evolved from fusions of an ancestral karyotype with 2n =. these findings make c. hystrix the primary resource for testing genetic hypotheses for further characterizing the evolution of modern cucumber.  this is the first broad-based comparative analysis of synteny between melon and cucumber. the consensus melon linkage map derived herein from two historic maps possesses the largest number of cross-species cucumber molecular markers currently mapped in the melon genome and provides a greater understanding of genomic relationships between these two important cucumis species. data support the hypothesis that cucumber chromosomes originate from fusions of chromosomes of an x = ancestral progenitor. however, many structural changes may have occurred in the evolution of the seven cucumber chromosomes. in depth cytogenetic and molecular investigations of x = cucumis species will likely provide further evidence of chromosome evolution in cucumber, melon and related taxons. 
a consensus melon linkage map was developed through map integration, which contained co-dominant markers in linkage groups including markers derived from the cucumber genome. in this study, comparative genetic mapping between cucumber and melon was conducted to examine syntenic relationships of their chromosomes. however, the marker orders in several syntenic blocks on these consensus linkage maps were not co-linear suggesting that more complicated structural changes beyond simple chromosome fusion events have occurred during the evolution of cucumber. further characterization of the genomic nature of cucumis species closely related to cucumber and melon might provide a better understanding of the evolutionary history leading to modern cucumber. using two melon mapping populations, and cucumber ssr markers were added onto previously reported f2- and ril-based genetic maps, respectively. it was determined that cucumber chromosome was syntenic to melon chromosome i. cucumber chromosomes and each contained genomic regions that were syntenic with melon chromosomes iii+v+xi and iii+viii+xi, respectively. likewise, cucumber chromosomes and each was syntenic with genomic regions of two melon chromosomes previously designated as ii+xii, iv+vi, vii+viii, and ix+x, respectively. cucumber, cucumis sativus l. and melon, c. melo l. are two important vegetable species in the genus cucumis. syntenic relationships between melon and cucumber chromosomes were inferred based on associations between markers on the consensus melon map and cucumber draft genome scaffolds. meanwhile, many structural changes may have occurred during the evolution of the remaining six cucumber chromosomes. comparative mapping conducted herein supported the hypothesis that cucumber chromosomes may be the result of chromosome fusion from a 24-chromosome progenitor species. cucumber is believed to have evolved from melon through chromosome fusion, but the details of this process are largely unknown. both species have an asian origin that diverged approximately nine million years ago.
 cucumber, cucumis sativus l. and melon, c. melo l. are two important vegetable species in the genus cucumis. both species have an asian origin that diverged approximately nine million years ago. cucumber is believed to have evolved from melon through chromosome fusion, but the details of this process are largely unknown. in this study, comparative genetic mapping between cucumber and melon was conducted to examine syntenic relationships of their chromosomes.  using two melon mapping populations, and cucumber ssr markers were added onto previously reported f2- and ril-based genetic maps, respectively. a consensus melon linkage map was developed through map integration, which contained co-dominant markers in linkage groups including markers derived from the cucumber genome. syntenic relationships between melon and cucumber chromosomes were inferred based on associations between markers on the consensus melon map and cucumber draft genome scaffolds. it was determined that cucumber chromosome was syntenic to melon chromosome i. cucumber chromosomes and each contained genomic regions that were syntenic with melon chromosomes iii+v+xi and iii+viii+xi, respectively. likewise, cucumber chromosomes and each was syntenic with genomic regions of two melon chromosomes previously designated as ii+xii, iv+vi, vii+viii, and ix+x, respectively. however, the marker orders in several syntenic blocks on these consensus linkage maps were not co-linear suggesting that more complicated structural changes beyond simple chromosome fusion events have occurred during the evolution of cucumber.  comparative mapping conducted herein supported the hypothesis that cucumber chromosomes may be the result of chromosome fusion from a 24-chromosome progenitor species. except for a possible inversion, cucumber chromosome has largely remained intact in the past nine million years since its divergence from melon. meanwhile, many structural changes may have occurred during the evolution of the remaining six cucumber chromosomes. further characterization of the genomic nature of cucumis species closely related to cucumber and melon might provide a better understanding of the evolutionary history leading to modern cucumber. cucumbermeloncucumismicrosatellitecomparative mappingchromosome evolution 