| Cucumber(Cucumis sativus L., 2n=2x=14), which belongs to the family Cucurbitaceae, is an economically important crop as well as a model system to study biologically relevant characters such as sex determination studies and plant vascular biology. High-resolution cytogenetic map not only can provide important biological information on genome organization but also provide a solid foundation for genetic and genomic research. Here, the cytogenetic maps of four cucumber chromosomes, 1 and 3–5, were constructed by fluorescence in situ hybridization(FISH) analysis on cucumber pachytene chromosomes. Our study not only provides essential information for the improvement of sequence assembly but also offers molecular tools for cucumber genomics research, comparative genomics and evolutionary study. In order to further understand the evolution of Cucumis genus, we investigated the locations of 5S and 45 S r DNA in 15 species in Cucumis by FISH. The results list as follows:1. To construct the molecular cytogenetic maps of the remaining four cucumber chromosomes, we selected a set of fosmid clones distributed at regular intervals across the chromosome-level cucumber draft genome assembly maps. We first determined the physical order of adjacent fosmid clones based on their positions in draft genome assembly map by dual-color FISH on somatic metaphase chromosomes. On the basis of these results, multi-fosmid FISH probe cocktails were developed and hybridized to the pachytene chromosomes together with the cucumber centromere-specific DNA probe Type III. The cocktails produced alternate red/green signals of all clones and marked centromeres on each chromosome.2. Together with previously constructed cytogenetic maps of three chromosomes. Cucumber has a complete cytogenetic map with 76 anchoring points between the genetic, the cytogenetic and the draft genome assembly map. To compare our pachytene FISH map directly to the genetic linkage and the draft genome assembly map, we used a standardized map unit-relative map position(RMP) to produce the comparative alignments. We found that the linear order of markers in the linkage groups was in complete with the order of the corresponding fosmid clones along the chromosomes except for 2-10,2-11. The majority of loci showed good RMP agreement but in some loci on chromosome 5. When compared the distributions of fosmid clones on the 9930 draft genome assembly map and our cytogenetic map. The RMPs were showing comparable distributions along the given chromosomes. The linear orders of the loci along a given chromosome were congruent between cytogenetic map and draft genome assembly map except for 5–1 and 5–2, 7–1 and 7–2. Between two maps, 4-4, 4-5, 4-6, 4-7 show big difference of RMP values.3. The distribution of 45 S r DNA among 16 species is both conserved and polymorphic. The copy numbers of 45 S r DNA loci was discrepant in the different chromosomes of the same species. The signals were detected on the satellite, pericentromeric and telomere. The number of 45 S r DNA is in relation with polyploidy.4. The 5S r DNA loci maintained high homogeneity in the number(except one hexaploid species), distribution and the copy numbers in 16 species. The locis of 45 S r DNA and 5S r DNA are on the same chromosome in 75% species. The signals were detected on the pericentromeric and telomere. |
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