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, 16 (1), 730

Chromosomal Structures and Repetitive Sequences Divergence in Cucumis Species Revealed by Comparative Cytogenetic Mapping

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Chromosomal Structures and Repetitive Sequences Divergence in Cucumis Species Revealed by Comparative Cytogenetic Mapping

Yunxia Zhang et al. BMC Genomics.

Abstract

Background: Differentiation and copy number of repetitive sequences affect directly chromosome structure which contributes to reproductive isolation and speciation. Comparative cytogenetic mapping has been verified an efficient tool to elucidate the differentiation and distribution of repetitive sequences in genome. In present study, the distinct chromosomal structures of five Cucumis species were revealed through genomic in situ hybridization (GISH) technique and comparative cytogenetic mapping of major satellite repeats.

Results: Chromosome structures of five Cucumis species were investigated using GISH and comparative mapping of specific satellites. Southern hybridization was employed to study the proliferation of satellites, whose structural characteristics were helpful for analyzing chromosome evolution. Preferential distribution of repetitive DNAs at the subtelomeric regions was found in C. sativus, C hystrix and C. metuliferus, while majority was positioned at the pericentromeric heterochromatin regions in C. melo and C. anguria. Further, comparative GISH (cGISH) through using genomic DNA of other species as probes revealed high homology of repeats between C. sativus and C. hystrix. Specific satellites including 45S rDNA, Type I/II, Type III, Type IV, CentM and telomeric repeat were then comparatively mapped in these species. Type I/II and Type IV produced bright signals at the subtelomeric regions of C. sativus and C. hystrix simultaneously, which might explain the significance of their amplification in the divergence of Cucumis subgenus from the ancient ancestor. Unique positioning of Type III and CentM only at the centromeric domains of C. sativus and C. melo, respectively, combining with unique southern bands, revealed rapid evolutionary patterns of centromeric DNA in Cucumis. Obvious interstitial telomeric repeats were observed in chromosomes 1 and 2 of C. sativus, which might provide evidence of the fusion hypothesis of chromosome evolution from x = 12 to x = 7 in Cucumis species. Besides, the significant correlation was found between gene density along chromosome and GISH band intensity in C. sativus and C. melo.

Conclusions: In summary, comparative cytogenetic mapping of major satellites and GISH revealed the distinct differentiation of chromosome structure during species formation. The evolution of repetitive sequences was the main force for the divergence of Cucumis species from common ancestor.

Figures

Fig. 1
Fig. 1
Phylogenetic relationship of the five Cucumis species used in comparative cytogenetic analysis. Values for age estimates (Mya) are placed above the branches
Fig. 2
Fig. 2
Distribution of repetitive sequences along chromosomes revealed by self-GISH in Cucumis species. a C. sativus; b C. hystrix; c C. melo; d C. metuliferus; e C. anguria. Red signals in (a), (b), (c), (d), and (e) represent the signals produced by genomic DNA themselves. Green signals in (a), (b), (d), and (e) represent the signals produced by Arabidopsis type telomere probes. Green signals in (c) represent the signals produced by C. melo centromere probe, CentM. Scale bars = 5 μm. Arrows in (a)-2 show interstitial telomere signals. Arrows in (c)-3 and (d)-3 show the nucleolar organizing regions (NORs)
Fig. 3
Fig. 3
Distribution of conserved homologous sequences detected by reciprocal comparative GISH in Cucumis species. Each row represents the metaphase chromosomes from the same species, and the species was showed at left side; each column represents the signal patterns using total genomic DNA probe from one species, and the species used as probes was showed on the top. Green signals pointed by arrows in self-GISH pictures show the 45S rDNA loci. Scale bars = 5 μm
Fig. 4
Fig. 4
FISH mapping of two types of satellites on metaphase chromosomes of C. sativus and C. hystrix. a Signals of Type I/II on C. sativus. b Signals of Type IV on C. sativus. c Merged picture from (a) and (b). (d) Signals of Type I/II on C. hystrix. e Signals of Type IV on C. hystrix. f Merged picture from (d) and (e). Scale bars = 5 μm
Fig. 5
Fig. 5
Southern hybridization of specific satellites. Genomic DNA of each lane stands for five Cucumis species, C. sativus, C. hystrix, C. melo, C. metuliferus and C. anguria, respectively. Each blot was probed separately with satellites Type I/II, Type IV, CentM, and 45S rDNA
Fig. 6
Fig. 6
Distribution of gene density along the chromosome 5 of cucumber (a) and chromosome five of melon (b). The blue line show the overall trend of gene density along chromosome, and the gray shadow parts show the rough heterochromatin region according to FISH results. The “physical distance” on x-axis means the end to end distance (from telomere to telomere)
Fig. 7
Fig. 7
Idiograms of five Cucumis species (left) and information of GISH signals and satellite repeats distribution (right)

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