The genus Cucumis, includes the cucumber (2n = 14), melon (2n = 24), and other wild species, which is a good model for studying genome organization and evolution due to their variation in genome size and basic chromosome number. In this study, five Cucumis species with different geographical origins and basic chromosome numbers (i.e., C. sativus, C. hystrix, C. melo, C. anguria, and C. metuliferus) were used to identify and characterize the repetitive DNA in detail using a phylogenetic method. Comparative cyto-molecular genetic analysis of repetitive DNA was carried out using a graph-based clustering method, construction of Neighbor-Joining tree and fluorescence in situ hybridization (FISH). The results revealed that the five Cucumis species had differences in the repeat content of their genome, as well as in the composition of repetitive DNA and their genomic proportions. Three species from subgenus Melo showed a decreased tendency in both repeat types and genomic proportions, while two species from subgenus Cucumis also showed a decreased tendency in repeat types, but an increased tendency in genomic proportions. Phylogenic analysis of Cucumis Ty1/Copia, Ty3/Gypsy, and 45S rDNA ITS regions revealed that C. sativus, C. hystrix, and C. melo were closely related species, which C. sativus and C. hystrix were closer, while C. anguria and C. metuliferus were closer to each other and further from the other three species. Differential accumulation and elimination of different repeat types divergently shaped the genomic architecture of these five Cucumis species, contributing to the genome's evolution and diversification. Overall, these results enhance our understanding of the genomes of these five Cucumis species, and contribute to a more holistic view of genome evolution and phylogenetics of this genus.

黄瓜属（Cucumis）包括黄瓜（2 n  = 14），瓜（2 n  = 24）和其他野生物种，由于它们在基因组大小和基本染色体数目上的变化，这是研究基因组组织和进化的良好模型。在这项研究中，五个具有不同地理起源和基本染色体数的黄瓜属物种（即，C。sativus，C。hystrix，C。melo，C。anguria和C. metuliferus）使用系统发育方法详细地鉴定和表征了重复性DNA。使用基于图的聚类方法，Neighbor-Joining树的构建和荧光原位杂交（FISH）对重复DNA进行了比较性的细胞分子遗传分析。结果表明，五个黄瓜属物种在其基因组的重复含量，重复DNA的组成及其基因组比例方面均存在差异。从亚属三个品种梅洛表现出两种类型的重复和基因组的比例下降趋势，而从亚属两个品种黄瓜也显示重复类型的下降趋势，但在基因组的比例增加的趋势。系统发育分析黄瓜Ty1导/ Copia进一步，TY3 /吉普赛人和45S rDNA的ITS区透露C.黄瓜，红锥，和香瓜密切相关的物种，其中C.黄瓜和红锥更接近，而C. anguria和Ç metuliferus彼此靠近，距离其他三个物种更远。差异积累和不同重复类型的消除会不同地塑造这五个黄瓜属物种的基因组结构，从而促进基因组的进化和多样化。总体而言，这些结果增强了我们对这五个黄瓜的基因组的了解 物种，并有助于更全面地了解该属的基因组进化和系统发育。