Cytological Distinctions Between Timun Suri and Cucumber Discovered by Fluorescence In Situ Hybridization (FISH) Using 45S Ribosomal DNA Gene

Agus Budi Setiawan, Aziz Purwantoro, Ari Wibowo


The genus Cucumis including timun suri, melon and cucumber, is an important horticultural crop of flowering plants. The dispute of timun suri terminology is leading to false-positive results in the nomenclature of timun suri in Indonesia. Although molecular research on these species has been widely conducted, detailed information and precise evidence based on the molecular cytogenetic approach are poorly investigated. The FISH technique was applied to reveal the cytological distinctions among these species. Here, this research conducted physical mapping of 45S ribosomal DNA (rDNA) on six accessions of Cucumis. The chromosome number of cucumber is 14 chromosomes, while timun suri and melon are 24 chromosomes. The number of 45S rDNA loci in cucumber, melon and timun suri was highly conserved. All cucumber accessions in this study had nine to ten 45S rDNA loci with strong and weak signal intensities located at proximal regions of the short arms. In melon and timun suri the signals of two pairs of 45S rDNA were located at the terminal and interstitial regions of the short arms. These were clear shreds of evidence to confirm that timun suri was cytogenetically closed to melon instead of cucumber. It confirmed that timun suri cannot be classified as a cucumber


45S rDNA; Cucumber; Cucumis melo var. momordica; FISH; Timun suri

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Acosta, M. C., Moscone, E. A., & Cocucci, A. A. (2016). Using chromosomal data in the phylogenetic and molecular dating framework: Karyotype evolution and diversification in Nierembergia (Solanaceae) influenced by historical changes in sea level. Plant Biology, 18(3), 514–526.

Amosova, A. V., Bolsheva, N. L., Zoshchuk, S. A., Twardovska, M. O., Yurkevich, O. Y., Andreev, I. O., … Muravenko, O. V. (2017). Comparative molecular cytogenetic characterization of seven Deschampsia (Poaceae) species. PLoS ONE, 12(4), e0175760.

Cabrero, J., & Camacho, J. P. M. (2008). Location and expression of ribosomal RNA genes in grasshoppers: Abundance of silent and cryptic loci. Chromosome Research, 16, 595–607.

Chen, J.-F., Luo, X.-D., Qian, C.-T., Jahn, M. M., Staub, J. E., Zhuang, F.-Y., … Ren, G. (2004). Cucumis monosomic alien addition lines: Morphological, cytological, and genotypic analyses. Theoretical and Applied Genetics, 108, 1343–1348.

Chen, J.-F., Staub, J. E., Adelberg, J. W., & Jiang, J. (1999). Physical mapping of 45S rRNA genes in Cucumis species by fluorescence in situ hybridization. Canadian Journal of Botany, 77(3), 389–393.

Chen, J.-F., Staub, J. E., Qian, C., Jiang, J., Luo, X., & Zhuang, F. (2003). Reproduction and cytogenetic characterization of interspecific hybrids derived from Cucumis hystrix Chakr. x Cucumis sativus L. Theoretical and Applied Genetics, 106, 688–695.

Chen, J.-F., Staub, J. E., Tashiro, Y., Isshiki, S., & Miyazaki, S. (1997). Successful interspecific hybridization between Cucumis sativus L. and C. hystrix Chakr. Euphytica, 96, 413–419.

Chen, J.-F., Staub, J., Adelberg, J., Lewis, S., & Kunkle, B. (2002). Synthesis and preliminary characterization of a new species (amphidiploid) in Cucumis. Euphytica, 123, 315–322.

De Melo, N. F., & Guerra, M. (2003). Variability of the 5S and 45S rDNA sites in Passiflora L. species with distinct base chromosome numbers. Annals of Botany, 92(2), 309–316.

Dhillon, N. P. S., Ranjana, R., Singh, K., Eduardo, I., Monforte, A. J., Pitrat, M., … Singh, P. P. (2007). Diversity among landraces of Indian snapmelon (Cucumis melo var. momordica). Genetic Resources and Crop Evolution, 54, 1267–1283.

Dubcovsky, J., & Dvorák, J. (1995). Ribosomal RNA multigene loci: Nomads of the Triticeae genomes. Genetics, 140(4), 1367–1377. Retrieved from

Ganal, M., & Hemleben, V. (1986). Comparison of the ribosomal RNA genes in four closely related Cucurbitaceae. Plant Systematics and Evolution, 154(1), 63–77.

Gerlach, W. L., & Bedbrook, J. R. (1979). Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucleic Acids Research, 7(7), 1869–1885.

Gong, Z., Xue, C., Zhang, M., Guo, R., Zhou, Y., & Shi, G. (2013). Physical localization and DNA methylation of 45S rRNA gene loci in Jatropha curcas L. PLoS ONE, 8(12), e84284.

Han, Y.-H., Zhang, Z.-H., Liu, J.-H., Lu, J.-Y., Huang, S.-W., & Jin, W.-W. (2008). Distribution of the tandem repeat sequences and karyotyping in cucumber (Cucumis sativus L.) by fluorescence in situ hybridization. Cytogenetic and Genome Research, 122, 80–88.

Hanson, R. E., Islam-Faridi, M. N., Percival, E. A., Crane, C. F., Ji, Y., McKnight, T. D., … Price, H. J. (1996). Distribution of 5S and 18S-28S rDNA loci in a tetraploid cotton (Gossypium hirsutum L.) and its putative diploid ancestors. Chromosoma, 105, 55–61.

Hayashi, M., Miyahara, A., Sato, S., Kato, T., Yoshikawa, M., Taketa, M., … Harada, K. (2001). Construction of a genetic linkage map of the model legume Lotus japonicus using an intraspecific F2 population. DNA Research, 8(6), 301–310.

Huda, I. N., & Daryono, B. S. (2013). Analisis variasi genetik melon (Cucumis melo L.) kultivar gama melon basket dengan metode random amplified polymorphic DNA. Biogenesis: Jurnal Ilmiah Biologi, 1(1), 41–50.

Jiang, J., & Gill, B. S. (2006). Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome, 49(9), 1057–1068.

Kato, A., Lamb, J. C., & Birchler, J. A. (2004). Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proceedings of the National Academy of Sciences of the United States of America, 101(37), 13554–13559.

Koo, D.-H., Nam, Y.-W., Choi, D., Bang, J.-W., de Jong, H., & Hur, Y. (2010). Molecular cytogenetic mapping of Cucumis sativus and C. melo using highly repetitive DNA sequences. Chromosome Research, 8, 325–336.

Li, K., Wang, H., Wang, J., Sun, J., Li, Z., & Han, Y. (2016). Divergence between C. melo and African Cucumis species identified by chromosome painting and rDNA distribution pattern. Cytogenetic and Genome Research, 150(2), 150–155.

Li, Z.-Y., Fu, M.-L., Hu, F.-F., Huang, S.-F., & Song, Y.- C. (2006). Visualization of the ribosomal DNA (45S rDNA) of Indica rice with FISH on some phases of cell cycle and extended DNA fibers. Biocell, 30(1), 27–32.

Liu, C., Liu, J., Li, H., Zhang, Z., Han, Y., Huang, S., & Jin, W. (2010). Karyotyping in melon (Cucumis melo L.) by cross-species fosmid fluorescence in situ hybridization. Cytogenetic and Genome Research, 129(1–3), 241–249.

Lou, Q., Zhang, Y., He, Y., Li, J., Jia, L., Cheng, C., … Chen, J. (2014). Single-copy gene-based chromosome painting in cucumber and its application for chromosome rearrangement analysis in Cucumis. Plant Journal, 78(1), 169–179.

Manohar, S. H., & Murthy, H. N. (2012). Estimation of phenotypic divergence in a collection of Cucumis melo, including shelf-life of fruit. Scientia Horticulturae, 148, 74–82.

Marcon, A. B., Leão Barros, I. C., & Guerra, M. (2005). Variation in chromosome numbers, CMA bands and 45S rDNA sites in species of Selaginella (Pteridophyta). Annals of Botany, 95(2), 271–276.

Navrátilová, A., Neumann, P., & Macas, J. (2003). Karyotype analysis of four Vicia species using in situ hybridization with repetitive sequences. Annals of Botany, 91(7), 921–926.

Neves, N., Delgado, M., Silva, M., Caperta, A., MoraisCecílio, L., & Viegas, W. (2005). Ribosomal DNA heterochromatin in plants. Cytogenetic and Genome Research, 109(1–3), 104–111.

Pedrosa-Harand, A., de Almeida, C. C. S., Mosiolek, M., Blair, M. W., Schweizer, D., & Guerra, M. (2006). Extensive ribosomal DNA amplification during Andean common bean (Phaseolus vulgaris L.) evolution. Theoretical and Applied Genetics, 112, 924–933.

Penner, G. A., Bush, A., Wise, R., Kim, W., Domier, L., Kasha, K., … Fedak, G. (1993). Reproducibility of random amplified polymorphic DNA (RAPD) analysis among laboratories. Genome Research, 2, 341–345.

Pitrat, M., Chauvet, M., & Foury, C. (1999). Diversity, history and production of cultivated cucurbits. Acta Horticulturae, 492, 21–28.

Rahayu, S. E., & Hartana, A. (2002). Biosistematika Cucumis (Cucurbitaceae) di Jawa. Floribunda, 2(2), 38–43. Retrieved from

Raskina, O., Belyayev, A., & Nevo, E. (2004a). Activity of the En/Spm-like transposons in meiosis as a base for chromosome repatterning in a small, isolated, peripheral population of Aegilops speltoides Tausch. Chromosome Research, 12(2), 153–161.

Raskina, O., Belyayev, A., & Nevo, E. (2004b). Quantum speciation in Aegilops: Molecular cytogenetic evidence from rDNA cluster variability in natural populations. Proceedings of the National Academy of Sciences of the United States of America, 101(41), 14818–14823.

Roa, F., & Guerra, M. (2012). Distribution of 45S rDNA sites in chromosomes of plants: Structural and evolutionary implications. BMC Evolutionary Biology, 12, 225.

Schwarzacher, T., & Heslop-Harrison, P. (2000). Practical in situ hybridization. Oxford: BIOS Scientific Publishers. Retrieved from

Sebastian, P., Schaefer, H., Telford, I. R. H., & Renner, S. S. (2010). Cucumber (Cucumis sativus) and melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia. Proceedings of the National Academy of Sciences of the United States of America, 107(32), 14269–14273.

Setiawan, A. B. (2018). Molecular cytogenetic studies on satellite DNA and retrotransposon in Cucumis species (Thesis). Chiba University.

Setiawan, A. B., Teo, C. H., Kikuchi, S., Sassa, H., & Koba, T. (2018). An improved method for inducing prometaphase chromosomes in plants. Molecular Cytogenetics, 11, 32.

She, C.-W., Jiang, X.-H., Ou, L.-J., Liu, J., Long, K.-L., Zhang, L.-H., … Hu, J.-C. (2015). Molecular cytogenetic characterisation and phylogenetic analysis of the seven cultivated Vigna species (Fabaceae). Plant Biology, 17(1), 268–280.

Singh, A. K., Kumar, S., Singh, H., Rai, V. P., Singh, B. D., & Pandey, S. (2015). Genetic diversity in Indian snapmelon (Cucumis melo var. momordica) accessions revealed by ISSR markers. Plant OMICS, 8(1), 9–16. Retrieved from

Skroch, P., & Nienhuis, J. (1995). Impact of scoring error and reproducibility RAPD data on RAPD based estimates of genetic distance. Theoretical and Applied Genetics, 91, 1086–1091.

Vaio, M., Speranza, P., Valls, J. F., Guerra, M., & Mazzella, C. (2005). Localization of the 5S and 45S rDNA sites and cpDNA sequence analysis in species of the quadrifaria group of Paspalum (Poaceae, Paniceae). Annals of Botany, 96(2), 191–200.

Wendel, J. F., Schnabel, A., & Seelanan, T. (1995). Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proceedings of the National Academy of Sciences of the United States of America, 92(1), 280–284.

Zhang, Y., Cheng, C., Li, J., Yang, S., Wang, Y., Li, Z., … Lou, Q. (2015). Chromosomal structures and repetitive sequences divergence in Cucumis species revealed by comparative cytogenetic mapping. BMC Genomics, 16, 730.

Zhang, Z.-T., Yang, S.-Q., Li, Z.-A., Zhang, Y.-X., Wang, Y.-Z., Cheng, C. Y., … Lou, Q. F. (2016). Comparative chromosomal localization of 45S and 5S rDNAs and implications for genome evolution in Cucumis. Genome, 59(7), 449–457.

Zhao, X., Lu, J., Zhang, Z., Hu, J., Huang, S., & Jin, W. (2011). Comparison of the distribution of the repetitive DNA sequences in three variants of Cucumis sativus reveals their phylogenetic relationships. Journal of Genetics and Genomics, 38(1), 39–45.


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