Research Article
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Year 2019, Volume 1, Issue 1, 68 - 76, 19.08.2019
https://doi.org/10.38058/ijsl.592537

Abstract

References

  • Arumuganathan, K., Earle, E. 1991. Nuclear DNA content of some important plant species, Plant Molecular Biology Reporter, 9: 208.
  • Carvalho, N., Canela, F.M., Leite, P.H.S., Ferreira, M.A., Oliveira, V.R., et al. 2017. Analysis of genetic variability of commercial melon cultivars using SSR molecular markers, Genetics and Molecular Research, 16(3): gmr16039739.
  • Galpaz, N., Gonda, I., Shem‐Tov, D., Barad, O., Tzuri, G., et al. 2018. Deciphering genetic factors that determine melon fruit‐quality traits using RNA‐Seq‐based high‐resolution QTL and eQTL mapping, The Plant Journal, 94(1): 169-191.
  • Garcia-Mas, J., Benjak, A., Sanseverino, W., Bourgeois, M., Mir, G. et al. 2012. The genome of melon (Cucumis melo L.), Proceedings of the National Academy of Sciences, 109(29): 11872-11877.
  • Gómez-Aix, C., Pascual, L., Cañizares, J., Sánchez-Pina, M.A., Aranda, M.A. 2016. Transcriptomic profiling of melon necrotic spot virus-infected melon plants revealed virus strain and plant cultivar-specific alterations, BMC Genomics, 17(1): 429.
  • Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W.J., et al. 2013. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions, Nature Genetics, 45(1): 51.
  • Huala, E., Dickerman, A.W., Garcia-Hernandez, M., Weems, D., Reiser, L. et al. 2001. The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant, Nucleic Acids Research, 29: 102-105.
  • Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., et al. 2009. The genome of the cucumber, Cucumis sativus L, Nature Genetics, 41: 1275-1281.
  • Huang, H.X., Yu, T., Li, J. X., Qu, S.P., Wang, M.M., et al. 2019. Characterization of Cucurbita maxima fruit metabolomic profiling and transcriptome to reveal fruit quality and ripening gene expression patterns, Journal of Plant Biology, 62(3): 203-216.
  • Jat, G.S., Munshi, A.D., Behera, T.K., Choudhary, H., Dash, P., et al. 2019. Genetics and molecular mapping of gynoecious (F) locus in cucumber (Cucumis sativus L.), The Journal of Horticultural Science and Biotechnology, 94(1): 24-32.
  • Jeffrey, C. 1980. A review of the Cucurbitaceae. Botanical Journal of the Linnean Society, 81(3): 233-247.
  • Jeffrey, C. 2001. Cucurbitaceae. In: Hanelt, P. (Ed). Mansfeld’s Encyclopedia of Agricultural and Horticultural Crops. Springer. pp. 1510–1557.
  • Jiang, H., Tian, H., Yan, C., Jia, L., Wang, Y., et al. 2019. RNA-seq analysis of watermelon (Citrullus lanatus) to identify genes involved in fruit cracking, Scientia Horticulturae, 248: 248-255.
  • Kalendar, R., Amenov, A., Daniyarov, A. 2019. Use of retrotransposon-derived genetic markers to analyse genomic variability in plants, Functional Plant Biology, 46(1): 15-29.
  • Kalendar, R., Flavell, A.J., Ellis, T.H.N., Sjakste, T., Moisy, C. et al. 2011. Analysis of plant diversity with retrotransposon-based molecular markers, Heredity, 106(4): 520.
  • Karimi, H.R., Bagheriyan, S., Esmaelizadeh, M., & Estaji, A., 2016, Genetic relationships among melons using RAPD markers, International Journal of Vegetable Science, 22(2): 200-208.
  • Kazazian, H.H. 2004. Mobile elements: drivers of genome evolution, Science, 303(5664): 1626-1632.
  • Kidwell, K.K., Osborn, T.C. 1992. Simple plant DNA Isolation Procedures, In: Beckmann, J.S., Osborn, T.C. (Eds.) Plant Genomes: Methods for Genetic and Physical Mapping. Kluwer Academic Publishers, Dordrecht, The Netherlands. pp. 1-13.
  • Kyriacou, M.C., Leskovar, D.I., Colla, G., Rouphael, Y. 2018. Watermelon and melon fruit quality: The genotypic and agro-environmental factors implicated. Scientia Horticulturae, 234: 393-408.
  • Lanciano, S., Mirouze, M. 2018. Transposable elements: all mobile, all different, some stress responsive, some adaptive?, Current Opinion in Genetics & Development, 49: 106-114.
  • Leigh, F., Kalendar, R., Lea, V., Lee, D., Donini, P., et al. 2003. Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques, Molecular Genetics and Genomics, 269(4): 464-474.
  • Liu, L., Sun, T., Liu, X., Guo, Y., Huang, X., et al. 2019. Genetic analysis and mapping of a striped rind gene (st3) in melon (Cucumis melo L.), Euphytica, 215(2): 20.
  • Marakli, S., Calis, A., Gozukirmizi, N. 2019. Determination of barley-specific retrotransposons’ movements in Pinus nigra ssp. pallasiana varieties: pyramidata and Seneriana, Russian Journal of Genetics, 55(1): 71-78.
  • Martin, A., Troadec, C., Boualem, A., Rajab, M., Fernandez, R., et al. 2009. A transposon-induced epigenetic change leads to sex determination in melon, Nature, 461: 1135-1138.
  • Meyer, R.S., Purugganan, M.D. 2013. Evolution of crop species: genetics of domestication and diversification. Nature Reviews Genetics, 14(12): 840.
  • Morgante, M., De Paoli, E., Radovic, S. 2007. Transposable elements and the plant pan-genomes, Current Opinion in Plant Biology, 10: 149-155.
  • Pandey, A., Khan, M.K., Isik, R., Turkmen, O., Acar, R., et al. 2019. Genetic diversity and population structure of watermelon (Citrullus sp.) genotypes, 3 Biotech, 9(6): 210.
  • Pawełkowicz, M.E., Skarzyńska, A., Pląder, W., Przybecki, Z., 2019, Genetic and molecular bases of cucumber (Cucumis sativus L.) sex determination, Molecular Breeding, 39(3): 50.
  • Renner, S.S., Schaefer, H., Kocyan, A. 2007. Phylogenetics of Cucumis (Cucurbitaceae): cucumber (C. sativus) belongs in an Asian/Australian clade far from melon (C. melo), BMC Evolutionary Biology, 7: 58.
  • Sebastian, P., Schaefer, H., Telford, I.R., Renner, S.S. 2010. Phylogenetic relationships among domesticated and wild species of Cucumis (Cucurbitaceae): The sister species of melon is from Australia, Proceedings of the National Academy of Sciences of the United States of America, 107: 14269-14273.
  • Sun, Y., Fan, M., He, Y. 2019. Transcriptome analysis of watermelon leaves reveals candidate genes responsive to Cucumber green mottle mosaic virus infection, International Journal of Molecular Sciences, 20(3): 610.
  • TÜİK, 2018, http://www.tuik.gov.tr (July, 2018).
  • Yilmaz, S., Marakli, S., Yuzbasioglu, G., Gozukirmizi, N. 2018. Short-term mutagenicity test by using IRAP molecular marker in rice grown under herbicide treatment, Biotechnology and Biotechnological Equipment, 32(4): 923-928.
  • Zaitoun, S.Y.A., Jamous, R.M., Shtaya, M.J., Mallah, O.B., Eid, I.S., et al. 2018. Characterizing Palestinian snake melon (Cucumis melo var. flexuosus) germplasm diversity and structure using SNP and DArTseq markers, BMC Plant Biology, 18(1): 246.
  • Zhang, Y., Yang, T., Li, M., Xu, Y., Lin, F. et al., 2018. Analysis and evaluation of fructose content in watermelon germplasm resources, Southwest China Journal of Agricultural Sciences, 31(4): 786-795.
  • Zhang, W.W., Pan, J.S., He, H.L., Zhang, C., Li, Z., et al. 2012. Construction of a high density integrated genetic map for cucumber (Cucumis sativus L.), Theoretical and Applied Genetics, 124(2): 249-259.
  • Zhang, W., He, H., Guan, Y., Du, H., Yuan, L., et al. 2010. Identification and mapping of molecular markers linked to the tuberculate fruit gene in the cucumber (Cucumis sativus L.), Theoretical and Applied Genetics, 120(3): 645-654.
  • Zhu, W.Y., Huang, L., Chen, L., Yang, J.T., Wu, J.N., et al. 2016. A high-density genetic linkage map for cucumber (Cucumis sativus L.): based on specific length amplified fragment (SLAF) sequencing and QTL analysis of fruit traits in cucumber. Frontiers in Plant Science, 7: 437.

Retrotransposon Analyses in Cucurbitaceae family

Year 2019, Volume 1, Issue 1, 68 - 76, 19.08.2019
https://doi.org/10.38058/ijsl.592537

Abstract

Retrotransposons are class I mobile elements, moving via an RNA intermediate. There are many retrotransposon-based molecular markers. Here, Nikita and Sukkula retrotransposons were investigated in Cucumis sativus L., Citrullus lanatus and Cucumis melo L. by using IRAP (Inter-Retrotransposon Amplified Polymorphism) molecular marker method. These barley-specific retrotransposons were identified in three plant species for the first time. Moreover, band profiles of the retrotransposons were similar in plants, indicating homomorphic band profiles. Findings could provide valuable information for understanding genomes of these plants and evolutionary relationships among them.

References

  • Arumuganathan, K., Earle, E. 1991. Nuclear DNA content of some important plant species, Plant Molecular Biology Reporter, 9: 208.
  • Carvalho, N., Canela, F.M., Leite, P.H.S., Ferreira, M.A., Oliveira, V.R., et al. 2017. Analysis of genetic variability of commercial melon cultivars using SSR molecular markers, Genetics and Molecular Research, 16(3): gmr16039739.
  • Galpaz, N., Gonda, I., Shem‐Tov, D., Barad, O., Tzuri, G., et al. 2018. Deciphering genetic factors that determine melon fruit‐quality traits using RNA‐Seq‐based high‐resolution QTL and eQTL mapping, The Plant Journal, 94(1): 169-191.
  • Garcia-Mas, J., Benjak, A., Sanseverino, W., Bourgeois, M., Mir, G. et al. 2012. The genome of melon (Cucumis melo L.), Proceedings of the National Academy of Sciences, 109(29): 11872-11877.
  • Gómez-Aix, C., Pascual, L., Cañizares, J., Sánchez-Pina, M.A., Aranda, M.A. 2016. Transcriptomic profiling of melon necrotic spot virus-infected melon plants revealed virus strain and plant cultivar-specific alterations, BMC Genomics, 17(1): 429.
  • Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W.J., et al. 2013. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions, Nature Genetics, 45(1): 51.
  • Huala, E., Dickerman, A.W., Garcia-Hernandez, M., Weems, D., Reiser, L. et al. 2001. The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant, Nucleic Acids Research, 29: 102-105.
  • Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., et al. 2009. The genome of the cucumber, Cucumis sativus L, Nature Genetics, 41: 1275-1281.
  • Huang, H.X., Yu, T., Li, J. X., Qu, S.P., Wang, M.M., et al. 2019. Characterization of Cucurbita maxima fruit metabolomic profiling and transcriptome to reveal fruit quality and ripening gene expression patterns, Journal of Plant Biology, 62(3): 203-216.
  • Jat, G.S., Munshi, A.D., Behera, T.K., Choudhary, H., Dash, P., et al. 2019. Genetics and molecular mapping of gynoecious (F) locus in cucumber (Cucumis sativus L.), The Journal of Horticultural Science and Biotechnology, 94(1): 24-32.
  • Jeffrey, C. 1980. A review of the Cucurbitaceae. Botanical Journal of the Linnean Society, 81(3): 233-247.
  • Jeffrey, C. 2001. Cucurbitaceae. In: Hanelt, P. (Ed). Mansfeld’s Encyclopedia of Agricultural and Horticultural Crops. Springer. pp. 1510–1557.
  • Jiang, H., Tian, H., Yan, C., Jia, L., Wang, Y., et al. 2019. RNA-seq analysis of watermelon (Citrullus lanatus) to identify genes involved in fruit cracking, Scientia Horticulturae, 248: 248-255.
  • Kalendar, R., Amenov, A., Daniyarov, A. 2019. Use of retrotransposon-derived genetic markers to analyse genomic variability in plants, Functional Plant Biology, 46(1): 15-29.
  • Kalendar, R., Flavell, A.J., Ellis, T.H.N., Sjakste, T., Moisy, C. et al. 2011. Analysis of plant diversity with retrotransposon-based molecular markers, Heredity, 106(4): 520.
  • Karimi, H.R., Bagheriyan, S., Esmaelizadeh, M., & Estaji, A., 2016, Genetic relationships among melons using RAPD markers, International Journal of Vegetable Science, 22(2): 200-208.
  • Kazazian, H.H. 2004. Mobile elements: drivers of genome evolution, Science, 303(5664): 1626-1632.
  • Kidwell, K.K., Osborn, T.C. 1992. Simple plant DNA Isolation Procedures, In: Beckmann, J.S., Osborn, T.C. (Eds.) Plant Genomes: Methods for Genetic and Physical Mapping. Kluwer Academic Publishers, Dordrecht, The Netherlands. pp. 1-13.
  • Kyriacou, M.C., Leskovar, D.I., Colla, G., Rouphael, Y. 2018. Watermelon and melon fruit quality: The genotypic and agro-environmental factors implicated. Scientia Horticulturae, 234: 393-408.
  • Lanciano, S., Mirouze, M. 2018. Transposable elements: all mobile, all different, some stress responsive, some adaptive?, Current Opinion in Genetics & Development, 49: 106-114.
  • Leigh, F., Kalendar, R., Lea, V., Lee, D., Donini, P., et al. 2003. Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques, Molecular Genetics and Genomics, 269(4): 464-474.
  • Liu, L., Sun, T., Liu, X., Guo, Y., Huang, X., et al. 2019. Genetic analysis and mapping of a striped rind gene (st3) in melon (Cucumis melo L.), Euphytica, 215(2): 20.
  • Marakli, S., Calis, A., Gozukirmizi, N. 2019. Determination of barley-specific retrotransposons’ movements in Pinus nigra ssp. pallasiana varieties: pyramidata and Seneriana, Russian Journal of Genetics, 55(1): 71-78.
  • Martin, A., Troadec, C., Boualem, A., Rajab, M., Fernandez, R., et al. 2009. A transposon-induced epigenetic change leads to sex determination in melon, Nature, 461: 1135-1138.
  • Meyer, R.S., Purugganan, M.D. 2013. Evolution of crop species: genetics of domestication and diversification. Nature Reviews Genetics, 14(12): 840.
  • Morgante, M., De Paoli, E., Radovic, S. 2007. Transposable elements and the plant pan-genomes, Current Opinion in Plant Biology, 10: 149-155.
  • Pandey, A., Khan, M.K., Isik, R., Turkmen, O., Acar, R., et al. 2019. Genetic diversity and population structure of watermelon (Citrullus sp.) genotypes, 3 Biotech, 9(6): 210.
  • Pawełkowicz, M.E., Skarzyńska, A., Pląder, W., Przybecki, Z., 2019, Genetic and molecular bases of cucumber (Cucumis sativus L.) sex determination, Molecular Breeding, 39(3): 50.
  • Renner, S.S., Schaefer, H., Kocyan, A. 2007. Phylogenetics of Cucumis (Cucurbitaceae): cucumber (C. sativus) belongs in an Asian/Australian clade far from melon (C. melo), BMC Evolutionary Biology, 7: 58.
  • Sebastian, P., Schaefer, H., Telford, I.R., Renner, S.S. 2010. Phylogenetic relationships among domesticated and wild species of Cucumis (Cucurbitaceae): The sister species of melon is from Australia, Proceedings of the National Academy of Sciences of the United States of America, 107: 14269-14273.
  • Sun, Y., Fan, M., He, Y. 2019. Transcriptome analysis of watermelon leaves reveals candidate genes responsive to Cucumber green mottle mosaic virus infection, International Journal of Molecular Sciences, 20(3): 610.
  • TÜİK, 2018, http://www.tuik.gov.tr (July, 2018).
  • Yilmaz, S., Marakli, S., Yuzbasioglu, G., Gozukirmizi, N. 2018. Short-term mutagenicity test by using IRAP molecular marker in rice grown under herbicide treatment, Biotechnology and Biotechnological Equipment, 32(4): 923-928.
  • Zaitoun, S.Y.A., Jamous, R.M., Shtaya, M.J., Mallah, O.B., Eid, I.S., et al. 2018. Characterizing Palestinian snake melon (Cucumis melo var. flexuosus) germplasm diversity and structure using SNP and DArTseq markers, BMC Plant Biology, 18(1): 246.
  • Zhang, Y., Yang, T., Li, M., Xu, Y., Lin, F. et al., 2018. Analysis and evaluation of fructose content in watermelon germplasm resources, Southwest China Journal of Agricultural Sciences, 31(4): 786-795.
  • Zhang, W.W., Pan, J.S., He, H.L., Zhang, C., Li, Z., et al. 2012. Construction of a high density integrated genetic map for cucumber (Cucumis sativus L.), Theoretical and Applied Genetics, 124(2): 249-259.
  • Zhang, W., He, H., Guan, Y., Du, H., Yuan, L., et al. 2010. Identification and mapping of molecular markers linked to the tuberculate fruit gene in the cucumber (Cucumis sativus L.), Theoretical and Applied Genetics, 120(3): 645-654.
  • Zhu, W.Y., Huang, L., Chen, L., Yang, J.T., Wu, J.N., et al. 2016. A high-density genetic linkage map for cucumber (Cucumis sativus L.): based on specific length amplified fragment (SLAF) sequencing and QTL analysis of fruit traits in cucumber. Frontiers in Plant Science, 7: 437.

Details

Primary Language English
Subjects Basic Sciences
Journal Section Research Articles
Authors

Sevgi MARAKLİ>

0000-0001-5796-7819
Türkiye

Publication Date August 19, 2019
Published in Issue Year 2019, Volume 1, Issue 1

Cite

Bibtex @research article { ijsl592537, journal = {International Journal of Science Letters}, eissn = {2687-4733}, address = {Amasya University, Central Research Laboratory, 05100 İpekköy-AMASYA}, publisher = {Amasya University}, year = {2019}, volume = {1}, number = {1}, pages = {68 - 76}, doi = {10.38058/ijsl.592537}, title = {Retrotransposon Analyses in Cucurbitaceae family}, key = {cite}, author = {Marakli, Sevgi} }
APA Marakli, S. (2019). Retrotransposon Analyses in Cucurbitaceae family . International Journal of Science Letters , 1 (1) , 68-76 . DOI: 10.38058/ijsl.592537
MLA Marakli, S. "Retrotransposon Analyses in Cucurbitaceae family" . International Journal of Science Letters 1 (2019 ): 68-76 <https://dergipark.org.tr/en/pub/ijsl/issue/47946/592537>
Chicago Marakli, S. "Retrotransposon Analyses in Cucurbitaceae family". International Journal of Science Letters 1 (2019 ): 68-76
RIS TY - JOUR T1 - Retrotransposon Analyses in Cucurbitaceae family AU - SevgiMarakli Y1 - 2019 PY - 2019 N1 - doi: 10.38058/ijsl.592537 DO - 10.38058/ijsl.592537 T2 - International Journal of Science Letters JF - Journal JO - JOR SP - 68 EP - 76 VL - 1 IS - 1 SN - -2687-4733 M3 - doi: 10.38058/ijsl.592537 UR - https://doi.org/10.38058/ijsl.592537 Y2 - 2019 ER -
EndNote %0 International Journal of Science Letters Retrotransposon Analyses in Cucurbitaceae family %A Sevgi Marakli %T Retrotransposon Analyses in Cucurbitaceae family %D 2019 %J International Journal of Science Letters %P -2687-4733 %V 1 %N 1 %R doi: 10.38058/ijsl.592537 %U 10.38058/ijsl.592537
ISNAD Marakli, Sevgi . "Retrotransposon Analyses in Cucurbitaceae family". International Journal of Science Letters 1 / 1 (August 2019): 68-76 . https://doi.org/10.38058/ijsl.592537
AMA Marakli S. Retrotransposon Analyses in Cucurbitaceae family. IJSL. 2019; 1(1): 68-76.
Vancouver Marakli S. Retrotransposon Analyses in Cucurbitaceae family. International Journal of Science Letters. 2019; 1(1): 68-76.
IEEE S. Marakli , "Retrotransposon Analyses in Cucurbitaceae family", International Journal of Science Letters, vol. 1, no. 1, pp. 68-76, Aug. 2019, doi:10.38058/ijsl.592537