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Year 2022, Volume: 9 Issue: 3, 251 - 258, 30.09.2022

Aysel Özgül Koral Mine Türktaş

https://doi.org/10.54287/gujsa.1142153

Abstract

References

  • Ahmadi, S. H., Agharezaee, M., Kamgar-Haghighi, A. A., & Sepaskhah, A. R. (2017). Compatibility of root growth and tuber production of potato cultivars with dynamic and static water-saving irrigation managements. Soil Use and Management, 33(1), 106-119. doi:10.1111/sum.12317
  • Aversano, R., Contaldi, F., Ercolano, M. R., Grosso, V., Iorizzo, M., Tatino, F., Xumerle, L., Molin, A. D., Avanzato, C., Ferrarini, A., Delledonne, M., Sanseverino, W., Cigliano, R. A., Capella-Gutierrez, S.,
  • Gabaldón, T., Frusciante, L., Bradeen, J. M., & Carputo, D. (2015). The Solanum commersonii genome sequence provides insights into adaptation to stress conditions and genome evolution of wild potato relatives. The Plant Cell, 27(4), 954-968. doi:10.1105/tpc.114.135954
  • Chapman, H. W. (1958). Tuberization in the Potato Plant. Physiologia Plantarum, 11, 215-224. doi:10.1111/j.1399-3054.1958.tb08460.x
  • Cheng, H.-Y., Wang, Y., Tao, X., Fan, Y.-F., Dai, Y., Yang, H., & Ma, X.-R. (2016). Genomic Profiling of Exogenous Abscisic Acid-Responsive MicroRNAs in Tomato (Solanum lycopersicum). BMC Genomics, 17(1), 423. doi:10.1186/s12864-016-2591-8
  • Chi, M., Liu, C., Su, Y., Tong, Y., & Liu, H. (2015). Bioinformatic Prediction of Upstream MicroRNAs of PPO and Novel MicroRNAs in Potato. Canadian Journal of Plant Science, 95(5), 871-877. doi:10.4141/cjps-2014-308
  • de Oliveira, A. S., Boiteux, L. S., Kormelink, R., & Resende, R. O. (2018). The Sw-5 Gene Cluster: Tomato Breeding and Research Toward Orthotospovirus Disease Control. Frontiers in Plant Science, 9, 1055. doi:10.3389/fpls.2018.01055
  • Dilsiz, S., & Yorgancılar, M. (2018). Patates (Solanum Tuberosum L.) Bitkisinde Sakkaroz ve Oksin-Sitokinin Uygulamalarının Mikro Yumru Oluşumuna Etkileri. Selçuk Tarım ve Gıda Bilimleri Dergisi, 32(3), 274-281. doi:10.15316/SJAFS.2018.94
  • Fujii, H., Chinnusamy, V., Rodrigues, A., Rubio, S., Antoni, R., Park, S.-Y., Cutler, S. R., Sheen, J., Rodriguez, P. L., & Zhu, J.-K. (2009). In vitro Reconstitution of an Abscisic acid Signalling Pathway. Nature, 462, 660-664. doi:10.1038/nature08599
  • Hajjar, R., & Hodgkin, T. (2007). The Use of Wild Relatives in Crop Improvement: A Survey Of Developments over The Last 20 Years. Euphytica, 156(1-2), 1-13. doi:10.1007/s10681-007-9363-0
  • Hanneman, R. E. Jr., & Bamberg, J. B. (1986). Inventory of Tuber-Bearing Solanum Species. Bulletin 533 of Research Division of the College of Agriculture and Life Sciences, University of Wisconsin, Madison USA.
  • Johnson, K. L., Cassin, A. M., Lonsdale, A., Wong, G. K.-S., Soltis, D. E., Miles, N. W., Melkonian, M., Melkonian, B., Deyholos, M. K., Leebens-Mack, J., Rothfels, C. J., Stevenson, D. W., Graham, S. W., Wang, X., Wu, S., Pires, J. C., Edger, P. P., Carpenter, E. J., Bacic, A., … Schultz, C. J. (2017). Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes. Plant Physiology, 174(2), 904-921. doi:10.1104/pp.17.00295
  • Jia, Q., Kong, D., Li, Q., Sun, S., Song, J., Zhu, Y., Liang, K., Ke, Q., Lin, W., Huang, J. (2019). The Function of Inositol Phosphatases in Plant Tolerance to Abiotic Stress. International Journal of Molecular Sciences, 20(16), 3999. doi:10.3390/ijms20163999
  • Kondhare, K. R., Malankar, N. N., Devani, R. S., & Banerjee, A. K. (2018). Genome-Wide Transcriptome Analysis Reveals Small RNA Profiles Involved in Early Stages of Stolon-to-Tuber Transitions in Potato under Photoperiodic Conditions. BMC Plant Biology, 18(1), 284. doi:10.1186/s12870-018-1501-4
  • Kondhare, K. R., Natarajan, B., & Banerjee, A. K. (2020). Molecular Signals that Govern Tuber Development in Potato. The International Journal of Developmental Biology, 64(1-2-3), 133-140. doi:10.1387/ijdb.190132ab
  • Kim, J., Jung, J.-H., Reyes, J. L., Kim, Y.-S., Kim, S.-Y., Chung, K.-S., Kim, J. A., Lee, M., Lee, Y., Narry Kim, V., Chua, N.-H., & Park, C.-M. (2005). microRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. The Plant Journal, 42(1), 84-94. doi:10.1111/j.1365-313X.2005.02354.x
  • Lakhotia, N., Joshi, G., Bhardwaj, A. R., Katiyar-Agarwal, S., Agarwal, M., Jagannath, A., Goel, S., & Kumar, A. (2014). Identification and Characterization of miRNAome in Root, Stem, Leaf and Tuber Developmental Stages of Potato (Solanum tuberosum L.) by High-Throughput Sequencing. BMC Plant Biology, 14(1), 6. doi:10.1186/1471-2229-14-6
  • Liu, Y., Teng, C., Xia, R., & Meyers, B. C. (2020). PhasiRNAs in Plants: Their Biogenesis, Genic Sources, and Roles in Stress Responses, Development, and Reproduction. The Plant Cell, 32(10), 3059-3080. doi:10.1105/tpc.20.00335
  • Marín-González, E., & Suárez-López, P. (2012). "And yet it moves": Cell-to-Cell and Long-Distance Signaling by Plant MicroRNAs. Plant Science, 196, 18-30. doi:10.1016/j.plantsci.2012.07.009
  • Marschner, H., Sattelmacher, B. & Bangerth, F. (1984). Growth Rate of Potato Tubers and Endogeneous Contents of Indolylacetic Acid. Physiologia Plantarum, 60(1), 16-20. doi:10.1111/j.1399-3054.1984.tb04242.x
  • Natarajan, B., Bhogale, S. & Banerjee, A. K. (2017). The Essential Role of MicroRNAs in Potato Tuber Development: a mini review. Indian Journal of Plant Physiology, 22(4), 401-410. doi:10.1007/s40502-017-0324-x
  • Ross, H. A., Wright, K. M., McDougall, G. J., Roberts, A. G., Chapman, S. N., Morris, W. L., Hancock, R. D., Stewart, D., Tucker, G. A., James, E. K., & Taylor, M. A. (2011). Potato Tuber Pectin Structure is Influenced by Pectin Methyl Esterase Activity and Impacts on Cooked Potato Texture. Journal of Experimental Botany, 62(1), 371-381. doi:10.1093/jxb/erq280
  • Seo, E., Kim, T., Park, J. H., Yeom, S.-I., Kim, S., Seo, M.-K., Shin, C., & Choi, D. (2018). Genome-Wide Comparative Analysis in Solanaceous Species Reveals Evolution of Micrornas Targeting Defense Genes in Capsicum spp. DNA Research : An International Journal for Rapid Publication of Reports on Genes and Genomes, 25(6), 561-575. doi:10.1093/dnares/dsy025
  • Shanmugavadivel, P. S., Soren, K. R., Konda, A. K., Chaturvedi, S. K., & Singh, N. P. (2016). Identification of Potential Stress Responsive Micrornas and Their Targets in Cajanus spp. Agri Gene, 1, 33-37. doi:10.1016/j.aggene.2016.06.001
  • Xia, R., Meyers, B. C., Liu, Z., Beers, E. P., Ye, S., & Liu, Z. (2013). MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots. The Plant Cell, 25(5), 1555-1572. doi:10.1105/tpc.113.110957
  • Yan, C., Wang, Q., Zhang, N., Wang, J., Ren, X., Xue, B., Pu, X., Xu, Z., & Liao, H. (2020). High-Throughput MicroRNA and mRNA Sequencing Reveals that MicroRNAs May Be Involved in Pectinesterase-Mediated Cold Resistance in Potato. Phyton-International Journal of Experimental Botany, 89(3), 561-586. doi:10.32604/phyton.2020.010322

In silico Analyzes of miRNAs Associated with Root and Tuber in S. commersonii

Year 2022, Volume: 9 Issue: 3, 251 - 258, 30.09.2022

Aysel Özgül Koral Mine Türktaş

https://doi.org/10.54287/gujsa.1142153

Abstract

Potato is an industrial plant that is produced and consumed globally due to its cheapness, high yield in the unit area, high nutritional values. It is used in many different fields. It has been stated that wild species with various characteristics can be used in studies to increase productivity because they have greater rate of genetic variation than their domesticated relatives. One of the wild species of potato found in nature is S. commersonii Dunal. It is more resistant to many stresses than cultivated potato S. tuberosum L. Also, its tuber has better quality due to the fact that it contains a higher proportion of dry matter. With the aim of determining the effects of miRNAs in tuber production and root characteristics relation we aimed to detect miRNAs in two transcriptome libraries of S. commersonii. In this study miRNAs were evaluated for the first time in the wild potato transcriptome data using in silico analysis. A number of miRNAs were identified, and their potential roles in tuber were discussed.

Keywords

Bioinformatics miRNA Root Solanum Commersonii Tuber

References

  • Ahmadi, S. H., Agharezaee, M., Kamgar-Haghighi, A. A., & Sepaskhah, A. R. (2017). Compatibility of root growth and tuber production of potato cultivars with dynamic and static water-saving irrigation managements. Soil Use and Management, 33(1), 106-119. doi:10.1111/sum.12317
  • Aversano, R., Contaldi, F., Ercolano, M. R., Grosso, V., Iorizzo, M., Tatino, F., Xumerle, L., Molin, A. D., Avanzato, C., Ferrarini, A., Delledonne, M., Sanseverino, W., Cigliano, R. A., Capella-Gutierrez, S.,
  • Gabaldón, T., Frusciante, L., Bradeen, J. M., & Carputo, D. (2015). The Solanum commersonii genome sequence provides insights into adaptation to stress conditions and genome evolution of wild potato relatives. The Plant Cell, 27(4), 954-968. doi:10.1105/tpc.114.135954
  • Chapman, H. W. (1958). Tuberization in the Potato Plant. Physiologia Plantarum, 11, 215-224. doi:10.1111/j.1399-3054.1958.tb08460.x
  • Cheng, H.-Y., Wang, Y., Tao, X., Fan, Y.-F., Dai, Y., Yang, H., & Ma, X.-R. (2016). Genomic Profiling of Exogenous Abscisic Acid-Responsive MicroRNAs in Tomato (Solanum lycopersicum). BMC Genomics, 17(1), 423. doi:10.1186/s12864-016-2591-8
  • Chi, M., Liu, C., Su, Y., Tong, Y., & Liu, H. (2015). Bioinformatic Prediction of Upstream MicroRNAs of PPO and Novel MicroRNAs in Potato. Canadian Journal of Plant Science, 95(5), 871-877. doi:10.4141/cjps-2014-308
  • de Oliveira, A. S., Boiteux, L. S., Kormelink, R., & Resende, R. O. (2018). The Sw-5 Gene Cluster: Tomato Breeding and Research Toward Orthotospovirus Disease Control. Frontiers in Plant Science, 9, 1055. doi:10.3389/fpls.2018.01055
  • Dilsiz, S., & Yorgancılar, M. (2018). Patates (Solanum Tuberosum L.) Bitkisinde Sakkaroz ve Oksin-Sitokinin Uygulamalarının Mikro Yumru Oluşumuna Etkileri. Selçuk Tarım ve Gıda Bilimleri Dergisi, 32(3), 274-281. doi:10.15316/SJAFS.2018.94
  • Fujii, H., Chinnusamy, V., Rodrigues, A., Rubio, S., Antoni, R., Park, S.-Y., Cutler, S. R., Sheen, J., Rodriguez, P. L., & Zhu, J.-K. (2009). In vitro Reconstitution of an Abscisic acid Signalling Pathway. Nature, 462, 660-664. doi:10.1038/nature08599
  • Hajjar, R., & Hodgkin, T. (2007). The Use of Wild Relatives in Crop Improvement: A Survey Of Developments over The Last 20 Years. Euphytica, 156(1-2), 1-13. doi:10.1007/s10681-007-9363-0
  • Hanneman, R. E. Jr., & Bamberg, J. B. (1986). Inventory of Tuber-Bearing Solanum Species. Bulletin 533 of Research Division of the College of Agriculture and Life Sciences, University of Wisconsin, Madison USA.
  • Johnson, K. L., Cassin, A. M., Lonsdale, A., Wong, G. K.-S., Soltis, D. E., Miles, N. W., Melkonian, M., Melkonian, B., Deyholos, M. K., Leebens-Mack, J., Rothfels, C. J., Stevenson, D. W., Graham, S. W., Wang, X., Wu, S., Pires, J. C., Edger, P. P., Carpenter, E. J., Bacic, A., … Schultz, C. J. (2017). Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes. Plant Physiology, 174(2), 904-921. doi:10.1104/pp.17.00295
  • Jia, Q., Kong, D., Li, Q., Sun, S., Song, J., Zhu, Y., Liang, K., Ke, Q., Lin, W., Huang, J. (2019). The Function of Inositol Phosphatases in Plant Tolerance to Abiotic Stress. International Journal of Molecular Sciences, 20(16), 3999. doi:10.3390/ijms20163999
  • Kondhare, K. R., Malankar, N. N., Devani, R. S., & Banerjee, A. K. (2018). Genome-Wide Transcriptome Analysis Reveals Small RNA Profiles Involved in Early Stages of Stolon-to-Tuber Transitions in Potato under Photoperiodic Conditions. BMC Plant Biology, 18(1), 284. doi:10.1186/s12870-018-1501-4
  • Kondhare, K. R., Natarajan, B., & Banerjee, A. K. (2020). Molecular Signals that Govern Tuber Development in Potato. The International Journal of Developmental Biology, 64(1-2-3), 133-140. doi:10.1387/ijdb.190132ab
  • Kim, J., Jung, J.-H., Reyes, J. L., Kim, Y.-S., Kim, S.-Y., Chung, K.-S., Kim, J. A., Lee, M., Lee, Y., Narry Kim, V., Chua, N.-H., & Park, C.-M. (2005). microRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. The Plant Journal, 42(1), 84-94. doi:10.1111/j.1365-313X.2005.02354.x
  • Lakhotia, N., Joshi, G., Bhardwaj, A. R., Katiyar-Agarwal, S., Agarwal, M., Jagannath, A., Goel, S., & Kumar, A. (2014). Identification and Characterization of miRNAome in Root, Stem, Leaf and Tuber Developmental Stages of Potato (Solanum tuberosum L.) by High-Throughput Sequencing. BMC Plant Biology, 14(1), 6. doi:10.1186/1471-2229-14-6
  • Liu, Y., Teng, C., Xia, R., & Meyers, B. C. (2020). PhasiRNAs in Plants: Their Biogenesis, Genic Sources, and Roles in Stress Responses, Development, and Reproduction. The Plant Cell, 32(10), 3059-3080. doi:10.1105/tpc.20.00335
  • Marín-González, E., & Suárez-López, P. (2012). "And yet it moves": Cell-to-Cell and Long-Distance Signaling by Plant MicroRNAs. Plant Science, 196, 18-30. doi:10.1016/j.plantsci.2012.07.009
  • Marschner, H., Sattelmacher, B. & Bangerth, F. (1984). Growth Rate of Potato Tubers and Endogeneous Contents of Indolylacetic Acid. Physiologia Plantarum, 60(1), 16-20. doi:10.1111/j.1399-3054.1984.tb04242.x
  • Natarajan, B., Bhogale, S. & Banerjee, A. K. (2017). The Essential Role of MicroRNAs in Potato Tuber Development: a mini review. Indian Journal of Plant Physiology, 22(4), 401-410. doi:10.1007/s40502-017-0324-x
  • Ross, H. A., Wright, K. M., McDougall, G. J., Roberts, A. G., Chapman, S. N., Morris, W. L., Hancock, R. D., Stewart, D., Tucker, G. A., James, E. K., & Taylor, M. A. (2011). Potato Tuber Pectin Structure is Influenced by Pectin Methyl Esterase Activity and Impacts on Cooked Potato Texture. Journal of Experimental Botany, 62(1), 371-381. doi:10.1093/jxb/erq280
  • Seo, E., Kim, T., Park, J. H., Yeom, S.-I., Kim, S., Seo, M.-K., Shin, C., & Choi, D. (2018). Genome-Wide Comparative Analysis in Solanaceous Species Reveals Evolution of Micrornas Targeting Defense Genes in Capsicum spp. DNA Research : An International Journal for Rapid Publication of Reports on Genes and Genomes, 25(6), 561-575. doi:10.1093/dnares/dsy025
  • Shanmugavadivel, P. S., Soren, K. R., Konda, A. K., Chaturvedi, S. K., & Singh, N. P. (2016). Identification of Potential Stress Responsive Micrornas and Their Targets in Cajanus spp. Agri Gene, 1, 33-37. doi:10.1016/j.aggene.2016.06.001
  • Xia, R., Meyers, B. C., Liu, Z., Beers, E. P., Ye, S., & Liu, Z. (2013). MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots. The Plant Cell, 25(5), 1555-1572. doi:10.1105/tpc.113.110957
  • Yan, C., Wang, Q., Zhang, N., Wang, J., Ren, X., Xue, B., Pu, X., Xu, Z., & Liao, H. (2020). High-Throughput MicroRNA and mRNA Sequencing Reveals that MicroRNAs May Be Involved in Pectinesterase-Mediated Cold Resistance in Potato. Phyton-International Journal of Experimental Botany, 89(3), 561-586. doi:10.32604/phyton.2020.010322
There are 26 citations in total.

Details

Primary Language English
Journal Section Biology
Authors

Aysel Özgül Koral 0000-0002-1206-5130

Mine Türktaş 0000-0001-8089-3774

Publication Date September 30, 2022
Submission Date July 7, 2022
Published in Issue Year 2022 Volume: 9 Issue: 3

Cite

APA Koral, A. Ö., & Türktaş, M. (2022). In silico Analyzes of miRNAs Associated with Root and Tuber in S. commersonii. Gazi University Journal of Science Part A: Engineering and Innovation, 9(3), 251-258. https://doi.org/10.54287/gujsa.1142153
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