Genome-wide Identification of PMEI Genes in Wild Olives (Olea europaea sylvestris L.) by Bioinformatic Analysis
DOI:
https://doi.org/10.24925/turjaf.v12i6.1005-1018.6757Keywords:
wild olive, bioinformatics, PMEI, genome-wideAbstract
In the present study, 47 PMEI type 1 genes and 57 PMEI type 2 genes were identified with bioinformatic analysis. The PMEI genes were localized separately on chromosomes 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21 and 22, but mainly at the level of the scaffold. The biological functions of the PMEI type 1 genes were found to be in the areas of biological regulation, metabolism and cellular functions. Their cellular localization appears to be associated with cell parts. For the PMEI type 2 genes, the biological functions were determined as biological regulation, metabolic and cellular functions. A total of 393 Arabidopsis miRNAs targeting 47 olive PMEI type 1 genes were identified. Two specific miRNAs targeting the OePMEI1-07 gene were found (ath-miR8168 and ath-miR774b-5p). For the PMEI type 2 genes, 269 Arabidopsis miRNAs were found, including 14 specific miRNAs targeting OPMEI2-02, OPMEI2-03, OPMEI2-27, OPMEI2-28, OPMEI2-29, OPMEI2-30, OPMEI2-40 and OPMEI2-54. These results suggest that PMEI genes in olives may not only play a role in cell development, germ cell formation and plant growth, but also play an important role in abiotic and biotic stress conditions in the olive.
References
Aabidine, A. Z. E., Charafi, J., Grout, C., Doligez, A., Santoni, S., Moukhli, A., Jay-Allemand, C., El Modafar, C. & Khadari, B. (2010). Construction of a genetic linkage map for the olive based on AFLP and SSR markers. Crop science, 50(6), 2291-2302.
Ayed, R. B., Ennouri, K., & Rebai, A. (2018). Involvement of SNP marker located on the Calcium binding protein gene in adaptive traits and organoleptic performances of the olive tree. Journal of Fundamental and Applied Sciences, 10(1), 328-343.
Bailey, T. L., Johnson, J., Grant, C. E., & Noble, W. S. (2015). The MEME suite. Nucleic acids research, 43(W1), W39-W49.
Beiki, A. H., Saboor, S., & Ebrahimi, M. (2012). A new avenue for classification and prediction of olive cultivars using supervised and unsupervised algorithms.
Belaj, A., Satovic, Z., Ismaili, H., Panajoti, D., Rallo, L., & Trujillo, I. (2003). RAPD genetic diversity of Albanian olive germplasm and its relationships with other Mediterranean countries. Euphytica, 130, 387-395.
Ben Ayed, R., Ben Hassen, H., Ennouri, K., & Rebai, A. (2016). Genetic markers analyses and bioinformatic approaches to distinguish between olive tree (Olea europaea L.) cultivars. Interdisciplinary Sciences: Computational Life Sciences, 8, 366-373.
Brake, M., Migdadi, H., Al-Gharaibeh, M., Ayoub, S., Haddad, N., & El Oqlah, A. (2014). Characterization of Jordanian olive cultivars (Olea europaea L.) using RAPD and ISSR molecular markers. Scientia Horticulturae, 176, 282-289.
Büyük, İ., Inal, B., Ilhan, E., Tanriseven, M., Aras, S., & Erayman, M. (2016). Genome-wide identification of salinity responsive HSP70 s in common bean. Molecular biology reports, 43, 1251-1266.
Cao, J. Y., Xu, Y. P., & Cai, X. Z. (2020). Integrated miRNAome and transcriptome analysis reveals argonaute 2-mediated defense responses against the devastating phytopathogen Sclerotinia sclerotiorum. Frontiers in Plant Science, 11, 500.
Coculo, D., & Lionetti, V. (2022). The plant invertase/pectin methylesterase inhibitor superfamily. Frontiers in Plant science, 13, 863892.
Conesa, A., Götz, S., García-Gómez, J. M., Terol, J., Talón, M., & Robles, M. (2005). Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18), 3674-3676.
Dai, X., Zhuang, Z., & Zhao, P. X. (2018). psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic acids research, 46(W1), W49-W54.
De la Rosa, R., Angiolillo, A., Guerrero, C., Pellegrini, M., Rallo, L., Besnard, G., Berville, A., Martin, A. & Baldoni, L. (2003). A first linkage map of olive (Olea europaea L.) cultivars using RAPD, AFLP, RFLP and SSR markers. Theoretical and Applied Genetics, 106(7), 1273-1282.
Deytieux-Belleau, C., Vallet, A., Donèche, B., & Geny, L. (2008). Pectin methylesterase and polygalacturonase in the developing grape skin. Plant Physiology and Biochemistry, 46(7), 638-646.
Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S. E., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server (pp. 571-607). Humana press.
Hu, B., Jin, J., Guo, A. Y., Zhang, H., Luo, J., & Gao, G. (2015). GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 31(8), 1296-1297.
Husna, N., Putri, A. E., & Martha, D. F. (2021). Genome-wide identification and characterization of the pectin methylesterase (PME) and pectin methylesterase inhibitor (PMEI) gene family in the banana A-genome (Musa acuminata) and B-genome (Musa balbisiana). Research Journal of Biotechnology Vol, 16, 2.
Keegstra, K. (2010). Plant cell walls. Plant physiology, 154(2), 483-486.
Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature protocols, 10(6), 845-858.
Kozomara, A., Birgaoanu, M., & Griffiths-Jones, S. (2019). miRBase: from microRNA sequences to function. Nucleic acids research, 47(D1), D155-D162.
Li, B., Wang, H., He, S., Ding, Z., Wang, Y., Li, N., Hao, X., Wang, L., Yang, Y. & Qian, W. (2022). Genome-wide identification of the PMEI gene family in tea plant and functional analysis of CsPMEI2 and CsPMEI4 through ectopic overexpression. Frontiers in Plant Science, 12, 807514.
Maldonado, N. G., López, M. J., Caudullo, G., & De Rigo, D. (2016). Olea europaea in Europe: Distribution, habitat, usage and threats. European Atlas of Forest Tree Species, Publ. Off. EU, Luxembourg. pp. 01534b.
NCBI. 2022. https://www.ncbi.nlm.nih.gov/gene/
Ozturk, M., Altay, V., Gönenç, T. M., Unal, B. T., Efe, R., Akçiçek, E., & Bukhari, A. (2021). An overview of olive cultivation in Turkey: Botanical features, eco-physiology and phytochemical aspects. Agronomy, 11(2), 295.
Qiagen, 2022. CLC Genomic Workbench 21. https://digitalinsights.qiagen.com/.
Rakhmetullina, A., Ivashchenko, A., Pyrkova, A., Uteulin, K., & Zielenkiewicz, P. (2023). In silico analysis of maize and wheat miRNAs as potential regulators of human gene expression. ExRNA, 5.
Sesli, M., & Yegenoglu, E. D. (2017). Genetic relationships in wild olives (Olea europaea ssp. oleaster) by ISSR and RAPD markers. Biotechnology & Biotechnological Equipment, 31(5), 897-904.
Sevindik, E. (2019). In silico analysis of putative polyphenol oxidases in olive using bioinformatics tools. Bangladesh Journal of Botany, 48(1), 17-24.
Showalter, A. M. (1993). Structure and function of plant cell wall proteins. The plant cell, 5(1), 9.
Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: molecular evolutionary genetics analysis version 11. Molecular biology and evolution, 38(7), 3022-3027.
Vidal, E. A., Tamayo, K. P., & Gutierrez, R. A. (2010). Gene networks for nitrogen sensing, signaling, and response in Arabidopsis thaliana. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 2(6), 683-693.
Wang, L., Gao, Y., Wang, S., Zhang, Q., & Yang, S. (2021). Genome-wide identification of PME genes, evolution and expression analyses in soybean (Glycine max L.). BMC Plant Biology, 21(1), 1-20.
Wang, Y., Zhang, D., Huang, L., Zhang, Z., Gao, J., Liu, W., Gan, H., Guo, X., Shan, C. & Hu, J. (2022). Research progress of pectin methylesterase and its inhibitors. Current Protein and Peptide Science, 23(10), 684-696.
Wong, D. (2008). Enzymatic deconstruction of backbone structures of the ramified regions in pectins. The protein journal, 27, 30-42.
WUR (2022). MapChart. https://www.wur.nl/en/show/mapchart.htm
Xue, C., Guan, S. C., Chen, J. Q., Wen, C. J., Cai, J. F., & Chen, X. (2020). Genome wide identification and functional characterization of strawberry pectin methylesterases related to fruit softening. BMC plant biology, 20(1), 1-17.
Zhang, P., Wang, H., Qin, X., Chen, K., Zhao, J., Zhao, Y., & Yue, B. (2019). Genome-wide identification, phylogeny and expression analysis of the PME and PMEI gene families in maize. Scientific reports, 9(1), 19918.
Downloads
Published
How to Cite
Issue
Section
License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
