بررسی گستره ژنومی خانواده ژنی CIPK در گیاه هالوفیت آلوروپوس لیتورالیس (.Aeluropus littoralis L)

Albrecht, V., Weinl, S., Blazevic, D., D'angelo, C., Batistic, O., Kolukisaoglu, Ü., Bock, R., Schulz, B., Harter, K., Kudla, J., 2003. The calcium sensor CBL1 integrates plant responses to abiotic stresses. The Plant Journal. 36, 457-470.

Armenteros, J.J.A., Tsirigos, K.D., Sønderby, C.K., Petersen, T.N., Winther, O., Brunak, S., Von Heijne, G., Nielsen, H., 2019. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nature biotechnology. 37, 420-423.

Bailey, T.L., Boden, M., Buske, F.A., Frith, M., Grant, C.E., Clementi, L., Ren, J., Li, W.W., Noble, W.S., 2009. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research. 37, 202-208.

Barhoumi, Z., Djebali, W., Smaoui, A., Chaïbi, W., Abdelly, C., 2007. Contribution of NaCl excretion to salt resistance of Aeluropus littoralis (Willd) Parl. Journal of Plant Physiology. 164, 842-850.

Ben-Saad, R., Ben-Ramdhan, W., Zouari, N., Azaza, J., Mieulet, D., Guiderdoni, E., Ellouz, R., Hassairi, A., 2012. Marker-free transgenic durum wheat cv. Karim expressing the AlSAP gene exhibits a high level of tolerance to salinity and dehydration stresses. Molecular Breeding. 30, 521-533.

Bowe, L.M., Coat, G., Depamphilis, C.W., 2000. Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers. Proceedings of the National Academy of Sciences. 97, 4092-4097.

Dodd, A.N., Kudla, J., Sanders, D., 2010. The language of calcium signaling. Annual Review of Plant Biology. 61, 593-620.

El-Gebali, S., Mistry, J., Bateman, A., Eddy, S.R., Luciani, A., Potter, S.C., Qureshi, M., Richardson, L.J., Salazar, G.A., Smart, A., 2019. The Pfam protein families database in 2019. Nucleic acids research. 47, D427-D432.

Evrard, A., 2013. Cell type-specific transcriptional responses of plants to salinity Doctoral Thesis. Faculty of Sciences, the University of Adelaide and Montpellier SupAgro, USA.

Fatemi, F., Hashemi-Petroudi, S.H., Nematzadeh, G., Askari, H., Abdollahi, M.R., 2019. Exploiting differential gene expression to discover ionic and osmotic-associated transcripts in the halophyte grass Aeluropus littoralis. Biological Procedures Online. 21, 1-6.

Felsenstein, J., 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39, 783-791.

Gasteiger, E., Hoogland, C., Gattiker, A., Wilkins, M.R., Appel, R.D., Bairoch, A., 2005. Protein identification and analysis tools on the ExPASy server. In: Walker, J.M. (ed.), The proteomics protocols handbook. Humana Press, New York, United States, pp. 571-607.

Hall, T., Biosciences, I., Carlsbad, C., 2011. BioEdit: an important software for molecular biology. GERF Bull Biosci. 2, 60-61.

Hashemi-Petroudi, S., Nematzadeh, G., Mohammadi, S., Kuhlmann, M., 2020. Expression pattern analysis of heat shock transcription factors (HSFs) gene family in Aeluropus littoralis under salinity stress. Environmental Stresses in Crop Sciences. 13(2), 571-81. [In Persian with English summary].

Hashemi-Petroudi, S.H., Mohammadi, S., 2020. Identification of the ERF gene family in Aeluropus littoralis halophyte plant and analysis of their expression pattern in response to salt stress. Crop Biotechnology. 9, 53-66. [In Persian with English summary].

Hashemi-Petroudi, S.H., Nematzadeh, G., Kuhlmann, M., 2019. Identification and analysis of a DEVIL paralog gene cluster in Aeluropus littoralis by a comparative genomic approach. Crop Biotechnology. 9, 75-87. [In Persian with English summary].

Hashemi, S.H., Arab, M., Dolatabadi, B., Kuo, Y.-T., Baez, M.A., Himmelbach, A., Nematzadeh, G., Maibody, S.a.M.M., Schmutzer, T., Mälzer, M., 2022. Initial Description of the Genome of Aeluropus Littoralis, a Halophile Grass. Frontiers in Plant Science. 13, 906462

Horton, P., Park, K.-J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C., Nakai, K., 2007. WoLF PSORT: protein localization predictor. Nucleic Acids Research. 35, 585-587.

Hu, B., Jin, J., Guo, A.-Y., Zhang, H., Luo, J., Gao, G., 2014. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 31, 1296-1297.

Hu, W., Xia, Z., Yan, Y., Ding, Z., Tie, W., Wang, L., Zou, M., Wei, Y., Lu, C., Hou, X., 2015. Genome-wide gene phylogeny of CIPK family in cassava and expression analysis of partial drought-induced genes. Frontiers in Plant Science. 6, 914.

Hulo, N., Bairoch, A., Bulliard, V., Cerutti, L., De Castro, E., Langendijk-Genevaux, P.S., Pagni, M., Sigrist, C.J., 2006. The PROSITE database. Nucleic Acids Research. 34(suppl_1), D227-D230.

Jalili, M.M., Haddad, M.A., Housaindokht, M.R., 2019. Biocomputational investigations of dtructural and functional properties of cry proteins for malaria biocontrol. Biological Journal of Microorganism. 8(29), 25-40.

Ji, H., Pardo, J.M., Batelli, G., Van Oosten, M.J., Bressan, R.A., Li, X., 2013. The Salt Overly Sensitive (SOS) pathway: established and emerging roles. Molecular plant. 6, 275-286.

Jones, P., Binns, D., Chang, H.-Y., Fraser, M., Li, W., Mcanulla, C., Mcwilliam, H., Maslen, J., Mitchell, A., Nuka, G., 2014. InterProScan 5: genome-scale protein function classification. Bioinformatics. 30, 1236-1240.

Kim, B.G., Waadt, R., Cheong, Y.H., Pandey, G.K., Dominguez‐Solis, J.R., Schültke, S., Lee, S.C., Kudla, J., Luan, S., 2007. The calcium sensor CBL10 mediates salt tolerance by regulating ion homeostasis in Arabidopsis. The Plant Journal. 52, 473-484.

Kolukisaoglu, Ü., Weinl, S., Blazevic, D., Batistic, O., Kudla, J., 2004. Calcium sensors and their interacting protein kinases: genomics of the Arabidopsis and rice CBL-CIPK signaling networks. Plant Physiology. 134, 43-58.

Letunic, I., Bork, P., 2018. 20 years of the SMART protein domain annotation resource. Nucleic Acids Research. 46, D493-D496.

Li, J., Jiang, M.-M., Ren, L., Liu, Y., Chen, H.-Y., 2016. Identification and characterization of CBL and CIPK gene families in eggplant (Solanum melongena L.). Molecular Genetics and Genomics. 291, 1769-1781.

Ma, X., Gai, W.-X., Qiao, Y.-M., Ali, M., Wei, A.-M., Luo, D.-X., Li, Q.-H., Gong, Z.-H., 2019. Identification of CBL and CIPK gene families and functional characterization of CaCIPK1 under Phytophthora capsici in pepper (Capsicum annuum L.). BMC Genomics. 20, 775.

Ma, X., Li, Q.-H., Yu, Y.-N., Qiao, Y.-M., Gong, Z.-H., 2020. The CBL–CIPK Pathway in Plant Response to Stress Signals. International Journal of Molecular Sciences. 21, 5668.

Mao, D., Chen, C., 2012. Colinearity and similar expression pattern of rice DREB1s reveal their functional conservation in the cold-responsive pathway. PloS one. 7, e47275.

Mo, C., Wan, S., Xia, Y., Ren, N., Zhou, Y., Jiang, X., 2018. Expression patterns and identified protein-protein interactions suggest that cassava CBL-CIPK signal networks function in responses to abiotic stresses. Frontiers in Plant Science. 9, 269.

Mohanta, T.K., Kumar, P., Bae, H., 2017. Genomics and evolutionary aspect of calcium signaling event in calmodulin and calmodulin-like proteins in plants. BMC Plant Biology. 17, 38.

Monihan, S.M., Magness, C.A., Yadegari, R., Smith, S.E., Schumaker, K.S., 2016. Arabidopsis CALCINEURIN B-LIKE10 functions independently of the SOS pathway during reproductive development in saline conditions. Plant Physiology. 171, 369-379.

Nuruzzaman, M., Manimekalai, R., Sharoni, A.M., Satoh, K., Kondoh, H., Ooka, H., Kikuchi, S., 2010. Genome-wide analysis of NAC transcription factor family in rice. Gene. 465, 30-44.

Pandey, G.K., Kanwar, P., Singh, A., Steinhorst, L., Pandey, A., Yadav, A.K., Tokas, I., Sanyal, S.K., Kim, B.-G., Lee, S.-C., 2015. Calcineurin B-like protein-interacting protein kinase CIPK21 regulates osmotic and salt stress responses in Arabidopsis. Plant Physiology. 169, 780-792.

Podell, S., Gribskov, M., 2004. Predicting N-terminal myristoylation sites in plant proteins. BMC Genomics. 5, 37.

Scherf, U., Ross, D.T., Waltham, M., Smith, L.H., Lee, J.K., Tanabe, L., Kohn, K.W., Reinhold, W.C., Myers, T.G., Andrews, D.T., 2000. A gene expression database for the molecular pharmacology of cancer. Nature Genetic. 24, 236.

Shi, J., Kim, K.-N., Ritz, O., Albrecht, V., Gupta, R., Harter, K., Luan, S., Kudla, J., 1999. Novel protein kinases associated with calcineurin B–like calcium sensors in Arabidopsis. The Plant Cell. 11, 2393-2405.

Sigrist, C.J., De Castro, E., Cerutti, L., Cuche, B.A., Hulo, N., Bridge, A., Bougueleret, L., Xenarios, I., 2012. New and continuing developments at PROSITE. Nucleic Acids Research. 41, D344-D347.

Su, W., Ren, Y., Wang, D., Huang, L., Fu, X., Ling, H., Su, Y., Huang, N., Tang, H., Xu, L., 2020. New insights into the evolution and functional divergence of the CIPK gene family in Saccharum. BMC Genomics. 21, 1-20.

Tamura, K., Stecher, G., Peterson, D., Filipski, A., Kumar, S., 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution. 30, 2725-2729.

Yang, Y., Zhang, C., Tang, R.-J., Xu, H.-X., Lan, W.-Z., Zhao, F., Luan, S., 2019. Calcineurin B-Like proteins CBL4 and CBL10 mediate two independent salt tolerance pathways in Arabidopsis. International Journal of Molecular Sciences. 20, 2421.

Yin, X., Wang, Q., Chen, Q., Xiang, N., Yang, Y., Yang, Y., 2017. Genome-wide identification and functional analysis of the calcineurin B-like protein and calcineurin B-like protein-interacting protein kinase gene families in turnip (Brassica rapa var. rapa). Frontiers in Plant Science. 8, 1191.

Younesi-Melerdi, E., Nematzadeh, G., Pakdin-Parizi, A., 2020. Expression analysis of some genes involved in signaling networks of Aeluropus littoralis (Gouan) Parl. under salinity stress. Environmental Stresses in Crop Sciences. 13, 1259-1270. [In Persian with English summary].

Yu, Q., An, L., Li, W., 2014. The CBL–CIPK network mediates different signaling pathways in plants. Plant cell reports. 33, 203-214.

Zhang, H., Yang, B., Liu, W.-Z., Li, H., Wang, L., Wang, B., Deng, M., Liang, W., Deyholos, M.K., Jiang, Y.-Q., 2014. Identification and characterization of CBL and CIPK gene families in canola (Brassica napus L.). BMC Plant Biology. 14, 8.

Zhao, J., Yu, A., Du, Y., Wang, G., Li, Y., Zhao, G., Wang, X., Zhang, W., Cheng, K., Liu, X., 2019. Foxtail millet (Setaria italica L.) P. Beauv) CIPKs are responsive to ABA and abiotic stresses. Plos one. 14, e0225091.