تحلیل جامع ژنومی، تکاملی و ساختاری خانواده‌های ژنی دارای موتیف LysM در غلات

Abedi, A., Hajiahmadi, Z., Kordrostami, M., Esmaeel, Q. & Jacquard, C. 2021. Analyses of Lysin-motif Receptor-like Kinase (LysM-RLK) Gene Family in Allotetraploid Brassica napus L. and Its Progenitor Species: An In Silico Study. Cells, 11, 37.  https://doi.org/10.3390/cells11010037

Akcapinar, G. B., Kappel, L., Sezerman, O. U. & Seidl-Seiboth, V. J. C. g. 2015. Molecular diversity of LysM carbohydrate-binding motifs in fungi. Curr Genet, 61, 103-113.  https://doi.org/10.1007/s00294-014-0471-9

Ao, Y., Li, Z., Feng, D., Xiong, F., Liu, J., Li, J. F., Wang, M., Wang, J., Liu, B. & Wang, H. B. 2014. Os CERK 1 and Os RLCK 176 play important roles in peptidoglycan and chitin signaling in rice innate immunity. The Plant Journal, 80, 1072-1084.  https://doi.org/10.1111/tpj.12710

Berendzen, K. W., Weiste, C., Wanke, D., Kilian, J., Harter, K. & Dröge-Laser, W. 2012. Bioinformatic cis-element analyses performed in Arabidopsis and rice disclose bZIP-and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription. BMC plant biology, 12, 1-19.  https://doi.org/10.1186/1471-2229-12-125

Buendia, L., Girardin, A., Wang, T., Cottret, L. & Lefebvre, B. J. F. i. p. s. 2018. LysM receptor-like kinase and LysM receptor-like protein families: an update on phylogeny and functional characterization. Front Plant Sci, 9, 1531. https://doi.org/10.3389/fpls.2018.01531

Chanwala, J., Kumari, K., Jha, D. K., Giri, M. K. & Dey, N. J. P. S. 2025. Pearl millet WRKY transcription factor PgWRKY52 positively regulates salt stress tolerance through ABA-MeJA mediated transcriptional regulation. Plant Stress, 16, 100814.  https://doi.org/10.1016/j.stress.2025.100814

Chen, C., Chen, H., Zhang, Y., Thomas, H. R., Frank, M. H., He, Y. & Xia, R. J. M. p. 2020a. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant, 13, 1194-1202.  https://doi.org/10.1016/j.molp.2020.06.009

Chen, D., Li, G., Liu, J., Wisniewski, M., Droby, S., Levin, E., Huang, S., Liu, Y. J. M. G. & Genomics 2020b. Multiple transcriptomic analyses and characterization of pathogen-related core effectors and LysM family members reveal their differential roles in fungal growth and pathogenicity in Penicillium expansum. Molecular Genetics and Genomics, 295, 1415-1429.  https://doi.org/10.1007/s00438-020-01710-9

Chen, Z., Shen, Z., Zhao, D., Xu, L., Zhang, L. & Zou, Q. 2020c. Genome-wide analysis of LysM-containing gene family in wheat: Structural and phylogenetic analysis during development and defense. Genes, 12, 31.  https://doi.org/10.3390/genes12010031

Chen, Z., Shen, Z., Zhao, D., Xu, L., Zhang, L. & Zou, Q. J. G. 2020d. Genome-wide analysis of LysM-containing gene family in wheat: Structural and phylogenetic analysis during development and defense. Genes (Basel), 12, 31.  https://doi.org/10.3390/genes12010031

Crumière, M., de Vallée, A., Rascle, C., Gillet, F. x., Nahar, S., van Kan, J. A., Bruel, C., Poussereau, N. & Choquer, M. J. J. o. B. M. 2025. A LysM Effector Mediates Adhesion and Plant Immunity Suppression in the Necrotrophic Fungus Botrytis cinerea. J Basic Microbiol, 65, e2400552.  https://doi.org/10.1002/jobm.202400552

Desai, H., Hamid, R., Ghorbanzadeh, Z., Bhut, N., Padhiyar, S. M., Kheni, J. & Tomar, R. S. J. S. r. 2021. Genic microsatellite marker characterization and development in little millet (Panicum sumatrense) using transcriptome sequencing. Sci Rep, 11, 20620.  https://doi.org/10.1038/s41598-021-00100-4

Desaki, Y., Miyata, K., Suzuki, M., Shibuya, N. & Kaku, H. J. I. I. 2018. Plant immunity and symbiosis signaling mediated by LysM receptors. Innate Immun, 24, 92-100.  https://doi.org/10.1177/1753425917738885

Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L. & Mistry, J. J. N. a. r. 2014. Pfam: the protein families database. Nucleic Acids Res, 42, D222-D230.  https://doi.org/10.1093/nar/gkt1223

Ghorbanzadeh, Z., Hamid, R., Jacob, F., Mirzaei, M., Zeinalabedini, M., Abdirad, S., Atwell, B. J., Haynes, P. A., Ghaffari, M. R. & Salekdeh, G. H. J. J. o. P. G. R. 2023. MicroRNA profiling of root meristematic zone in contrasting genotypes reveals novel insight into in rice response to water deficiency. Journal of Plant Growth Regulation, 42, 3814-3834.  https://doi.org/10.1007/s00344-022-10842-8

Gibelin‐Viala, C., Amblard, E., Puech‐Pages, V., Bonhomme, M., Garcia, M., Bascaules‐Bedin, A., Fliegmann, J., Wen, J., Mysore, K. S. & le Signor, C. 2019. The Medicago truncatula LysM receptor‐like kinase LYK9 plays a dual role in immunity and the arbuscular mycorrhizal symbiosis. New Phytologist, 223, 1516-1529.  https://doi.org/10.1111/nph.15891

Gong, B.-Q., Wang, F.-Z. & Li, J.-F. J. T. i. p. s. 2020. Hide-and-seek: chitin-triggered plant immunity and fungal counterstrategies. Trends Plant Sci, 25, 805-816.  https://doi.org/10.1016/j.tplants.2020.03.006

Gong, X., Han, D., Zhang, L., Yin, G., Yang, J., Jia, H., Cao, Z., Dong, J., Liu, Y. & Gu, S. J. J. o. I. A. 2025. Comprehensive analysis of the LysM protein family and functional characterization of the key LysM effector StLysM1, which modulates plant immunity in Setosphaeria turcica. Journal of Integrative Agriculture, 24, 1860-1874  https://doi.org/10.1016/j.jia.2024.06.006

Grabherr, H. M. 2011. Characterisation of the role of LysM receptor-like kinases and the CHIA chitinase in the perception of peptidoglycan and in the innate immunity of Arabidopsis thaliana. PhD. Thesis, Universität Tübingen.

Grote, U., Fasse, A., Nguyen, T. T. & Erenstein, O. J. F. i. S. F. S. 2021. Food security and the dynamics of wheat and maize value chains in Africa and Asia. Front. Sustain. Food Syst, 4, 617009.  https://doi.org/10.3389/fsufs.2020.617009

Guo, J., Gong, B. Q. & Li, J. F. J. T. P. J. 2021. Arabidopsis lysin motif/F‐box‐containing protein InLYP1 fine‐tunes glycine metabolism by degrading glycine decarboxylase GLDP2. Plant J, 106, 394-408.  https://doi.org/10.1111/tpj.15171

Gust, A. A. J. P. p. 2015. Peptidoglycan perception in plants. PLoS Pathog, 11, e1005275.  https://doi.org/10.1371/journal.ppat.1005275

Hamid, R., Ghorbanzadeh, Z., Jacob, F., Nekouei, M. K., Zeinalabedini, M., Mardi, M., Sadeghi, A. & Ghaffari, M. R. J. B. P. B. 2024a. Decoding drought resilience: a comprehensive exploration of the cotton Eceriferum (CER) gene family and its role in stress adaptation. BMC Plant Biol, 24, 468.  https://doi.org/10.1186/s12870-024-05172-8

Hamid, R., Jacob, F., Ghorbanzadeh, Z., Mardi, M., Ariaeenejad, S., Zeinalabedini, M. & Ghaffari, M. R. J. P. G. 2024b. Genome-wide identification and characterization of FORMIN genes in cotton: Implications for abiotic stress tolerance. 40, 100474.

He, J., Zhang, C., Dai, H., Liu, H., Zhang, X., Yang, J., Chen, X., Zhu, Y., Wang, D. & Qi, X. J. M. P. 2019. A LysM receptor heteromer mediates perception of arbuscular mycorrhizal symbiotic signal in rice. Mol Plant, 12, 1561-1576. ttps://doi.org/10.1016/j.molp.2019.https://doi.org/10.015

Hu, S.-P., Li, J.-J., Dhar, N., Li, J.-P., Chen, J.-Y., Jian, W., Dai, X.-F. & Yang, X.-Y. 2021a. Lysin motif (LysM) proteins: interlinking manipulation of plant immunity and fungi. International journal of molecular sciences, 3114, 22.  https://doi.org/10.3390/ijms22063114

Hu, S.-P., Li, J.-J., Dhar, N., Li, J.-P., Chen, J.-Y., Jian, W., Dai, X.-F. & Yang, X.-Y. J. I. j. o. m. s. 2021b. Lysin motif (LysM) proteins: interlinking manipulation of plant immunity and fungi. Int J Mol Sci, 22, 311.  https://doi.org/10.3390/ijms22063114

Ji, L., Yang, X. & Qi, F. 2022. Distinct responses to pathogenic and symbionic microorganisms: the role of plant immunity. International Journal of Molecular Sciences, 23, 10427.  https://doi.org/10.3390/ijms231810427

Kaur, A., Pati, P. K., Pati, A. M. & Nagpal, A. K. 2017. In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa. PloS one, 12, e0184523.  https://doi.org/10.1371/journal.pone.0184523

Kumar, S., Stecher, G., Suleski, M., Sanderford, M., Sharma, S. & Tamura, K. 2024. MEGA12: Molecular Evolutionary Genetic Analysis version 12 for adaptive and green computing. Molecular Biology and Evolution, 41, msae263.  https://doi.org/10.1093/molbev/msae263

Levin, E., Ballester, A. R., Raphael, G., Feigenberg, O., Liu, Y., Norelli, J., Gonzalez-Candelas, L., Ma, J., Dardick, C. & Wisniewski, M. J. P. O. 2017. Identification and characterization of LysM effectors in Penicillium expansum. PLoS One, 12, e0186023.  https://doi.org/10.1371/journal.pone.0186023

Li, Q., Qi, J., Qin, X., Hu, A., Fu, Y., Chen, S. & He, Y. J. S. H. 2021. Systematic identification of lysin-motif receptor-like kinases (LYKs) in Citrus sinensis, and analysis of their inducible involvements in citrus bacterial canker and phytohormone signaling. Scientia Horticulturae, 276, 109755.  https://doi.org/10.1016/j.scienta.2020.109755

Liao, D., Sun, X., Wang, N., Song, F. & Liang, Y. J. F. i. P. S. 2018. Tomato LysM receptor-like kinase SlLYK12 is involved in arbuscular mycorrhizal symbiosis. Front. Plant Sci, 9, 1004.  https://doi.org/10.3389/fpls.2018.01004

Liu, B., Li, J.-F., Ao, Y., Qu, J., Li, Z., Su, J., Zhang, Y., Liu, J., Feng, D. & Qi, K. J. T. P. C. 2012. Lysin motif–containing proteins LYP4 and LYP6 play dual roles in peptidoglycan and chitin perception in rice innate immunity. Plant Cell, 24, 3406-3419.  https://doi.org/10.1105/tpc.112.102475

Liu, L., Xu, L., Jia, Q., Pan, R., Oelmüller, R., Zhang, W., Wu, C. J. P. S. & Behavior 2019. Arms race: diverse effector proteins with conserved motifs. Plant Signal Behav, 14, 1557008.  https://doi.org/10.1080/15592324.2018.1557008

Liu, L., Yahaya, B. S., Li, J. & Wu, F. J. F. i. P. S. 2024. Enigmatic role of auxin response factors in plant growth and stress tolerance. Front Plant Sci, 15, 1398818.  https://doi.org/10.3389/fpls.2024.1398818

Liu, M., Gao, N., Zhao, Y., Wu, Y. & Yuan, Z. 2022. Wheat Lysin-Motif-Containing Proteins Characterization and Gene Expression Patterns under Abiotic and Biotic Stress. Phyton, 91, 2367 . https://doi.org/10.32604/phyton.2022.0214

Meng, Y., Li, J., Yuan, W., Liu, R., Xu, L. & Huang, L. 2024. Pseudomonas thivervalensis K321, a promising and effective biocontrol agent for managing apple Valsa canker triggered by Valsa mali. Pesticide Biochemistry and Physiology, 204, 106095.  https://doi.org/10.1016/j.pestbp.2024.106095

Miryala, S. K., Anbarasu, A. & Ramaiah, S. 2018. Discerning molecular interactions: a comprehensive review on biomolecular interaction databases and network analysis tools. Gene, 642, 84-94.  https://doi.org/10.1016/j.gene.2017.11.028

Nakagawa, T., Okazaki, S. & Shibuya, N. 2014. Genes involved in pathogenesis and defense responses. The Lotus japonicus Genome, 163-169.

Nazarian-Firouzabadi, F., Joshi, S., Xue, H. & Kushalappa, A. C. J. M. B. R. 2019. Genome-wide in silico identification of LysM-RLK genes in potato (Solanum tuberosum L.). Mol Biol Rep, 46, 5005-5017.  https://doi.org/10.1007/s11033-019-04951-z

Peng, X., Wang, J., Peng, W., Wu, F.-X. & Pan, Y. J. B. i. b. 2017. Protein–protein interactions: detection, reliability assessment and applications. Brief Bioinform, 18, 798-819.  https://doi.org/10.1093/bib/bbw066

Petutschnig, E. K., Jones, A. M., Serazetdinova, L., Lipka, U. & Lipka, V. 2010. The lysin motif receptor-like kinase (LysM-RLK) CERK1 is a major chitin-binding protein in Arabidopsis thaliana and subject to chitin-induced phosphorylation. Journal of Biological Chemistry, 285, 28902-28911.  https://doi.org/10.1074/jbc.M110.116657

Ren, W., Zhang, C., Wang, M., Zhang, C., Xu, X., Huang, Y., Chen, Y., Lin, Y. & Lai, Z. 2022. Genome-wide identification, evolution analysis of LysM gene family members and their expression analysis in response to biotic and abiotic stresses in banana (Musa L.). Gene, 845, 146849.  https://doi.org/10.1016/j.gene.2022.146849

Roudaire, T., Marzari, T., Landry, D., Löffelhardt, B., Gust, A. A., Jermakow, A., Dry, I., Winckler, P., Héloir, M.-C. & Poinssot, B. 2023a. The grapevine LysM receptor-like kinase VvLYK5-1 recognizes chitin oligomers through its association with VvLYK1-1. Frontiers in Plant Science, 14, 1130782. https://doi.org/10.3389/fpls.2023.1130782

Singh, K., Upadhyay, S. K. J. E. & Botany, E. 2021. LysM domain-containing proteins modulate stress response and signalling in Triticum aestivum L. 189, 104558.  Environmental and Experimental Botany,  https://doi.org/10.1016/j.envexpbot.2021.104558

Tombuloglu, G., Tombuloglu, H., Cevik, E., Sabit, H. J. P. & Pathology, M. P. 2019. Genome-wide identification of Lysin-Motif Receptor-Like Kinase (LysM-RLK) gene family in Brachypodium distachyon and docking analysis of chitin/LYK binding. Physiological and Molecular Plant Pathology, 106, 217-225.  https://doi.org/10.1016/j.pmpp.2019.03.002

Wan, J., Tanaka, K., Zhang, X.-C., Son, G. H., Brechenmacher, L., Nguyen, T. H. N. & Stacey, G. 2012. LYK4, a lysin motif receptor-like kinase, is important for chitin signaling and plant innate immunity in Arabidopsis. Plant physiology, 160, 396-406.  https://doi.org/10.1104/pp.112.201699

Wan, J., Zhang, X.-C., Neece, D., Ramonell, K. M., Clough, S., Kim, S.-y., Stacey, M. G. & Stacey, G. J. T. P. C. 2008. A LysM receptor-like kinase plays a critical role in chitin signaling and fungal resistance in Arabidopsis. Plant Cell, 20, 471-481.  https://doi.org/10.1105/tpc.107.056754

Wang, Y., Mostafa, S., Zeng, W. & Jin, B. J. I. J. o. M. S. 2021. Function and mechanism of jasmonic acid in plant responses to abiotic and biotic stresses. Int J Mol Sci, 22, 8568.  https://doi.org/10.3390/ijms22168568

Wong, J. E., Nadzieja, M., Madsen, L. H., Bücherl, C. A., Dam, S., Sandal, N. N., Couto, D., Derbyshire, P., Uldum-Berentsen, M. & Schroeder, S. J. P. o. t. N. A. o. S. 2019. A Lotus japonicus cytoplasmic kinase connects Nod factor perception by the NFR5 LysM receptor to nodulation. Proc Natl Acad Sci U S A, 116, 14339-14348.  https://doi.org/10.1073/pnas.1815425116

Xu, B. & Timko, M. J. P. m. b. 2004. Methyl jasmonate induced expression of the tobacco putrescine N-methyltransferase genes requires both G-box and GCC-motif elements. Plant Molecular Biology, 55, 743-761.  https://doi.org/10.1007/s11103-004-1962-8

Xu, J., Wang, G., Wang, J., Li, Y., Tian, L., Wang, X. & Guo, W. J. B. p. b. 2017. The lysin motif-containing proteins, Lyp, Lyk7 and LysMe3, play important roles in chitin perception and defense against Verticillium dahliae in cotton. BMC Plant Biol, 17, 1-18.  https://doi.org/10.1186/s12870-017-1096-1

Yang, H., Bayer, P. E., Tirnaz, S., Edwards, D. & Batley, J. J. B. 2020. Genome-wide identification and evolution of receptor-like kinases (RLKs) and receptor like proteins (RLPs) in Brassica juncea. Biology (Basel), 10, 17.  https://doi.org/10.3390/biology10010017

Zhang, L., Li, S., Fang, X., An, H. & Zhang, X. 2023. Genome-wide analysis of LysM gene family members and their expression in response to Colletotrichum fructicola infection in Octoploid strawberry (Fragaria× ananassa). Frontiers in Plant Science, 13, 1105591.  https://doi.org/10.3389/fpls.2022.1105591

Zhou, D., Chen, X., Chen, X., Xia, Y., Liu, J. & Zhou, G. J. F. i. M. 2023. Plant immune receptors interact with hemibiotrophic pathogens to activate plant immunity. Front Microbiol, 14, 1252039.  https://doi.org/10.3389/fmicb.2023.1252039

Zhou, Z., Tian, Y., Cong, P. & Zhu, Y. J. P. S. 2018. Functional characterization of an apple (Malus x domestica) LysM domain receptor encoding gene for its role in defense response. Plant Sci, 269, 56-65.  https://doi.org/10.1016/j.plantsci.2018.01.006

Zhu, Q., Zhang, X.-L., Nadir, S., DongChen, W.-H., Guo, X.-Q., Zhang, H.-X., Li, C.-Y., Chen, L.-J. & Lee, D.-S. 2017a. A LysM domain-containing gene OsEMSA1 involved in embryo sac development in rice (Oryza sativa L.). Frontiers in Plant Science, 8, 1596.  https://doi.org/10.3389/fpls.2017.01596

Zhu, Q., Zhang, X.-L., Nadir, S., DongChen, W.-H., Guo, X.-Q., Zhang, H.-X., Li, C.-Y., Chen, L.-J. & Lee, D.-S. J. F. i. P. S. 2017b. A LysM domain-containing gene OsEMSA1 involved in embryo sac development in rice (Oryza sativa L.). Front Plant Sci, 8, 1596.  https://doi.org/10.3389/fpls.2017.01596