[1] Bennett J. 1991. Protein phosphorylation in green plant chloroplasts. Annual Review of Plant Physiology and Plant Molecular Biology 42:281−311 doi: 10.1146/annurev.pp.42.060191.001433
[2] Stone JM, Walker JC. 1995. Plant protein kinase families and signal transduction. Plant Physiology 108:451−57 doi: 10.1104/pp.108.2.451
[3] Champion A, Kreis M, Mockaitis K, Picaud A, Henry Y. 2004. Arabidopsis kinome: after the casting. Functional & Integrative Genomics 4:163−87 doi: 10.1007/s10142-003-0096-4
[4] Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. 2002. The protein kinase complement of the human genome. Science 298:1912−34 doi: 10.1126/science.1075762
[5] Hanks SK, Quinn AM, Hunter T. 1988. The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. Science 241:42−52 doi: 10.1126/science.3291115
[6] Lehti-Shiu MD, Shiu SH. 2012. Diversity, classification and function of the plant protein kinase superfamily. Philosophical Transactions of the Royal Society B - Biological Sciences 367:2619−39 doi: 10.1098/rstb.2012.0003
[7] Liu J, Chen N, Grant JN, Cheng ZM, Stewart CN Jr, et al. 2015. Soybean kinome: functional classification and gene expression patterns. Journal of Experimental Botany 66:1919−34 doi: 10.1093/jxb/eru537
[8] Zhu K, Wang X, Liu J, Tang J, Cheng Q, et al. 2018. The grapevine kinome: annotation, classification and expression patterns in developmental processes and stress responses. Horticulture Research 5:19 doi: 10.1038/s41438-018-0027-0
[9] Hanada K, Zou C, Lehti-Shiu MD, Shinozaki K, Shiu SH. 2008. Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiology 148:993−1003 doi: 10.1104/pp.108.122457
[10] Lehti-Shiu MD, Zou C, Hanada K, Shiu SH. 2009. Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes. Plant Physiology 150:12−26 doi: 10.1104/pp.108.134353
[11] Dardick C, Chen J, Richter T, Ouyang S, Ronald P. 2007. The rice kinase database. A phylogenomic database for the rice kinome. Plant Physiology 143:579−86 doi: 10.1104/pp.106.087270
[12] Gish LA, Clark SE. 2011. The RLK/Pelle family of kinases. The Plant Journal 66:117−27 doi: 10.1111/j.1365-313X.2011.04518.x
[13] Zhu K, Fan P, Mo Z, Tan P, Feng G, et al. 2020. Identification, expression and co-expression analysis of R2R3-MYB family genes involved in graft union formation in pecan (Carya illinoinensis). Forests 11:917 doi: 10.3390/f11090917
[14] Guo W, Chen J, Li J, Huang J, Wang Z, et al. 2020. Portal of Juglandaceae: A comprehensive platform for Juglandaceae study. Horticulture Research 7:35 doi: 10.1038/s41438-020-0256-x
[15] Huang Y, Xiao L, Zhang Z, Zhang R, Wang Z, et al. 2019. The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition. Gigascience 8:giz036 doi: 10.1093/gigascience/giz036
[16] Panchy N, Lehti-Shiu M, Shiu SH. 2016. Evolution of gene duplication in plants. Plant Physiology 171:2294−316 doi: 10.1104/pp.16.00523
[17] Cannon SB, Mitra A, Baumgarten A, Young ND, May G. 2004. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biology 4:10 doi: 10.1186/1471-2229-4-10
[18] Zhu K, Chen F, Liu J, Chen X, Hewezi T, et al. 2016. Evolution of an intron-poor cluster of the CIPK gene family and expression in response to drought stress in soybean. Scientific Reports 6:28225 doi: 10.1038/srep28225
[19] Chen X, Ding Y, Yang Y, Song C, Wang B, et al. 2021. Protein kinases in plant responses to drought, salt, and cold stress. Journal of Integrative Plant Biology 63:53−78 doi: 10.1111/jipb.13061
[20] Ferreira-Neto JRC, Borges AN da C, da Silva MD, Morais DA de L, Bezerra-Neto JP, et al. 2021. The cowpea kinome: genomic and transcriptomic analysis under biotic and abiotic stresses. Frontiers in Plant Science 12:667013 doi: 10.3389/fpls.2021.667013
[21] Zhu J. 2016. Abiotic stress signaling and responses in plants. Cell 167:313−24 doi: 10.1016/j.cell.2016.08.029
[22] Bundó M, Coca M. 2017. Calcium-dependent protein kinase OsCPK10 mediates both drought tolerance and blast disease resistance in rice plants. Journal of Experimental Botany 68:2963−75 doi: 10.1093/jxb/erx145
[23] Andrási N, Rigó G, Zsigmond L, Pérez-Salamó I, Papdi C, et al. 2019. The mitogen-activated protein kinase 4-phosphorylated heat shock factor A4A regulates responses to combined salt and heat stresses. Journal of Experimental Botany 70:4903−18 doi: 10.1093/jxb/erz217
[24] Wei K, Wang Y, Zhong X, Pan S. 2014. Protein kinase structure, expression and regulation in maize drought signaling. Molecular Breeding 34:583−602 doi: 10.1007/s11032-014-0059-6
[25] Zhu K, Liu H, Chen X, Cheng Q, Cheng ZM. 2018. The kinome of pineapple: catalog and insights into functions in crassulacean acid metabolism plants. BMC Plant Biology 18:199 doi: 10.1186/s12870-018-1389-z
[26] Hindle MM, Martin SF, Noordally ZB, van Ooijen G, Barrios-Llerena ME, et al. 2014. The reduced kinome of Ostreococcus tauri: core eukaryotic signalling components in a tractable model species. BMC Genomics 15:640 doi: 10.1186/1471-2164-15-640
[27] Zulawski M, Schulze G, Braginets R, Hartmann S, Schulze WX. 2014. The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification. BMC Genomics 15:548 doi: 10.1186/1471-2164-15-548
[28] Dievart A, Gottin C, Périn C, Ranwez V, Chantret N. 2020. Origin and diversity of plant receptor-like kinases. Annual Review of Plant Biology 71:131−56 doi: 10.1146/annurev-arplant-073019-025927
[29] Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, et al. 2005. Modeling gene and genome duplications in eukaryotes. PNAS 102:5454−59 doi: 10.1073/pnas.0501102102
[30] Zhang Z, Li J, Zhao X, Wang J, Wong GKC, et al. 2006. KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics 4:259−63 doi: 10.1016/S1672-0229(07)60007-2
[31] Hou J, Wei S, Pan H, Zhuge Q, Yin T. 2019. Uneven selection pressure accelerating divergence of Populus and Salix. Horticulture Research 6:37 doi: 10.1038/s41438-019-0121-y
[32] Antolín-Llovera M, Ried MK, Binder A, Parniske M. 2012. Receptor kinase signaling pathways in plant-microbe interactions. Annual Review of Phytopathology 50:451−73 doi: 10.1146/annurev-phyto-081211-173002
[33] Liang X, Zhou JM. 2018. Receptor-like cytoplasmic kinases: central players in plant receptor kinase–mediated signaling. Annual Review of Plant Biology 69:267−99 doi: 10.1146/annurev-arplant-042817-040540
[34] Chandran AKN, Yoo YH, Cao P, Sharma R, Sharma M, et al. 2016. Updated Rice Kinase Database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes. Rice 9:40 doi: 10.1186/s12284-016-0106-5
[35] Nodine MD, Yadegari R, Tax FE. 2007. RPK1 and TOAD2 are two receptor-like kinases redundantly required for Arabidopsis embryonic pattern formation. Developmental Cell 12:943−56 doi: 10.1016/j.devcel.2007.04.003
[36] Li J. 2010. Multi-tasking of somatic embryogenesis receptor-like protein kinases. Current Opinion in Plant Biology 13:509−14 doi: 10.1016/j.pbi.2010.09.004
[37] Wang R, Li L, Cao Z, Zhao Q, Li M, et al. 2012. Molecular cloning and functional characterization of a novel apple MdCIPK6L gene reveals its involvement in multiple abiotic stress tolerance in transgenic plants. Plant Molecular Biology 79:123−35 doi: 10.1007/s11103-012-9899-9
[38] Meng D, Dong B, Niu L, Song Z, Wang L, et al. 2021. The pigeon pea CcCIPK14-CcCBL1 pair positively modulates drought tolerance by enhancing flavonoid biosynthesis. Plant Journal 106:1278−97 doi: 10.1111/tpj.15234
[39] Lu L, Chen X, Wang P, Lu Y, Zhang J, et al. 2021. CIPK11: a calcineurin B-like protein-interacting protein kinase from Nitraria tangutorum, confers tolerance to salt and drought in Arabidopsis. BMC Plant Biology 21:123 doi: 10.1186/s12870-021-02878-x
[40] Fujii H, Verslues PE, Zhu JK. 2011. Arabidopsis decuple mutant reveals the importance of SnRK2 kinases in osmotic stress responses in vivo. PNAS 108:1717−22 doi: 10.1073/pnas.1018367108
[41] Gao L, Xue H. 2012. Global analysis of expression profiles of rice receptor-like kinase genes. Molecular Plant 5:143−53 doi: 10.1093/mp/ssr062
[42] Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, et al. 2016. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Research 44:D279−D285 doi: 10.1093/nar/gkv1344
[43] Eddy SR. 1998. Profile hidden Markov models. Bioinformatics 14:755−63 doi: 10.1093/bioinformatics/14.9.755
[44] Letunic I, Khedkar S, Bork P. 2021. SMART: recent updates, new developments and status in 2020. Nucleic Acids Research 49:D458−D460 doi: 10.1093/nar/gkaa937
[45] Katoh K, Rozewicki J, Yamada KD. 2019. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20:1160−66 doi: 10.1093/bib/bbx108
[46] Price MN, Dehal PS, Arkin AP. 2009. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Molecular Biology and Evolution 26:1641−50 doi: 10.1093/molbev/msp077
[47] Yu CS, Chen YC, Lu CH, Hwang JK. 2006. Prediction of protein subcellular localization. Proteins 64:643−51 doi: 10.1002/prot.21018
[48] Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25:3389−402 doi: 10.1093/nar/25.17.3389
[49] Wang Y, Li J, Paterson AH. 2013. MCScanX-transposed: detecting transposed gene duplications based on multiple colinearity scans. Bioinformatics 29:1458−60 doi: 10.1093/bioinformatics/btt150
[50] Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947−48 doi: 10.1093/bioinformatics/btm404
[51] Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, et al. 2020. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant 13:1194−202 doi: 10.1016/j.molp.2020.06.009
[52] Kim D, Langmead B, Salzberg SL. 2015. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12:357−60 doi: 10.1038/nmeth.3317
[53] Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, et al. 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33:290−95 doi: 10.1038/nbt.3122
[54] Li B, Dewey CN. 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323 doi: 10.1186/1471-2105-12-323
[55] Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15:550 doi: 10.1186/s13059-014-0550-8
[56] Ernst J, Bar-Joseph Z. 2006. STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics 7:191 doi: 10.1186/1471-2105-7-191
[57] Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. 2003. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research 13:2498−504 doi: 10.1101/gr.1239303