The sugarcane and sorghum kinomes: insights into evolutionary expansion and diversification

The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, which were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between these species, this study offers insights about Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq, identifying significant similarities between Sbi and Ssp. Moreover, through coexpression networks, we inferred a core structure of kinase interactions with specific key elements. This study is the first to categorize the allele specificity of a kinome and provides a wide reservoir of molecular and genetic information, enhancing the understanding of the evolutionary history of Sbi and Ssp PKs. Highlight This study describes the catalog of kinase gene family in Saccharum spontaneum and Sorghum bicolor , providing a reservoir of molecular features and expression patterns based on RNA-Seq and co-expression networks. ### Competing Interest Statement The authors have declared no competing interest. * Aco : Aquilegia coerulea AGC : cyclic AMP-dependent protein kinase (cAPK), cGMP-dependent protein kinase, and lipid signaling kinase families Aly : Arabidopsis lyrata Ath : Arabidopsis thaliana B-lectin : D-mannose-binding lectin Bdi : Brachypodium distachyon CAMK : calcium- and calmodulin-regulated kinase Ccl : Citrus clementina CDS : DNA coding sequence CK1 : casein kinase 1 CMGC : cyclin-dependent kinase, mitogen-activated protein kinase, glycogen synthase kinase and cyclin-dependent kinase-like kinase Cpa : Carica papaya Cre : Chlamydomonas reinhardtii Csa : Cucumis sativus Csi : Citrus sinensis DUF26 : Domain of Unknown Function 26 Egr : Eucalyptus grandis ER : endoplasmic reticulum GM : gene model Gma : Glycine max GO : Gene Ontology GUB : galacturonan-binding HMM : hidden Markov model IRE1 : inositol-requiring kinase 1 Ka : Nonsynonymous substitution rates Ks : Synonymous substitution rates LRR : leucine-rich repeat LRRNT : leucine-rich repeat N-terminal domain Mes : Manihot esculenta Mgu : Mimulus guttatus Mtr : Medicago truncatula MW : molecular weight MYA : million years ago Osa : Oryza sativa PEK : pancreatic eukaryotic initiation factor-2alpha kinase PK : protein kinase pI : isoelectric point Ppa : Physcomitrella patens Ppe : Prunus persica Ptr : Populus trichocarpa Rco : Ricinus communis RLK : receptor-like kinase S-locus-glycop : S-locus glycoprotein Sbi : Sorghum bicolor Sit : Setaria italica Smo : Selaginella moellendorffii Ssp : Saccharum spontaneum STE : serine/threonine kinase TKL : tyrosine kinase-like kinase TPM : Transcripts per million Vca : Volvox carteri Vvi : Vitis vinifera WAK : wall-associated receptor kinase WGD : whole-genome duplication Zma : Zea mays