Pecan kinome: classification and expression analysis of all protein kinases in Carya illinoinensis

Protein kinases (PKs) are involved in plant growth and stress responses, and constitute one of the largest superfamilies due to numerous gene duplications. However, limited PKs have been functionally described in pecan, an economically important nut tree. Here, the comprehensive identification, annotation and classification of the entire pecan kinome are reported. A total of 967 PK genes were identified from the pecan genome, and further classified into 20 different groups and 121 subfamilies using the kinase domain sequences, which were verified by phylogenetic analysis. The receptor-like kinase (RLK) group contained 565 members, which constituted the largest group. Gene duplication contributed to the expansion of pecan kinome, 169 segmental duplication events including 285 PK genes were found, and the Ka/Ks ratio revealed they experienced strong negative selection. The RNA-Seq data of PK genes in pecan were further analyzed at the subfamily level, and different PK subfamilies performed various expression patterns across pecan embryo development or drought treatment, suggesting PK genes in pecan are involved in embryo development and drought stress response. Taken together, this study provides insight into the classification, expansion, evolution, and expression of pecan PKs. Our findings regarding expansion, expression and co-expression analyses lay a good foundation for future research to understand the roles of pecan PKs, and more efficiently determine the key candidate genes.