Abstract
The protein kinase (PK) gene family is one of the largest and most highly conserved gene families in plants and plays a role in nearly all biological functions. While a large number of genes have been predicted to encode PKs in soybean, a comprehensive functional classification and global analysis of expression patterns of this large gene family is lacking. In this study, we identified the entire soybean PK repertoire or kinome, which comprised 2166 putative PK genes, representing 4.67% of all soybean protein-coding genes. The soybean kinome was classified into 19 groups, 81 families, and 122 subfamilies. The receptor-like kinase (RLK) group was remarkably large, containing 1418 genes. Collinearity analysis indicated that whole-genome segmental duplication events may have played a key role in the expansion of the soybean kinome, whereas tandem duplications might have contributed to the expansion of specific subfamilies. Gene structure, subcellular localization prediction, and gene expression patterns indicated extensive functional divergence of PK subfamilies. Global gene expression analysis of soybean PK subfamilies revealed tissue- and stress-specific expression patterns, implying regulatory functions over a wide range of developmental and physiological processes. In addition, tissue and stress co-expression network analysis uncovered specific subfamilies with narrow or wide interconnected relationships, indicative of their association with particular or broad signalling pathways, respectively. Taken together, our analyses provide a foundation for further functional studies to reveal the biological and molecular functions of PKs in soybean.
Highlights
The protein kinase (PK) gene family is one of the largest and most highly conserved gene families in plants
The 2166 soybean PKs were classified into 19 groups in which receptor-like kinase (RLK) (1418), cyclindependent kinases (CMGC) (166), calcium- and calmodulin-regulated kinase (CAMK) (158), tyrosine kinase-like kinase (TKL) (115), STE (86), AGC (70), and casein kinase 1 (CK1) (32) comprised 2045 genes, representing 94% of the soybean kinome
The large size of the soybean PK superfamily could partly be attributed to the large genome size and two whole-genome-wide duplication (WGD) events that occurred 59 and 13 million years ago (Mya)
Summary
The protein kinase (PK) gene family is one of the largest and most highly conserved gene families in plants. Genome-wide identification of PKs in a number of plant species have indicated the presence of more than 3% of the annotated proteins coding for PKs, an indication of their functional importance (Lehti-Shiu et al, 2009; Lehti-Shiu and Shiu, 2012).
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