title: Soybean kinome: functional classification and gene expression patterns.
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.
authors.affiliation: Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
authors.forename: Jinyi
authors.initials: J
authors.lastname: Liu
authors.affiliation: Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
authors.forename: Nana
authors.initials: N
authors.lastname: Chen
authors.affiliation: Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
authors.forename: Joshua N
authors.initials: JN
authors.lastname: Grant
authors.affiliation: Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
authors.forename: Zong-Ming Max
authors.initials: ZM
authors.lastname: Cheng
authors.affiliation: Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
authors.forename: C Neal
authors.initials: CN
authors.lastname: Stewart
authors.affiliation: Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA thewezi@utk.edu.
authors.forename: Tarek
authors.initials: T
authors.lastname: Hewezi
mesh_terms: D000595:Amino Acid Sequence; D002874:Chromosome Mapping; D015870:Gene Expression; D018745:Genome, Plant / Q000235:genetics*; D005810:Multigene Family; D009928:Organ Specificity; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D011494:Protein Kinases / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D056916:Segmental Duplications, Genomic; D013025:Glycine max / Q000201:enzymology / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D011494:Protein Kinases
keywords: abiotic stress; biotic stress; co-expression network; collinearity analysis; duplication events; gene expression; soybean kinases.