Abstract
The protein kinase (PK, kinome) family is one of the largest families in plants and regulates almost all aspects of plant processes, including plant development and stress responses. Despite their important functions, comprehensive functional classification, evolutionary analysis and expression patterns of the cotton PK gene family has yet to be performed on PK genes. In this study, we identified the cotton kinomes in the Gossypium raimondii, Gossypium arboretum, Gossypium hirsutum and Gossypium barbadense genomes and classified them into 7 groups and 122–24 subfamilies using software HMMER v3.0 scanning and neighbor-joining (NJ) phylogenetic analysis. Some conserved exon-intron structures were identified not only in cotton species but also in primitive plants, ferns and moss, suggesting the significant function and ancient origination of these PK genes. Collinearity analysis revealed that 16.6 million years ago (Mya) cotton-specific whole genome duplication (WGD) events may have played a partial role in the expansion of the cotton kinomes, whereas tandem duplication (TD) events mainly contributed to the expansion of the cotton RLK group. Synteny analysis revealed that tetraploidization of G. hirsutum and G. barbadense contributed to the expansion of G. hirsutum and G. barbadense PKs. Global expression analysis of cotton PKs revealed stress-specific and fiber development-related expression patterns, suggesting that many cotton PKs might be involved in the regulation of the stress response and fiber development processes. This study provides foundational information for further studies on the evolution and molecular function of cotton PKs.
Highlights
The protein kinase (PK, kinome) family is one of the largest families in plants and regulates many signaling pathways that are triggered during stress and development processes [1]
We identified 1517, 1407, 2508 and 2745 PK genes with typical kinase domains (S1 Table) and excluded 70, 147, 363 and 390 sequences with atypical kinase domains in G. raimondii, G. arboretum, G. hirsutum and G. barbadense, respectively (S2 Table)
Cotton PKs were classified into seven groups: receptor-like kinase (RLK) (G. raimondii 1019, G. arboretum 913, and G. hirsutum 1681, and G. barbadense 1855), AGC (52, 55, 81, 96), calcium- and calmodulin-regulated kinase (CAMK) (114, 113, 189, 207), cyclin-dependent kinases (CMGC) (105, 100, 180, 182), STE (60, 59, 103, 112), tyrosine kinaselike kinase (TKL) (80, 80, 130, 143), and others (87, 87, 144, 150)
Summary
The protein kinase (PK, kinome) family is one of the largest families in plants and regulates many signaling pathways that are triggered during stress and development processes [1]. The common structural feature of PKs is their 250–300 amino acid catalytic domain, which uses the γ-phosphate of adenosine triphosphate (ATP) to phosphorylate serine, threonine or tyrosine residues of proteins [2]. Phylogenetic analyses of the PK family were initially conducted using the conserved feature of the catalytic domain [3].
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