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Background  The glycogen synthase kinase 3/shaggy kinase (GSK3) is a serine/threonine kinase with important roles in animals. Although  GSK3  genes have been studied for more than 30 years, plant  GSK  genes have been studied only since the last decade. Previous research has confirmed that plant  GSK  genes are involved in diverse processes, including floral development, brassinosteroid signaling, and responses to abiotic stresses.    Result  In this study, 20, 15 (including 5 different transcripts) and 10  GSK  genes were identified in  G. hirsutum ,  G. raimondii  and  G. arboreum , respectively. A total of 65 genes from  Arabidopsis , rice, and cotton were classified into 4 clades. High similarities were found in GSK3 protein sequences, conserved motifs, and gene structures, as well as good concordance in gene pairwise comparisons ( G. hirsutum  vs.  G. arboreum ,  G. hirsutum  vs.  G. raimondii , and  G. arboreum  vs.  G. raimondii ) were observed. Whole genome duplication (WGD) within At and Dt sub-genomes has been central to the expansion of the  GSK  gene family. Furthermore,  GhSK  genes showed diverse expression patterns in various tissues. Additionally, the expression profiles of  GhSKs  under different stress treatments demonstrated that many are stress-responsive genes. However, none were induced by brassinolide treatment. Finally, nine co-expression sub-networks were observed for  GhSKs  and the functional annotations of these genes suggested that some  GhSK s might be involved in cotton fiber development.    Conclusion  In this present work, we identified 45  GSK  genes from three cotton species, which were divided into four clades. The gene features, muti-alignment, conversed motifs, and syntenic blocks indicate that they have been highly conserved during evolution. Whole genome duplication was determined to be the dominant factor for  GSK  gene family expansion. The analysis of co-expressed sub-networks and tissue-specific expression profiles suggested functions of  GhSKs  during fiber development. Moreover, their different responses to various abiotic stresses indicated great functional diversity amongst the  GhSKs . Briefly, data presented herein may serve as the basis for future functional studies of GhSKs.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1526-8) contains supplementary material, which is available to authorized users.

bmc plant biology

Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress