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Plant specific transcription factors, SQUAMOSA promoter-binding protein-like (SPL), are involved in many biological processes. However, no systematical study has been reported in cotton. In this study, a total of 177  SPL  genes were identified, including 29, 30, 59 and 59  SPLs  in  Gossypium arboreum ,  G. raimondii ,  G. barbadense , and  G. hirsutum , respectively. These  SPL  genes were classified into eight phylogenetical groups. The gene structure, conserved motif, and clustering were highly conserved within each orthologs. Two zinc finger-like structures (Cys3His and Cys2HisCys) and NLS segments were existed in all GrSPLs. Segmental duplications play important roles in SPL family expansion, with 20 genes involved in segmental duplications and 2 in tandem duplications, and ten ortholog pairs in syntenic regions between  G. raimondii  and  A. thaliana . Several putative cis-elements, involved in light, stresses and phytohormones response, were found in the promoter regions of  GhSPLs , suggesting that plant responses to those environmental changes may be induced through targeting SPL transcription factors. RNA-seq analysis shows that SPL genes were differentially expressed in cotton; some were highly expressed during fiber initiation and early development. Comparing with other plants, SPL genes show subfunctionalization, lost and/or gain functions in cotton during long-term domestication and evolution.

Genome-wide identification and characterization of SPL transcription factor family and their evolution and expression profiling analysis in cotton