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Background  Fructose-1,6-bisphosphatase (FBP) is a key enzyme in the plant sucrose synthesis pathway, in the Calvin cycle, and plays an important role in photosynthesis regulation in green plants. However, no systemic analysis of FBPs has been reported in  Gossypium  species.    Results  A total of 41  FBP  genes from four  Gossypium  species were identified and analyzed. These  FBP  genes were sorted into two groups and seven subgroups. Results revealed that  FBP  family genes were under purifying selection pressure that rendered FBP family members as being conserved evolutionarily, and there was no tandem or fragmental DNA duplication in  FBP  family genes. Collinearity analysis revealed that a  FBP  gene was located in a translocated DNA fragment and the whole  FBP  gene family was under disequilibrium evolution that led to a faster evolutionary progress of the members in  G. barbadense  and in A t  subgenome than those in other  Gossypium  species and in the D t  subgenome, respectively, in this study. Through RNA-seq analyses and qRT-PCR verification, different  FBP  genes had diversified biological functions in cotton fiber development (two genes in 0 DPA and 1DPA ovules and four genes in 20–25 DPA fibers), in plant responses to  Verticillium  wilt onset (two genes) and to salt stress (eight genes).    Conclusion  The FBP gene family displayed a disequilibrium evolution pattern in  Gossypium  species, which led to diversified functions affecting not only fiber development, but also responses to  Verticillium  wilt and salt stress. All of these findings provide the foundation for further study of the function of  FBP  genes in cotton fiber development and in environmental adaptability.

Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species