Identification and comparative analysis of flowering genes in the Sugar pathway from five Gossypium species

Abstract

Flowering is a critical plant growth stage coordinated by internal and external factors. Changes to endogenous sugar levels can promote or inhibit flowering, but research on the regulation of flowering-related genes associated with the sugar pathway in cotton is limited. Here, a genome-wide study identified 165 flowering and sugar pathway-related genes in five cotton species: Gossypium herbaceum, G. arboreum, G. hirsutum, G. barbadense, and G. raimondii. The genes were phylogenetically classified into nine subfamilies and showed a high degree of conservation. Notably, no homologs of INDETERMINATE DOMAIN 8 (IDD8), SUCROSE-PROTON SYMPORTER 9 (SUC9), or AGP GALACTOSYLTRANSFERASE 2 (GALT2) were identified. A synteny analysis provided evidence of varying degrees of gene expansion, and a selection pressure analysis indicated that the genes had undergone purifying selection, with Ka/Ks ratios of <1. The similarity among the genes identified in G. herbaceum, G. arboreum, and G. raimondii was higher than between these species and the allopolyploid cotton species, indicating the earlier divergence of these genes. A network analysis of protein interaction revealed G. hirsutum proteins to be associated primarily with sugar synthesis, transport, and metabolism. Yeast two-hybrid assays demonstrated that GhTPS1–1 and GhHXK1–1 can interact with GhPGI1–1. RNA-sequencing data for 46 genes from eight tissue-types in G. hirsutum revealed that most were highly expressed in stems and flowers. This study provides a comprehensive phylogenetic and network analysis of flowering-related genes in the sugar pathway across five Gossypium species, laying a foundation for future in-depth research on the functional mechanisms of these genes.