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

Abstract

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.

UDP-Glucose Dehydrogenases: Identification, Expression, and Function Analyses in Upland Cotton (Gossypium hirsutum)

“…We identified 15 UGD genes each in G. hirsutum and G. barbadense and 6 UGD genes each in G. arboreum and G. raimondii ( Figure 1B ). These results indicate that UGD gene family in G. hirsutum and G. barbadense may expand through duplications during their evolutions, which is a common phenomenon in plant genome evolutions ( Schaper and Anisimova, 2015 ; Ge et al, 2020 ). On the other hand, gene losses in both allotetraploid diploid species are also observed ( Li et al, 2015 ; Hu et al, 2019 ).…”

“…The CDS and protein lengths of the UGD genes suggest that the UGD genes are in a conservative mode in genome evolution among the four Gossypium species. Ka/Ks value analysis reveals that the Ka/Ks values of most UGD homologous pairs are below 0.1 ( Figure 2 ), indicating purifying selection pressure of UGD gene family during its evolution ( Ge et al, 2020 ).…”

Association Mapping of Verticillium Wilt Disease in a Worldwide Collection of Cotton (Gossypium hirsutum L.)

“…Fructose-1,6bisphosphatase (FBP) is a key enzyme in the plant sucrose synthesis pathway in the Calvin cycle and plays an important role in the regulation of photosynthesis in green plants. In addition, it is associated with the fiber quality of cotton as well as salt stress and Verticillium wilt disease [37]. Marker A8451, with which we found a very strong association in the 10th and 12th chromosomes of the cotton genome, was located on the uncharacterized protein LOC107963741-LOC107960135.…”

Genome-wide identification of the MIOX gene family and their expression profile in cotton development and response to abiotic stress

“…Due to the rapid development of next generation sequencing, the whole genomes have been reported for the diploid D-genome of G. raimondii [15], A-genome of G. arboretum [16], G. herbaceum [17], and allopolyploid AD genome species of G. hirsutum [18], G. barbadense [18], G. darwinii, G. mustelinum and G. tomentosum [19]. The sequence of these genomes provides useful resources for studying the gene families and a series of families have been genome-wide analyzed in cotton [20,21].…”