Genome-Wide Characterization of Fructose 1,6-Bisphosphate Aldolase Genes and Expression Profile Reveals Their Regulatory Role in Abiotic Stress in Cucumber

Abstract

The fructose-1,6-bisphosphate aldolase (FBA) gene family exists in higher plants, with the genes of this family playing significant roles in plant growth and development, as well as response to abiotic stresses. However, systematic reports on the FBA gene family and its functions in cucumber are lacking. In this study, we identified five cucumber FBA genes, named CsFBA1-5, that are distributed randomly across chromosomes. Phylogenetic analyses involving these cucumber FBAs, alongside eight Arabidopsis FBA proteins and eight tomato FBA proteins, were conducted to assess their homology. The CsFBAs were grouped into two clades. We also analyzed the physicochemical properties, motif composition, and gene structure of the cucumber FBAs. This analysis highlighted differences in the physicochemical properties and revealed highly conserved domains within the CsFBA family. Additionally, to explore the evolutionary relationships of the CsFBA family further, we constructed comparative syntenic maps with Arabidopsis and tomato, which showed high homology but only one segmental duplication event within the cucumber genome. Expression profiles indicated that the CsFBA gene family is responsive to various abiotic stresses, including low temperature, heat, and salt. Taken together, the results of this study provide a theoretical foundation for understanding the evolution of and future research into the functional characterization of cucumber FBA genes during plant growth and development.

Keywords: abiotic stresses; cucumber; fructose-1,6-bisphosphate aldolase; genome-wide identification.

Figure 1

Evolutionary relationships of FBA family in cucumber, Arabidopsis, and tomato. (A) Phylogenetic tree of the relationship between the FBA proteins of cucumber, Arabidopsis, and tomato. C1 and C2 represent different subfamilies. The evolutionary history was inferred using the neighbor-joining method [46]. The optimal tree with a sum of branch length = 1.60678193 is shown. The tree is drawn to scale, with branch lengths (above the branches) in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the p-distance method [47] and are presented as the number of amino acid differences per site. The analysis involved 21 amino acid sequences. All positions containing gaps and missing data were eliminated, resulting in a final dataset comprising a total of 132 positions. Evolutionary analyses were conducted using MEGA7.0 [48]. (B) Multiple sequence alignment of the glycolysis domains of 21 FBA proteins from cucumber, A. thaliana, and tomato using 100 amino acids on either side of the structural domain.

Figure 2

Phylogenetic tree, gene structure, and motif pattern of CsFBA proteins. (A) The phylogenetic tree was constructed using the full-length sequences of CsFBA proteins with 1000 replicates on each node. (B) Green rectangles, yellow rectangles, and black lines indicate UTRs (non-coding regions), CDSs (coding sequences or exons), and introns, respectively. (C) The amino acid motifs (numbered 1–10) in CsFBA proteins are displayed in ten colored boxes, and black lines indicate amino acid length.

Figure 3

(A) Chromosomal location of CsFBAs. The colored rectangular bars represent the chromosomes of cucumber, and the 0–45 Mb scale represents chromosome length. (B) Synteny analysis of FBA genes on cucumber chromosomes. Seven cucumber chromosomes are colored in green with their names. The black line in the figure denotes the syntenic region of the cucumber genome.

Figure 4

Collinear analyses of FBA genes between cucumber, Arabidopsis, and tomato. The gray lines between cucumber and other plants represent collinear blocks in wide regions of the genomes, while blue lines show the orthologous relationship of FBA genes.

Figure 5

Expression patterns of the five CsFBA genes in cucumber seedlings after low-temperature treatment (A–E), heat treatment (F–J), and salt treatment (K–O). * Significant differences according to t-test (* p < 0.05, ** p < 0.01).