Genome-wide identification of the GATA gene family in melon (Cucumis melo) and analysis of their expression characteristics under biotic and abiotic stresses

Abstract

GATA transcription factors are an important class of transcription factors in plants, known for their roles in tissue development, signal transduction, and responses to biotic and abiotic stresses. To date, there have been no reports on the GATA gene family in melon (Cucumis melo). In this study, 24 CmGATA genes were identified from the melon genome. These family members exhibit significant differences in protein length, molecular weight, and theoretical isoelectric point and are primarily located in the nucleus. Based on the classification of Arabidopsis thaliana GATA members, the phylogenetic tree divided them into four groups: group I, group II, group III, and group IV, containing 10, 8, 4, and 2 genes, respectively. Notably, CmGATA genes within the same group have highly conserved protein motifs and similar exon-intron structures. The CmGATA family members are unevenly distributed across 10 chromosomes, with six pairs of segmentally duplicated genes and one pair of tandemly duplicated genes, suggesting that gene duplication may be the primary factor in the expansion of the CmGATA family. Melon shares 21, 4, 38, and 34 pairs of homologous genes with A. thaliana, Oryza sativa, Cucumis sativus, and Citrullus lanatus, respectively. The promoter regions are enriched with various cis-acting elements related to growth and development (eight types), hormone regulation (nine types), and stress responses (six types). Expression patterns indicate that different CmGATA family members are significantly expressed in seeds, roots, stems, leaves, tendrils, mesocarp, and epicarp, exhibiting distinct tissue-specific expression characteristics. Quantitative fluorescence analysis revealed that five genes, CmGATA3, CmGATA7, CmGATA16, CmGATA22, and CmGATA24, may be highly active under 48-h drought stress, while CmGATA1 and CmGATA22 may enhance melon resistance to heavy metal lead stress. Additionally, CmGATA22 and CmGATA24 are suggested to regulate melon resistance to Fusarium wilt infection. CmGATA22 appears to comprehensively regulate melon responses to both biotic and abiotic stresses. Lastly, potential protein interaction networks were predicted for the CmGATA family members, identifying CmGATA8 as a potential hub gene and predicting 2,230 target genes with enriched GO functions. This study preliminarily explores the expression characteristics of CmGATA genes under drought stress, heavy metal lead stress, and Fusarium wilt infection, providing a theoretical foundation for molecular mechanisms in melon improvement and stress resistance.

Keywords: Cucumis melo; Fusarium wilt infection; GATA gene family; drought stress; heavy metal lead stress.

Figure 1

Neighbor-joining phylogenetic tree of GATA family members in A. thaliana, C. melo, C. sativus, and C. lanatus. The four branch colors of the evolutionary tree represent the four groups. The solid circles in four different colors represent the genes of the four species, respectively.

Figure 2

Analysis of the phylogenetic tree, conserved motifs, domains, and gene structures of CmGATA family members. (A) Neighbor-Joining phylogenetic tree. (B) Conserved protein motifs. (C) Distribution of GATA domain positions. (D) Distribution of exons and introns. (E) Rectangle colors and corresponding types.

Figure 3

Analysis of CmGATA family members. (A) Gene chromosomal location analysis. The scale on the left represents the length of chromosomes, with ‘chr’ denoting the chromosome. Genetic intervals are set at 200 kb to calculate the gene density on each chromosome, with a gradient color from blue (low gene density) to red (high gene density) indicating this. Blank areas signify regions lacking gene distribution information. Green lines represent segmentally duplicated gene pairs. (B) Segmental duplication gene analysis. The arc shape represents chromosomes, with different colors corresponding to different chromosome numbers. The external red vertical scale indicates chromosome length. Red lines denote segmental gene pairs. (C) Analysis of GATA homologous gene pairs in melon, A. thaliana, O. sativa, C. sativus, and C. lanatus. Each horizontal line represents a chromosome, with numbers indicating the chromosome identifiers. Red lines denote the GATA homologous gene pairs.

Figure 4

Analysis of cis-acting elements in CmGATA family members. (A) Neighbor-joining phylogenetic tree. (B) Distribution of cis-acting elements analysis.

Figure 5

Analysis of expression patterns in CmGATA family members. Expression levels are normalized by row average, with a gradient from blue (low expression) to red (high expression).

Figure 6

Fluorescent quantitative expression bar graph of CmGATA genes under drought and heavy metal lead stress. (A) Drought stress. (B) Heavy metal lead stress.

Figure 7

Fluorescent quantitative expression bar graph of CmGATA genes after infection by Fusarium wilt. Yellow bars represent roots, green bars represent stems, and purple bars represent leaves.

Figure 8

Protein interaction and target gene analysis. (A) Protein interaction network of CmGATA family members. (B) Meaning of different colored lines in the interaction network. (C) GO enrichment bubble chart of CmGATA family members. FDR stands for false discovery rate. (D) Binding site profile of the Arabidopsis GATA12 transcription factor. (E) Statistical results of GO enrichment for target genes.

Figure 9

Predicted tertiary structure of CmGATA family member proteins.