Evolutionary Analysis of the Melon (Cucumis melo L.) GH3 Gene Family and Identification of GH3 Genes Related to Fruit Growth and Development

Abstract

The indole-3-acetic acid (IAA) auxin is an important endogenous hormone that plays a key role in the regulation of plant growth and development. In recent years, with the progression of auxin-related research, the function of the Gretchen Hagen 3 (GH3) gene has become a prominent research topic. However, studies focusing on the characteristics and functions of melon GH3 family genes are still lacking. This study presents a systematic identification of melon GH3 gene family members based on genomic data. The evolution of melon GH3 family genes was systematically analyzed by means of bioinformatics, and the expression patterns of the GH3 family genes in different melon tissues during different fruit developmental stages and with various levels of 1-naphthaleneacetic acid (NAA) induction were analyzed with transcriptomics and RT-qPCR. The melon genome contains 10 GH3 genes distributed across seven chromosomes, and most of these genes are expressed in the plasma membrane. According to evolutionary analysis and the number of GH3 family genes, these genes can be divided into three subgroups, and they have been conserved throughout the evolution of melon. The melon GH3 gene has a wide range of expression patterns across distinct tissue types, with expression generally being higher in flowers and fruit. Through promoter analysis, we found that most cis-acting elements contained light- and IAA-responsive elements. Based on the RNA-seq and RT-qPCR analyses, it can be speculated that CmGH3-5, CmGH3-6 and CmGH3-7 may be involved in the process of melon fruit development. In conclusion, our findings suggest that the GH3 gene family plays an important role in the development of melon fruit. This study provides an important theoretical basis for further research on the function of the GH3 gene family and the molecular mechanism underlying the development of melon fruit.

Keywords: GH3 gene family; evolutionary analysis; expression analysis; fruit development; melon.

Figure 1

Chromosome location of the melon GH3 genes.

Figure 2

Phylogenetic relationships of the GH3 gene family in plants. The GH3 gene family was identified in three Cucumis species (C. sativus, C. hystrix, and C. melo), three additional Cucurbitaceae species (bottle gourd, watermelon and squash) and two other non-Cucurbitaceae species, A. thaliana and rice. The GH3 gene family belonging to a given plant species is marked with the indicated leaf label decorations. Blocks of Groups 1–5 are highlighted with sky blue, orange, green, purple and pink, respectively. The white box represents C. hystrix GH3 genes. The green triangle represents rice GH3 genes. The red circle represents C. melo GH3 genes. The green triangle represents C. sativus GH3 genes. The blue tick represents watermelon GH3 genes. The white five-pointed star represents bottle gourd GH3 genes. The white circle represents squash GH3 genes. The white triangle represents A. thaliana GH3 genes.

Figure 3

Circos diagram of the GH3 gene for the eight plant species. The collinear gene pairs in melon are connected by red lines. The collinear gene pair between melon and cucumber is connected by a pink line. The collinear gene pair between melon and C. hystrix is connected by a green line. The collinear gene pair between melon and bottle gourd is connected by an orange line. The collinear gene pairs between melon and watermelon are connected by purple lines. The collinear gene pair between melon and squash is connected by a blue line. The collinear gene pair between melon and A. thaliana is connected by a light green line.

Figure 4

Evolutionary tree, gene structure and conservative motif analysis of the GH3 gene family in melon. Different motifs are displayed in different colored boxes as indicated on the right side, yellow indicates CDS, and gray line indicates introns.

Figure 5

Analysis of promoter cis-acting elements of CmGH3 genes. Cis-acting elements are represented by different colored boxes.

Figure 6

Expression analysis of GH3 genes in melon. (A) Tissue-specific expression analysis. (B) Expression analysis of melon in four developmental stages (10 DAA, 20 DAA, 30 DAA and fruit flesh).

Figure 7

GH3 gene expression analysis in the four melon developmental stages (fruit set, swelling melon, color change and maturity). Error bars represent the average of three replicates ± SE. The difference from the control group (fruit set stage) is statistically significant: * p < 0.05, ** p < 0.01.

Figure 8

Expression analysis of the GH3 genes in melon following NAA treatment. Error bars represent the average of three replicates ± SE. The difference from the control group (NAA treatment 0 h) was statistically significant: * p < 0.05, ** p < 0.01.

Figure 9

Tissue-specific expression analysis of GH3 genes in melon. Error bars represent the average of three replicates ± SE. The difference from the control group (root tissues) was statistically significant: ** p < 0.01.

Figure 10

CmGH3-5, CmGH3-6 and CmGH3-7 gene interaction network.