Identification of UGT gene family in grape
A total of 181 UGT genes were identified in the grape genome (Table 1). These UGTs were named VvUGT1 to VvUGT181 according to their chromosomal locations. They were unevenly distributed on 18 grape chromosomes except for 10 UGT members (Fig. 1). Among them, chromosome 5 contained the most UGT genes (26 members), followed chromosome 18 (23 members), and chromosome 12 (19 members). Only one member was mapped to chromosome 9. Notably, many clusters were observed on 18 chromosomes, such as Chr3, Chr5, Chr6, and Chr17 (Fig. 1). The physicochemical properties analysis showed that the length of VvUGTs ranged from 380 aa (VvUGT74) to 1397 aa (VvUGT181), with an average of approximately 486 aa. The predicted molecular weight of UGTs ranged from 42.60 kDa (VvUGT74) to 156.47 kDa (VvUGT181), averaging 54.07 kDa. Isoelectric point (PI) values were between 4.84 (VvUGT144) and 7.36 (VvUGT77), averaging 5.76. The instability index of most VvUGTs were found to be more than 40 and regarded as unstable proteins. Grand Average of Hydropathicity (GRAVY) scores of more than three quarters of VvUGT proteins were negative, suggesting their hydrophilicity (Table 1).
Analysis of phylogenetic, gene structure and conserved motif
To investigate the evolutionary relationship of the VvUGT gene family, a phylogenetic tree was constructed based on the UGT protein sequences from grape, Arabidopsis, tomato, mouse-ear hawkweed and maize. The phylogenetic tree revealed that 181 VvUGTs can be divided into 17 groups (A-P, R) (Fig. 2). Group E contained the largest VvUGT members (56), followed by group P (24). Group O was the smallest (only one VvUGT member). The group Q was observed only in maize, indicating that it may be monocotyledon-specific group.
Analysis of gene structure is helpful to understand the evolution of gene families. Thus, we analyzed genomic makeup of each VvUGT member (Fig. 3). There were 101 VvUGT genes with no introns and 80 with at least one intron. Of the 80 intron-containing VvUGT genes, 70 contained one intron, 6 had two introns, and the remaining genes possessed between three and five introns. Combined with the phylogenetic tree, most VvUGT genes within the same group possessed a comparable gene structure. For instance, there were no introns in R group, and almost members of group L contained one intron.
The distribution of conserved motifs of VvUGTs was performed by MEME online software (Fig. 3). A total of 20 conserved motifs were detected. Motif 1, 2, 3, 4, 5, 6, 7, 8, 10, 12 and 13 existed in most VvUGT proteins, but some motifs only were found in specific groups. For example, motif 20 was specific to group P and H. Motif 11, 14 and 18 only existed in group E. Additionally, motifs 5 and 15 located at the beginning and motif 9 was in the end of almost VvUGT sequences. In general, the same group shared analogous motifs, and this supported evolutionary classification of VvUGTs above.
Cis-regulatory elements in grape UGT gene promoters
To investigate the promoter features, 2000 bp upstream of VvUGT genes was analyzed (Fig. 4). Many kinds of cis-elements were identified and mainly divided into four categories, including light response, phytohormone response, stress response, and development (Fig. 4). All VvUGT gene promoters were found to contained the light responsive elements, such as Box 4, G-box, GT-motif, and I-box. This implied that the transcription regulation of VvUGT genes may influenced by light signals. The hormone-responsive elements comprised 11 types of elements, in which ABRE (ABA responsiveness), CGTCA-motif (MeJA-responsiveness), and TCA-element (SA responsiveness) were the most abundant, accounting for 25.9%, 22.5%, and 12.6%, respectively. Besides, stress-responsive and development-related elements were identified, such as low-temperature responsiveness (LTR), drought inducibility responsiveness (MBS), CAT-boxes, and circadian elements. The findings indicated that the VvUGT genes were closely associated with plant development and stress responses.
Interspecific and intraspecific collinearity analysis
In order to explore the expansion and evolution mechanisms of VvUGT gene family, gene duplication events in grape genome were analyzed (Fig. 5). In this study, MCScanX software was used to compare grape genome based on amino acid sequence homology. A total of 15 segmental-duplication gene pairs were identified, including VvUGT85/93, VvUGT85/98, VvUGT149/8, VvUGT1/41, VvUGT89/99, VvUGT191/3, VvUGT117/141, VvUGT65/69, VvUGT90/95, VvUGT109/66, VvUGT82/93, VvUGT82/97, VvUGT104/53, VvUGT85/94, and VvUGT86/94. In addition, analysis of intrachromosomal duplication revealed that 159 VvUGT genes were from tandem repeat events, leading to the paralogous gene clusters in the genome (Table S1). These results indicated that segmental duplication and tandem duplication acted important roles in the expansion of the VvUGT family.
To further explore the evolution of the VvUGT gene family, we performed collinearity analysis between Arabidopsis and grape (Fig. 6). There were a total of 27 collinear UGT gene pairs between Arabidopsis and grape genomes, in which 24 genes from Arabidopsis and 27 genes from grape. These VvUGTs were located on 13 chromosomes (chr2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, and 19), and chromosomes 6 and 18 contained more collinear VvUGT genes than any other chromosome. The nonuniformity distribution of VvUGT genes on the chromosome indicated that there were genetic variations in the evolution of grape.
Enrichment analysis of grape
In order to understand the biological processes of VvUGTs, functional enrichment analysis was conducted by TBtools (Fig. 7; 8). GO analysis found that VvUGT family members were mainly concentrated on transferase activity, such as quercetin 3-O-glucosyltransferase activity, quercetin 7-O-glucosyltransferase activity, hexosyltransferase activity, flavonoids and flavonoid metabolic processes and other pathways (Fig. 7). KEGG enrichment analysis identified some relevant metabolic pathways of VvUGT family, including glucosinolate biosynthesis, tryptophan metabolism, metabolism of terpenoids and polyketides, amino acid metabolism, anthocyanin biosynthesis, and other biosynthesis of various secondary metabolites (Fig. 8). Based on KEGG and GO results, we identified 14 VvUGT genes involved flavonoid synthesis pathway. They are VvUGT60, VvUGT61, VvUGT62, VvUGT63, VvUGT79, VvUGT80, VvUGT81, VvUGT124, VvUGT165, VvUGT166, VvUGT167, VvUGT168, VvUGT169, VvUGT170. These candidate VvUGT genes related to flavonoid biosynthesis will provide evidence for the further research on plant secondary metabolites regulation mechanism.
Expression profiles of VvUGTs in different tissues
The expression pattern of VvUGT genes in five tissues (root, stem, leaf, flower and berrypericarp) was analyzed based on chip data (Fig. 9). The results showed that a total of 60 VvUGT genes were expressed in all tissues. The expression level of VvUGT99 in the root was higher than that in other tissues. 8 VvUGTs (VvUGT87, VvUGT97, VvUGT116, VvUGT119, VvUGT120, VvUGT125, VvUGT129 and VvUGT134) exhibited high levels of expression in all tissues of grape, suggesting their crucial roles in the growth and development of grape. Both VvUGT124 and VvUGT79 showed high expression level in berrypericarp and flower, respectively.
Expression profiles of VvUGTs in fruits at different development stages
To understand a potential function for VvUGT genes in fruit development, we investigated transcriptome data from two grape cultivars, including ‘Muscat Blanc’ and ‘Muscat Rouge’, at three developmental stages (Fig. 10). The findings revealed that 32 VvUTGs were not detected in any stages, while 149 VvUGTs were expressed at different stages. Among them, 13 VvUGT genes showed high expression abundance in all stages, which they may function in fruit development. In ‘Muscat Blanc’, VvUGT10 and VvUGT12 showed high expression levels in the young fruit stage, and expression of VvUGT134 and VvUGT145 was high in fruit veraison. VvUGT10, VvUGT51, VvUGT134 and VvUGT145 were highly expressed in maturity. Similar situation was observed at maturity of Muscat Rouge. The expression levels of VvUGT10, VvUGT12 and VvUGT13 genes of Muscat Rouge is lower than that of Muscat Blanc in at young fruit stage, while VvUGT22 and VvUGT124 genes of Muscat Rouge showed higher expression abundance than that of Muscat Blanc at both veraison and maturity.
Expression profiles of VvUGTs under abiotic stress
In order to further analyze the expression characteristics of VvUGT genes under abiotic stress, we investigated the response of VvUGT genes to salt and drought stress in this study (Fig. 11). 24 VvUGT genes were expressed under salt and drought stress. Under salt stress, the expression levels of 8 genes (VvUGT12, VvUGT30, VvUGT36, VvUGT59, VvUGT104, VvUGT122, VvUGT124, and VvUGT133) decreased after 16 days under salt stress treatment. 7 genes (VvUGT25, VvUGT40, VvUGT69, VvUGT97, VvUGT107, VvUGT125, VvUGT179) showed an increasing trend under salt stress. Under drought stress, the expression of VvUGT125 was significantly upregulated, while VvUGT122 exhibited a remarkable decrease after 16 days. Overall, the trend of gene expression was similar between salt and drought stress.