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. 2024 Nov 13;24(1):1068.
doi: 10.1186/s12870-024-05775-1.

Genome-wide identification of the OVATE gene family and revelation of its expression profile and functional role in eight tissues of Rosa roxburghii Tratt

Yanlin An #  1 , Xueqi Li #  1 , Yani Chen  1 , Sixia Jiang  1 , Tingting Jing  2 , Feng Zhang  3
Affiliations

Genome-wide identification of the OVATE gene family and revelation of its expression profile and functional role in eight tissues of Rosa roxburghii Tratt

Yanlin An et al. BMC Plant Biol. .

Abstract

Background: The OVATE gene family is a new class of transcriptional repressors, which play an important regulatory role in plant growth and development. Many studies have proved that the OVATE gene family can regulate the development of plant tissues and organs and resist stress, but its quantity and functional role in Rosa roxburghii remain unknown.

Results: In this study, 14 OVATE family members were identified by re-annotating the genome of Rosa roxburghii, and these members were unevenly distributed on 6 chromosomes. Evolutionary analysis indicated that these family members were classified into three groups. In their promoter regions, many hormone-related cis-acting elements such as ABA, GA, and MeJA were identified. Segmental duplication is an important driving force for the expansion of the OVATE family in Rosa roxburghii. Transcriptome sequencing and RT-qPCR analysis showed that OVATE gene family had a specific tissue expression pattern in Rosa roxburghii. For instance, the expression level of gene Rr602241 in leaves was more than 4 times that of other tissues. The gene Rr101515 was highly expressed in FR1 and FR4 stages of fruit tree development, and was highly homologous to the gene regulating fruit shape in tomatoes. These results suggest that members of the OVATE gene family may have diverse functions in different tissues. Furthermore, based on the transcriptome data of eight tissues, a transcriptional regulatory co-expression network of different transcription factors and 14 OVATE genes was constructed.

Conclusion: In conclusion, our study provides the expression profiles of the OVATE family and reveals the potential functional roles of different members in the growth and development of Rosa roxburghii Tratt.

Keywords: Rosa roxburghii Tratt; Gene expression; OVATE gene family; Tissue growth and development; Transcriptome sequencing.

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Conflict of interest statement

Declarations Ethics approval and consent to participate Not applicable. The sampling of plant material was performed in compliance with institutional guidelines. The research conducted in this study required neither approval from an ethics committee, nor involved any human or animal subjects. Consent for publication Not applicable. Competing interests The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Distribution of the OVATE genes in the Rosa roxburghii genome. The left axis shows the length of each chromosome, and it was estimated in mega base (Mb)
Fig. 2
Fig. 2
Construction and analysis of the phylogenetic tree. An unrooted neighbor-joining phylogenetic tree was constructed based on the OVATE sequences in the genomes of Rosa roxburghii Tratt, Arabidopsis thaliana, apple and peach. The bootstrap test was set to 1,000 replicates
Fig. 3
Fig. 3
Motif, gene structure and cis-acting regulatory elements analysis of the OVATE gene family. (A) Protein motifs of OVATE genes. Six conservative motifs are shown in the figure. (B) Cis-acting regulatory elements analysis of the OVATE genes. Sequences of the 2000 bp above the start codon were used to identify cis-acting elements. (C) Gene structure of OVATE genes
Fig. 4
Fig. 4
Circle plot showing collinearity of OVATE gene family in Rosa roxburghii Tratt. Collinearity genes were highlighted with red curved lines
Fig. 5
Fig. 5
Synteny analysis of OVATE genes from Arabidopsis, Peach and Apple, Cabbage, Cotton
Fig. 6
Fig. 6
Differentially expressed genes among eight tissues of Rosa roxburghii and KEGG enrichment analysis. (A) Number of differentially expressed genes in different tissues. (B) KEGG enrichment analysis of differentially expressed genes in fruits at five developmental stages. (C) KEGG enrichment analysis of differentially expressed genes between fruits and flowers
Fig. 7
Fig. 7
The expression characteristics of OVATE gene family in eight tissues of Rosa roxburghii were analyzed based on transcriptome sequencing. Different letters above the bars represent significant differences at p < 0.05. ND means not detected
Fig. 8
Fig. 8
Expression of OVATE genes analyzed by RT-qPCR in different tissues of Rosa roxburghii. Different letters above the bars represent significant differences at p < 0.05. ND means not detected
Fig. 9
Fig. 9
Transcriptional regulatory network of OVATE gene family in Rosa roxburghii. The correlations between the expression of OVATE genes and that of different transcription factors are shown with colored lines (Pearson’s correlation test, P ≤ 0.05). The detailed expression correlations used for network construction are listed in Table S10
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