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. 2025 May 23:16:1588362.
doi: 10.3389/fpls.2025.1588362. eCollection 2025.

Pan-genome analysis of the R2R3-MYB genes family in Brassica napus unveils phylogenetic divergence and expression profiles under hormone and abiotic stress treatments

Haiyan Fan  1   2 , Jiawei Li  1   3 , Wencong Huang  1 , Aoshuang Liang  1 , Liqing Jing  2 , Jintao Li  2 , Qing-Yong Yang  1   3 , Kede Liu  1 , Zhiquan Yang  3
Affiliations

Pan-genome analysis of the R2R3-MYB genes family in Brassica napus unveils phylogenetic divergence and expression profiles under hormone and abiotic stress treatments

Haiyan Fan et al. Front Plant Sci. .

Abstract

Introduction: The R2R3-MYB transcription factors (TFs) are pivotal regulators of plant growth, development, and stress responses. However, their genetic diversity and functional roles in Brassica napus remain underexplored at a pan-genome scale.

Methods: We identified R2R3-MYB genes in 18 published rapeseed genomes and analyzed their genomic distribution patterns, gene duplication, selective pressure, gene structure, conserved motifs, and phylogenetic relationships using a pan-genome approach. Additionally, transcriptomic datasets from hormone treatments and drought/heat stress experiments were analyzed to identify hormone-responsive and stress-responsive genes.

Results: We systematically identified 7,552 R2R3-MYB genes from 18 B. napus genomes, which were grouped into 353 gene clusters based on the pan-genome approach, including 139 core, 121 softcore, 68 dispensable, and 25 private gene clusters. Similar to Arabidopsis, the B. napus R2R3-MYB genes can be clustered into 29 subgroups based on the phylogenetic tree, suggesting conserved functional roles in B. napus and A. thaliana. Cis-element profiling highlighted enrichment in hormone-responsive and stress-related elements in the promoter regions of the R2R3-MYB genes. Transcriptomic analyses identified 283 hormone-responsive and 266 stress-responsive R2R3-MYB genes, and 30 co-regulated genes under drought and heat stress implicate their roles in combined stress adaptation.

Discussion: These findings provide the first pan-genome resource for R2R3-MYB genes in B. napus, which can serve as pivotal targets for enhancing stress resilience in rapeseed breeding programs.

Keywords: R2R3-MYB; abiotic stresses; pan-genome analysis; phylogenetic relationship; plant hormones.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Figures

Figure 1
Figure 1
Number of R2R3-MYB genes in 18 Brassica napus genomes. The number of R2R3-MYB genes among each accession. Blue bars represent the number of R2R3-MYB genes in 18 genomes.
Figure 2
Figure 2
Distribution of R2R3-MYB genes across subgenomes and chromosomes in Brassica napus. (A) Number of R2R3-MYB genes in subgenomes An and Cn in the 18 genomes. Pink and blue boxes represent numbers of R2R3-MYB genes in subgenomes An and Cn, respectively. Black dots represent numbers of R2R3-MYB genes of 18 genomes. (B) Number of R2R3-MYB genes across chromosomes in 18 genomes. Boxes with different colors represent numbers of R2R3-MYB genes in A01-C09 chromosomes and black dots respresent numbers of R2R3-MYB genes of 18 genomes. (C) Chromosomal locations of R2R3-MYB genes in ZS11 genome. Blue to red regions in 19 chromosomes represent low to high gene density with the window size of 100 kb and the step size of 100 kb. Purple triangles represent R2R3-MYB genes.
Figure 3
Figure 3
The panR2R3-MYB genes constructed from the 18 Brassica napus genomes. (A) The number of pan-genome and core R2R3-MYB OGGs in the 18 genomes. Blue and pink boxes represent pan-genome and core OGGs, respectively. (B) Composition of OGGs at the pan-genome level. The histogram shows the frequency distribution of OGGs shared by different numbers of genomes. The pie chart shows the proportion of different groups of OGGs. Deep yellow, light yellow, blue and purple bars and pies represent core, softcore, dispensable and private OGGs, respectively. (C) The presence and absence of R2R3-MYB OGGs in the 18 genomes. Red and blue regions represent present and absent OGGs, respectively. (D) Percentage of different R2R3-MYB gene groups in each of the 18 genomes. Deep yellow, light yellow, blue and purple bars and pies represent core, softcore, dispensable and private OGGs, respectively. (E, F) Comparison of Ka/Ks ratios (E) and sequence diversities (F) in promoters between core and variable OGGs (two-sided Student’s t test). (G) Expression levels of core and variable R2R3-MYB genes in ZS11 across various tissues: Bud, Cotyledon, Leaf, Petal, Pollen, Root, Seed, Silique, and Stem. In (E–G), pink and blue boxes represent core and variable OGGs, respectively. .
Figure 4
Figure 4
Phylogenetic classification of A. thaliana and B. napus R2R3-MYB genes. Representative R2R3-MYB genes for 353 OGGs were included. The R2R3-MYB genes in B. napus were classified into four categories: core (red labels), softcore (purple labels), and dispensable (brown labels) and private (grey labels), based on their presence in 18 B. napus genomes, with R2R3-MYB genes in A. thaliana highlighted in blue. The subfamilies of S1–S25 represented subfamilies based on groups of R2R3-MYB proteins in A. thaliana and subfamilies are highlighted in different colors accordingly.
Figure 5
Figure 5
The number of up- and down-regulated DEGs under different hormone and abiotic stress treatments. (A) The number of up- and down-regulated DEGs under different hormone treatments. (B) The number of up- and down-regulated DEGs under different abiotic stress treatments. In (A, B), red and blue bars represent up- and down-regulated DEGs, respectively. .
Figure 6
Figure 6
Sequence characteristics of the R2 and R3 repeats in R2R3-MYB proteins in A. thaliana and B. napus. (A, B) Sequence characteristics of the R2 repeats in R2R3-MYB proteins in A. thaliana (A) and B. napus (B). (C, D) Sequence characteristics of the R3 repeats in R2R3-MYB proteins in A. thaliana (C) and B. napus (D). The bit score represents the information content of each amino acid at specific positions within the sequence. The locations of the three α-helices are indicated (helices 1 to 3). Conserved tryptophan residues (Trp, W) within the MYB domain are highlighted with red asterisks, while substituted residues in the R3 repeat are denoted by yellow asterisks.
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