Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Apr 25:12:e17304.
doi: 10.7717/peerj.17304. eCollection 2024.

Genome‑wide analysis of the MYB gene family in pumpkin

Minyan Xu #  1   2 , Jingjing Fu #  1 , Ying Ni  2 , Chenchen Zhang  1
Affiliations

Genome‑wide analysis of the MYB gene family in pumpkin

Minyan Xu et al. PeerJ. .

Abstract

The MYB gene family exerts significant influence over various biological processes and stress responses in plants. Despite this, a comprehensive analysis of this gene family in pumpkin remains absent. In this study, the MYB genes of Cucurbita moschata were identified and clustered into 33 groups (C1-33), with members of each group being highly conserved in terms of their motif composition. Furthermore, the distribution of 175 CmoMYB genes across all 20 chromosomes was found to be non-uniform. Examination of the promoter regions of these genes revealed the presence of cis-acting elements associated with phytohormone responses and abiotic/biotic stress. Utilizing quantitative real-time polymerase chain reaction (qRT-PCR), the expression patterns of 13 selected CmoMYB genes were validated, particularly in response to exogenous phytohormone exposure and various abiotic stressors, including ABA, SA, MeJA, and drought treatments. Expression analysis in different tissues showed that CmoMYB genes are expressed at different levels in different tissues, suggesting that they are functionally divergent in regulating growth and abiotic stresses. These results provide a basis for future studies to characterize the function of the MYB gene family under abiotic stresses in pumpkins.

Keywords: ABA; Abiotic/biotic stresses; Cis-acting elements; Gene; Genome-wide analysis; MYB; MeJA; Pumpkin; SA; Transcription factors.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1. The Neighbor-Joining phylogenetic tree of MYB proteins between C.moschata and Arabidopsis.
The phylogenetic tree was constructed based on the MYB domain alignment by the MEGA7.0 program with a bootstrap test (replicated 1,000 times). The proteins are clustered into 33 subgroups (e.g., C1), and 25 clades of AtMYBs are labeled in the evolutionary tree (e.g., S1). Filled purple circles represent the MYB proteins of C.moschata, and filled black circles represent the MYB proteins of Arabidopsis.
Figure 2
Figure 2. The conserved motifs and exon/intron structures of MYB genes.
(A) The distribution pattern of conserved motifs in the CmoMYBs was identified by the MEME web server. Motif distribution includes different colored boxes, each representing a unique numbered motif as indicated in the legend. The width differences among the boxes represent the motif length. (B) Exon/intron structures of MYB genes from C. moschata. TBtools software was used to visualize the above results. The exons and introns are presented as filled blue sticks and thin gray single lines, respectively. Upstream and downstream regions are represented by black bars at the two ends of sequences.
Figure 3
Figure 3. Cis-acting elements in the promoter region of ComMYB genes.
The cis-acting elements were identified by PlantCARE and visualized using the TBtools software. Different colors of the box indicate different cis-acting elements.
Figure 4
Figure 4. Expression levels of the selected 13 CmoMYB genes in different tissues.
Expression levels of the selected 13 CmoMYB genes (CmoMYB99, 165, 142, 154, 144, 116, 70, 46, 64, 59, 3, 29, and 9) in different tissues (Student’s t-test; *p < 0.05, ***p < 0.001).
Figure 5
Figure 5. ABA-induced expression patterns of 13 CmoMYB genes.
The uniformly sized three-leaf pumpkin seedlings were treated with 10 µM ABA. The leaves were harvested at the indicated times for RNA extraction and qRT-PCR analysis. The Cmoβ-actin gene was used as the normalization reference gene. The relative expression level of genes was calculated by the 2−∆∆CT method. Three experimental replicates were performed for each sample (Student’s t-test; *p < 0.05, **p < 0.01, ***p < 0.001).
Figure 6
Figure 6. The expression levels of 13 CmoMYB genes under JA (100 µM).
The three-leaf pumpkin seedlings leaves were harvested at the indicated times for RNA extraction and qRT-PCR analysis. The Cmoβ-actin gene was used as the normalization reference gene. The relative expression level of genes was calculated by the 2−∆∆CT method. Three experimental replicates were performed for each sample (Student’s t-test; *p < 0.05, **p < 0.01, ***p < 0.001).
Figure 7
Figure 7. SA-induced expression patterns of 13 CmoMYB genes.
The three-leaf pumpkin seedlings’ leaves were harvested at the indicated times after being treated with 100 µM SA for RNA extraction and qRT-PCR analysis. The Cmoβ-actin gene was used as the normalization reference gene. Three experimental replicates were performed for each sample (Student’s t-test; **p < 0.01, ***p < 0.001).
Figure 8
Figure 8. The expression levels of 13 CmoMYB genes under simulated drought (20% PEG6000).
The leaves were harvested at the indicated times for RNA extraction and qRT-PCR analysis. The Cmoβ-actin gene was used as the normalization reference gene. Three experimental replicates were performed for each sample (Student’s t-test; *p < 0.05, ***p < 0.001).
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Ambawat S, Sharma P, Yadav NR, Yadav RC. MYB transcription factor genes as regulators for plant responses: an overview. Physiology and Molecular Biology of Plants. 2013;19(3):307–321. doi: 10.1007/s12298-013-0179-1. - DOI - PMC - PubMed
    1. Arce-Rodríguez ML, Martínez O, Ochoa-Alejo N. Genome-wide identification and analysis of the MYB transcription factor gene family in chili pepper (Capsicum spp.) International Journal of Molecular Sciences. 2021;22(5):2229. doi: 10.3390/ijms22052229. - DOI - PMC - PubMed
    1. Ballester A-R, Molthoff J, Vos RD, Hekkert BtL, Orzaez D, Fernaݩndez-Moreno J-P, Tripodi P, Grandillo S, Martin C, Heldens J, Ykema M, Granell A, Bovy A. Biochemical and molecular analysis of pink tomatoes: deregulated expression of the gene encoding transcription factor SlMYB12 leads to pink tomato fruit color. Plant Physiology. 2009;152(1):71–84. doi: 10.1104/pp.109.147322. - DOI - PMC - PubMed
    1. Butt HI, Yang Z, Gong Q, Chen E, Wang X, Zhao G, Ge X, Zhang X, Li F. GaMYB85, an R2R3 MYB gene, in transgenic Arabidopsis plays an important role in drought tolerance. BMC Plant Biology. 2017;17(1):142. doi: 10.1186/s12870-017-1078-3. - DOI - PMC - PubMed
    1. Cao Y, Han Y, Li D, Lin Y, Cai Y. MYB transcription factors in chinese pear (Pyrus bretschneideri Rehd.): genome-wide identification, classification, and expression profiling during fruit development. Frontiers in Plant Science. 2016;7(10):7. doi: 10.3389/fpls.2016.00577. - DOI - PMC - PubMed

Publication types

MeSH terms

Grants and funding

This work was supported by the 2020 Outstanding Talent Support Program for Universities (No. gxyq2020086). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

LinkOut - more resources

-