Genome-Wide Screening of the MYB Genes in Coptis chinensis and Their Roles in Growth, Development, and Heavy Metal Resistance

Abstract

Background:Coptis chinensis is a traditional medicinal plant rich in bioactive compounds like berberine, known for its antibacterial, anti-inflammatory, and antioxidant properties. This study aims to analyze the MYB transcription factor family in C. chinensis to better understand their roles in plant growth, development, metabolism, and stress responses. Methods: We employed bioinformatics to conduct a genome-wide identification of MYB genes in C. chinensis, followed by analyses of physicochemical properties, phylogenetic relationships, gene structures, chromosomal localization, conserved motifs, cis-acting elements, and expression patterns. Results were validated using qRT-PCR. Results: A total of 129 CcMYB genes were identified across nine chromosomes. Phylogenetic analysis categorized these genes into 19 subgroups, notably highlighting the S6 subgroup, which lacks counterparts in Arabidopsis. Comparative genomics revealed segmental duplication among gene pairs. Transcriptomic analysis indicated that CcMYB21, CcMYB40, CcMYB105, and CcMYB116 had high expression levels in stems. Importantly, CcMYB94 expression significantly increased under cadmium stress, suggesting its role in stress regulation. Conclusions: This study offers a comprehensive analysis of the MYB gene family in C. chinensis, underscoring the significance of MYB transcription factors in enhancing the plant's medicinal value and stress tolerance, particularly against cadmium exposure. These insights pave the way for further exploration of specific MYB genes to improve stress resilience in C. chinensis.

Keywords: CcMYB; Coptis chinensis; biosynthesis; cadmium stress; genome-wide identification; qRT-PCR.

Figure 1

The location of MYB family genes on 9 chromosomes of C. chinensis genome; CcMYB genes are represented by black font. Different colors represent different gene densities: blue indicates low density, while red indicates high density (divided using a 1Mb window).

Figure 2

The phylogenetic tree constructed based on the 129 CcMYB genes of C. chinensis and 168 AtMYB genes of A. thaliana, with different colors representing different subfamilies.

Figure 3

Structural characteristics and conserved motifs of the CcMYB genes. (a) Phylogenetic relationships and the gene structures of the CcMYB gene. Coding sequence (CDS) regions are represented by green rectangles, untranslated regions (UTRs) are represented by yellow rectangles, and introns are represented by black lines. (b) Conserved protein motifs of the CcMYB genes.

Figure 4

Analysis of cis-acting elements in the promoter region of the CcMYB genes. A 2 kb sequence of the promoter region of the CcMYB genes was extracted and analyzed, and different cis-acting elements are marked with specific colors.

Figure 5

(a) Syntenic analysis of CcMYB genes in C. chinensis. Red lines represent segmental duplication CcMYB gene pairs in the genome, and chromosome numbers are labeled next to each chromosome. (b) Syntenic analysis of CcMYB genes between C. chinensis and A. vilmorinianum and between C. chinensis and A. thaliana, where red lines represent CcMYB genes with collinearity and blue lines indicate CcMYB genes with segmental duplication.

Figure 6

Transcriptome analysis of CcMYB genes in different tissues. (a) Expression patterns of 129 CcMYB genes in four different tissues of C. chinensis, where red indicates high expression levels and green indicates lower expression levels. (b) Volcano plot of differentially expressed CcMYB genes among different tissues, with red representing upregulated genes and blue representing downregulated genes. (c) Venn diagram of differentially expressed CcMYB genes among different tissues.

Figure 7

Trend analysis of CcMYB genes among different tissues. (a) Trend clustering statistics of four tissues: root, stem, leaf, and flower. Different colors represent different CcMYB. (b) Number of CcMYB genes in different trend categories.

Figure 8

Transcriptome analysis of CcMYB genes under control and heavy metal stress conditions. (a) Heatmap of the expression levels of CcMYB genes in different samples under control and heavy metal stress. (b) Volcano plot of differentially expressed CcMYB genes.

Figure 9

Verification of the expression levels of 9 randomly selected CcMYB genes in different tissues using qRT-PCR. (a, b, c, d) indicate significant differences between groups: the same letters indicate no significant difference between groups, while different letters indicate significant differences between groups.