Genome-wide identification and expression profiling of MYB transcription factors in Artemisia argyi

Abstract

Artemisia argyi, a significant medicinal plant in China, is known for its high content of essential oils, flavonoids, and other bioactive compounds. MYB transcription factors are the largest gene family in plants and are widely reported to play important roles in plant development, metabolism, defense, and stress resistance. However, the MYB family of A. argyi has not been systematically studied. The aim of this study was to comprehensively analyze the MYB gene family of A. argyi and explore its potential role in flavonoid biosynthesis. Here, the phylogeny, chromosome location, gene structure, cis-acting elements, expression patterns and Gene ontology (GO) annotation of MYB gene family members were investigated using bioinformatics methods based on the whole-genome and transcriptome data of A. argyi. In total, 227 AYMYB transcription factors were identified from A. argyi genome, including 22 1R-MYB, 165 R2R3-MYB, 16 3R-MYB, 5 4R-MYB and 19 atypical MYB members. These AYMYBs were unevenly distributed across the A. argyi genome. Subcellular localization prediction revealed that all the AYMYBs were localized in the nucleus. The protein motifs, conserved domains, and gene structures of AYMYBs were identified, and the results showed that AYMYBs from the same subfamily exhibited similar motifs and gene structures. Cis-acting elements and GO analysis suggested that AYMYBs may be involved in many biological processes related to plant development, metabolism, defense, and stress resistance. Moreover, quantitative real-time PCR (qRT-PCR) analysis showed that approximately 50 genes showed high expression levels in the leaves of A. argyi and AYMYBs showed specific expression patterns under MeJA treatment. Together, our research will offer useful information for future investigations into the functions of MYB genes in A. argyi, especially in regulating the process of flavonoid biosynthesis in leaves and in response to MeJA treatment.

Keywords: AYMYB; Artemisia argyi; Bioinformatics tools; Expression pattern; MeJA.

Fig. 1

Phylogenetic relationships of MYB proteins were analyzed between A. argyi and other species, such as Arabidopsis thaliana, Artemisia annua, Oryza sativa, Zea mays, Triticum aestivum, Salvia miltiorrhiza, Brassica oleracea, and Tanacetum cinerariifolium. The phylogenetic tree was constructed using MEGA 7.0, representing different classes in distinct colors

Fig. 2

Chromosomal distribution and collinearity analysis of AYMYBs. A. Chromosomal distribution of each AYMYB gene. B. Chromosomal relationships of AYMYBs. The gray blocks denoted the segments of A. argyi chromosomes. The gray lines in the background represent collinear blocks within the genome of A. argyi, while the red lines indicate syntenic AYMYB gene pairs. Here, ‘Chr’ denotes the chromosome

Fig. 3

Sequence analysis of AYMYBs. Phylogenetic relationships (A), conserved motifs (B), domains (C), and exon/intron organization (D) of AYMYB proteins or genes from A. argyi. UTR and CDS indicate non-translated regions and coding sequences, respectively

Fig. 4

Cis-acting element analysis of AYMYBs promoter regions. A. The proportion of cis-elements predicted in the promoters of AYMYBs. B. Numbers of cis-elements involved in light response, hormone response, biotic and abiotic stress, development, and tissue specificity

Fig. 5

GO analysis of AYMYBs in A. argyi

Fig. 6

Expression pattern analysis of AYMYBs in A. argyi. A. The expression profiles of AYMYBs in different tissues of A. argyi.B. The expression profiles of AYMYB genes under MeJA treatment. The color scale represents log10 expression values, with blue representing low expression and red indicating high expression. Leaf A represents 5 days of leaf buds; Leaf B represents 15 days of young leaves; Leaf C represents 30 days of mature leaves; Leaf D represents 45 days of old leaves

Fig. 7

qRT-PCR analysis of relative expression of AYMYBs in different A. argyi tissues. Leaf A represents 5 days of leaf buds; Leaf B represents 15 days of young leaves; Leaf C represents 30 days of mature leaves. Vertical bars indicate the mean ± SD calculated from three replicates. Different letters indicate significant differences among treatments in the same period using Duncan’s test (P < 0.05)

Fig. 8

qRT-PCR analysis of relative expression of AYMYBs under MeJA treatment of A. argyi at 0, 6, 12, 24 and 48 h. Vertical bars indicate the mean ± SD calculated from three replicates. Different letters indicate significant differences among treatments in the same period using Duncan’s test (P < 0.05)