Genome-wide organization and expression profiling of the R2R3-MYB transcription factor family in sea buckthorn (Hippophae rhamnoides L.)

Abstract

Background MYB transcription factor family involved in multifarious stages of plant growth and development until death, which is one of the largest and most versatile gene families in plants, therefore it is an important regulatory factor in plants. Sea buckthorn (Hippophae rhamnoides L.) is rich in many secondary metabolites and has high nutritional and medicinal value. With the completion of sea buckthorn genome sequencing, it has laid the foundation for us to explore the gene structure, evolutionary relationship and function prediction of sea buckthorn MYB gene family from the whole genome perspective. Results In this study, 161 R2R3-MYB genes were identified from the sea buckthorn genome. We systematically analyzed their gene structure, collinearity, phylogenetic relationships and expression pattern. According to the gene structure, conserved motifs and phylogenetic relationship of 161 HrMYB genes, all the HrMYB genes were divided into 28 subgroups. The phylogenetic tree of Hippophae rhamnoides L. and Arabidopsis thaliana R2R3-MYB genes showed that the sea buckthorn MYB gene family showed functional differentiation during evolution. Chromosomal localization results showed that the distribution of HrMYB genes were random. RNA-seq data from seven different tissues indicated that the HrMYB genes have significant spatiotemporal and tissue expression differences. QRT-PCR analysis showed that the selected genes which relate to flavonoid biosynthesis of sea buckthorn fruit expressed different degrees in different developmental stages of the fruit. Conclusion The sea buckthorn R2R3-MYB gene family was successfully identified from the whole genome sequence by a series of bioinformatics methods. The results firstly provide a more comprehensive insight for the phylogenetic relationships and expression patterns of the HrMYB genes. It will help us to further study their specific functions in the growth and development of sea buckthorn.

Identification and analysis of UGT genes associated with triterpenoid saponin in soapberry (Sapindus mukorossi Gaertn.)

“…Among the 42 genes, 45.2% had intron insertions (Fig. 1), a value lower than those of Hippophae rhamnoides (50.6%) [37], maize (60%) [20], and Arabidopsis thaliana (58%) [18], and similar to that of the Sapindaceae Dimocarpus longan (47.3%) [36]. Therefore, we speculate that intron insertion was gradually lost during the evolution of SmUGT s.…”

“…In other species, the expression of UGT genes changes as fruit development progresses. In Hippophae rhamnoides, most UGT genes are expressed at high levels in the early or middle stages of fruit development, and at lower levels in later stages [37]. In peach, 35% of UGT genes have the highest expression level in S1 (the first exponential growth phase, characterized by rapid cell division) [42].…”

Recent Advanced Metabolic and Genetic Engineering of Phenylpropanoid Biosynthetic Pathways

“…R2R3-MYB (185) transcription factors are reported in the genome of Mangrove, 34 MYB gene are mainly expressed in different tissues (root, leaves), which are related to various stresses (salinity and drought) [35]. Hippophae rhamnoides is the rich source of secondary metabolites, which has economic importance regarding medicinal and nutritional values, 161 R2R3-MYB TFs were obtained through its genome-wide analysis [36]. In a recent study, 111 StR2R3-MYB transcription factors are reported in potato [37].…”