Genome-wide analysis of R2R3-MYB transcription factors in Boehmeria nivea (L.) gaudich revealed potential cadmium tolerance and anthocyanin biosynthesis genes

Abstract

Gene family, especially MYB as one of the largest transcription factor family in plants, the study of its subfunctional characteristics is a key step in the study of plant gene function. The sequencing of ramie genome provides a good opportunity to study the organization and evolutionary characters of the ramie MYB gene at the whole genome level. In this study, a total of 105 BnGR2R3-MYB genes were identified from ramie genome and subsequently grouped into 35 subfamilies according to phylogeny divergence and sequences similarity. Chromosomal localization, gene structure, synteny analysis, gene duplication, promoter analysis, molecular characteristics and subcellular localization were accomplished using several bioinformatics tools. Collinearity analysis showed that the segmental and tandem duplication events is the dominant form of the gene family expansion, and duplications prominent in distal telomeric regions. Highest syntenic relationship was obtained between BnGR2R3-MYB genes and that of Apocynum venetum (88). Furthermore, transcriptomic data and phylogenetic analysis revealed that BnGMYB60, BnGMYB79/80 and BnGMYB70 might inhibit the biosynthesis of anthocyanins, and UPLC-QTOF-MS data further supported the results. qPCR and phylogenetic analysis revealed that the six genes (BnGMYB9, BnGMYB10, BnGMYB12, BnGMYB28, BnGMYB41, and BnGMYB78) were cadmium stress responsive genes. Especially, the expression of BnGMYB10/12/41 in roots, stems and leaves all increased more than 10-fold after cadmium stress, and in addition they may interact with key genes regulating flavonoid biosynthesis. Thus, a potential link between cadmium stress response and flavonoid synthesis was identified through protein interaction network analysis. The study thus provided significant information into MYB regulatory genes in ramie and may serve as a foundation for genetic enhancement and increased productivity.

Genome-wide identification of thaumatin-like protein family genes in Panax notoginseng and analysis of their responses to Fusarium solani infection

“…The gene duplication of PnTLPs in P. notoginseng genome was performed by MCscanX with the default parameters, and circus was used to locate all the PnTLP genes on the P. notoginseng chromosome by Tbtools version 1.120 (Du, Zhang, et al, 2022). The syntenic relationships between the PnTLP genes and TLP genes from A. thaliana and O. sativa were obtained also using McscanX and both results visualized in Tbtools (Feng, Abubakar, et al, 2023).…”

Comprehensive Analysis of WUSCEL-Related Homeobox Gene Family in Ramie (Boehmeria nivea) Indicates Its Potential Role in Adventitious Root Development

“…The potential involvement of the ramie WOX genes in adventitious root formation was investigated using quantitative real-time PCR and transcriptomic analysis of the ramie tissues grown using stem cuttings according to previous reports [43,44]. The transcriptome analysis of tissue-specific expression of the WOX genes was performed using four different ramie tissues (bud, leaf, stem, and root) sequenced by our laboratory, which was previously reported by Chen et al [3].…”

A Systematic Review on the Improvement of Cd Stress Tolerance in Ramie Crop, Limitations and Future Prospective

“…Previous studies have revealed that ramie crop has robust tolerance to Cd stress and can accumulate Cd ions from soil; hence, the use of ramie to prevent the Cd contamination of agricultural soils is of practical significance [27][28][29]. More significantly, ramie can accumulate a comparatively large number of heavy metals in its above-ground portion [30]. Ramie is a relatively tolerant crop against heavy metals stress, especially Cd stress, as it absorbs Cd from heavy metals-contaminated soils [27,30,31].…”

“…More significantly, ramie can accumulate a comparatively large number of heavy metals in its above-ground portion [30]. Ramie is a relatively tolerant crop against heavy metals stress, especially Cd stress, as it absorbs Cd from heavy metals-contaminated soils [27,30,31]. An earlier study showed that ramie has a certain degree of tolerance to soil Cd stress at a concentration of ≤20 mg/kg [32].…”

“…Still, this technique has limited applications in ramie, and this gap should be covered in future studies. On the other hand, TFs analysis revealed several genes involved in Cd tolerance [30,37] and can be used to develop tolerant cultivars using genetic engineering or editing using the CRISPR/Cas9 tool. All TFs belong to different families, which have still not been identified because of the diverse nature of the gene network.…”