Genome-wide analysis of the R2R3-MYB gene family in Spatholobus suberectus and identification of its function in flavonoid biosynthesis

Qin, Shuangshuang; Wei, Fan; Liang, Ying; Tang, Danfeng; Lin, Quan; Miao, Jianhua; Wei, Kunhua

doi:10.3389/fpls.2023.1219019

Cited by 4 publications

(1 citation statement)

References 54 publications

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“…The majority of MYB genes, included several motifs (1, 2, 3, 4, and 5) in Prunus avium ( Sabir et al., 2022 ). These motifs were conserved within specific subgroups, and proteins in the same subgroup that share these motifs likely ( Qin et al., 2023 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification, classification and expression analysis of MYB gene family in coconut (Cocos nucifera L.)

Li,

Guo,

Min Htwe

et al. 2024

Front. Plant Sci.

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MYB transcription factors regulate the growth, development, and secondary metabolism of plant species. To investigate the origin of color variations in coconut pericarp, we identified and analyzed the MYB gene family present in coconut. According to the sequence of MYB genes in Arabidopsis thaliana, homologous MYB gene sequences were found in the whole genome database of coconut, the conserved sequence motifs within MYB proteins were analyzed by Motif Elicitation (MEME) tool, and the sequences without conservative structure were eliminated. Additionally, we employed RNA-seq technology to generate gene expression signatures of the R2R3-MYB genes across distinctive coconut parts exhibiting diverse colors. To validate these profiles, we conducted quantitative PCR (qPCR). Through comprehensive genome-wide screening, we successfully identified a collection of 179 MYB genes in coconut. Subsequent phylogenetic analysis categorized these 179 coconut MYB genes into 4-subfamilies: 124 R2R3-MYB, 4 3R-MYB types, 4 4R-MYB type, and 47 unknown types. Furthermore, these genes were further divided into 34 subgroups, with 28 of these subgroups successfully classified into known subfamilies found in Arabidopsis thaliana. By mapping the CnMYB genes onto the 16 chromosomes of the coconut genome, we unveiled a collinearity association between them. Moreover, a preservation of gene structure and motif distribution was observed across the CnMYB genes. Our research encompassed a thorough investigation of the R2R3-MYB genes present in the coconut genome, including the chromosomal localization, gene assembly, conserved regions, phylogenetic associations, and promoter cis-acting elements of the studied genes. Our findings revealed a collection of 12 R2R3-MYB candidate genes, namely CnMYB8, CnMYB15, CnMYB27, CnMYB28, CnMYB61, CnMYB63, CnMYB68, CnMYB94, CnMYB101, CnMYB150, CnMYB153, and CnMYB164. These genes showed differential expressions in diverse tissues and developmental stages of four coconut species, such as CnMYB68, CnMYB101, and CnMYB28 exhibited high expression in majority of tissues and coconut species, while CnMYB94 and CnMYB164 showed lower expression. These findings shed light on the crucial functional divergence of CnMYB genes across various coconut tissues, suggesting these genes as promising candidate genes for facilitating color development in this important crop.

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Section: Discussionmentioning

confidence: 99%

Genome-wide identification, classification and expression analysis of MYB gene family in coconut (Cocos nucifera L.)

Li,

Guo,

Min Htwe

et al. 2024

Front. Plant Sci.

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In silico analysis of Phaseolus vulgaris L. metalloprotease FtsH gene: characterization and expression in drought and salt stress

Inal,

Muslu,

Yigider

et al. 2024

Genet Resour Crop Evol

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Proteases help plants maintain protein quality and break down protein subsets in reply to environmental, developmental, biotic, and abiotic stressors. Filamentation temperature-sensitive H (FtsH) is an ATP-dependent metalloprotease detected in both prokaryotes and eukaryotes cells. The present research, the FtsH gene in the bean, which has an important place in the legume family and is an important agricultural product, was characterized for the first time using various bioinformatic tools, and qRT-PCR measured its expression level. In the study, effectively identified and characterized 17 FtsH genes present in genome the of Phaseolus vulgaris. The MW of FtsH proteins varied from 71.16 to 147.07 kDa, their amino acid lengths ranged from 642 to 1284, and their pI values varied from 5.39 to 9.60. Interestingly, the distribution of these 17 distinct PvFtsH genes across the 8 chromosomes was not uniform, exhibiting an uneven pattern throughout the genome. A pair of segmental duplication fragments were found, revealing probable processes of gene expansion and evolution. Collinearity with related genes in Arabidopsis and rice was thoroughly examined to determine the evolutionary conservation and differentiation of PvFtsH genes. Additionally, we used RNAseq and qRT-PCR to investigate the expression patterns of PvFtsH in leaf tissue under salt and drought conditions. Our data showed unique expression patterns, suggesting PvFtsH may respond to environmental and physiological stressors. Overall, this work makes major contributions to our understanding of PvFtsH genes and their roles in the context of gene evolution, chromosomal distribution, and expression patterns under various environmental situations.

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Integrated multi-omics analysis reveals genes involved in flavonoid biosynthesis and trichome development of Artemisia argyi

Cui,

Huang,

et al. 2024

Plant Science

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Genome-wide analysis of the R2R3-MYB gene family in Spatholobus suberectus and identification of its function in flavonoid biosynthesis

Cited by 4 publications

References 54 publications

Genome-wide identification, classification and expression analysis of MYB gene family in coconut (Cocos nucifera L.)

Genome-wide identification, classification and expression analysis of MYB gene family in coconut (Cocos nucifera L.)

In silico analysis of Phaseolus vulgaris L. metalloprotease FtsH gene: characterization and expression in drought and salt stress

Integrated multi-omics analysis reveals genes involved in flavonoid biosynthesis and trichome development of Artemisia argyi

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