Large-scale analysis of putative Euphorbiaceae R2R3-MYB transcription factors identifies a MYB involved in seed oil biosynthesis

Cao, Yang; Fan, Tingting; Li-hu, Wang; Zhang, Lin; Li, Yanli

doi:10.1186/s12870-023-04163-5

Cited by 6 publications

(5 citation statements)

References 74 publications

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“…The visualization and plotting of the pressure analysis data were performed using the R package. For a more comprehensive understanding of the identification methods employed, please refer to Cao et al [ 43 ].…”

Section: Methodsmentioning

confidence: 99%

Molecular evolution analysis of MYB5 in Brassicaceae with specific focus on seed coat color of Brassica napus

Dai,

Liu,

Shen

et al. 2024

BMC Plant Biol

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Background MYB transcription factors are splay a vital role in plant biology, with previous research highlighting the significant impact of the R2R3-MYB-like transcription factor MYB5 on seed mucilage biosynthesis, trichome branching, and seed coat development. However, there is a dearth of studies investigating its role in the regulation of proanthocyanidin (PA) biosynthesis. Results In this study, a total of 51 MYB5 homologous genes were identified across 31 species belonging to the Brassicaceae family, with particular emphasis on Brassica napus for subsequent investigation. Through phylogenetic analysis, these genes were categorized into four distinct subclasses. Protein sequence similarity and identity analysis demonstrated a high degree of conservation of MYB5 among species within the Brassicaceae family. Additionally, the examination of selection pressure revealed that MYB5 predominantly underwent purifying selection during its evolutionary history, as indicated by the Ka/Ks values of all MYB5 homologous gene pairs being less than one. Notably, we observed a higher rate of non-synonymous mutations in orthologous genes compared to paralogous genes, and the Ka/Ks value displayed a stronger correlation with Ka. In B. napus, an examination of expression patterns in five tissues revealed that MYB5 exhibited particularly high expression in the black seed coat. The findings from the WGCNA demonstrated a robust correlation between MYB5 and BAN(ANR) associated with PA biosynthesis in the black seed coat, providing further evidence of their close association and co-expression. Furthermore, the results obtained from of the analysis of protein interaction networks offer supplementary support for the proposition that MYB5 possesses the capability to interact with transcriptional regulatory proteins, specifically TT8 and TT2, alongside catalytic enzymes implicated in the synthesis of PAs, thereby making a contribution to the biosynthesis of PAs. These findings imply a plausible and significant correlation between the nuique expression pattern of MYB5 and the pigmentation of rapeseed coats. Nevertheless, additional research endeavors are imperative to authenticate and substantiate these findings. Conclusions This study offers valuable insights into the genetic evolution of Brassicaceae plants, thereby serving as a significant reference for the genetic enhancement of Brassicaceae seed coat color.

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Section: Methodsmentioning

confidence: 99%

Molecular evolution analysis of MYB5 in Brassicaceae with specific focus on seed coat color of Brassica napus

Dai,

Liu,

Shen

et al. 2024

BMC Plant Biol

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“…For example, Jiang et al elucidated the mechanism of polysaccharide biosynthesis of Bletilla striata by combining genomic and transcriptomic data (Jiang et al, 2022a). Furthermore, multi-omics analysis of potential R2R3-MYB transcription factors within the Euphorbiaceae family has successfully identified a specific MYB gene significantly involved in the biosynthesis of seed oil (Cao et al, 2023).…”

Section: Elevating Plant Trait Predictionsmentioning

confidence: 99%

Editorial: Multi-omics and computational biology in horticultural plants: from genotype to phenotype, volume II

Cao,

Li,

Song

et al. 2024

Front. Plant Sci.

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Editorial on the Research TopicMulti-omics and computational biology in horticultural plants: from genotype to phenotype, volume II Horticulture, an integral component of the broader field of agriculture, has played a pivotal role in the development of human civilization. The shift from nomadic lifestyles to settled farming communities was greatly enabled by advancements in horticultural practices. This domain encompasses the scientific, technological, and artistic aspects of growing, breeding, processing, and commercializing various plant types, such as ornamental species, flowers, fruits, vegetables, nuts, seeds, and herbs. In recent years, there has been a surge in the sequencing of numerous horticultural plant genomes (Marks et al., 2021). The field of multi-omics and computational biology, particularly as they relate to horticultural plants and transition from genotype to phenotype, have experienced significant growth and diversification (Cao et al., 2022a). This progress has been driven by the incorporation of high-throughput technologies and innovative computational methods, yielding profound insights into plant physiological adaptation and biological mechanisms. The current Research Topic is focused on merging advanced omics and computational biology techniques to associate genotypes with phenotypes and link genetic markers to traits in various horticultural crops (Figure 1). This Research Topic showcases a collection of 24 scholarly articles. Within this assemblage, two pieces are comprehensive reviews, while the other 22 constitute original research papers. Among these, a pair delves into the genome sequencing of horticultural crops. Three articles focus on the study of fruit crops, another trio sheds light on vegetable research, and a single paper explores the realm of Chinese herbal medicine. Additionally, Frontiers in Plant Science frontiersin.org 01

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“…Gene duplication events may involve the expansion of gene members in peach [21,22,25]. Here, we constructed the gene duplication analysis of PpAHLs to reveal the evolutionary process.…”

Section: Gene Duplication Analysis Suggests the Large-scale Duplicati...mentioning

confidence: 99%

“…Given the distinct roles of AHL family members in various biological processes, the identification of AHL genes in peach will help us further understand their functions and lay the groundwork for their future application in the genetic improvement of peach. Similar features of many gene families including MYB [22], CHS [23], G3PAT [24], and PHD-finger [25] have helped to identify important target genes to improve fruit quality, stress tolerance, and other important economic traits. The purpose of this study was to systematically analyze the members of the AHL family in the model fruit tree peach, so as to increase our understanding of the functional diversity of AHL genes during plant development.…”

Section: Introductionmentioning

confidence: 99%

Dissection of AT-Hook Motif Nuclear-Localized Genes and Their Potential Functions in Peach Growth and Development

Zhao

Wang

2023

Forests

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The AT-hook motif nuclear-localized (AHL) family members play key roles in plant biological processes via protein–protein and protein-DNA interactions. Here, 22 non-redundant PpAHL genes were identified and analyzed in peach (Prunus persica), one of economically important non-timber forestry crops. The maximum-likelihood (ML) tree classified the PpAHLs into two clades (Clade-A and Clade-B) with three subfamilies: Type_I, Type_II, and Type_III. Exon–intron analysis exhibited that the PpAHLs from Type_I except one (Prupe.1G530300.1) lacked introns, and the PpAHLs from Type_II and Type_III gradually emerged with intron additions, indicating spatial expression patterns, evolutionarily distinct temporal patterns and, likely, neofunctionalization. Duplication event analysis suggested that PpAHLs in peach were mainly expanded through the large-scale duplication events. RNA-seq data showed that PpAHLs were induced by drought stress, and two genes (Prupe.1G530300.1 and Prupe.1G034400.1) from Type_I AHLs were induced at all time points, indicating that they might play key roles in the response to drought stress in peach. The tissue-specific expression pattern of PpAHLs exhibited their biological functions in the development of these specific tissues. In addition, the transient overexpression of Prupe.1G530300.1 and Prupe.1G034400.1 resulted in significant changes in sugar content, suggesting that they may be positive regulators of sugar accumulation in peach fruits. Our study provided novel insights into the roles of PpAHLs in plant development, which was helpful for the functional analysis of peach and related woody fruit trees, and for formulating new strategies for further breeding.

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Large-scale analysis of putative Euphorbiaceae R2R3-MYB transcription factors identifies a MYB involved in seed oil biosynthesis

Cited by 6 publications

References 74 publications

Molecular evolution analysis of MYB5 in Brassicaceae with specific focus on seed coat color of Brassica napus

Molecular evolution analysis of MYB5 in Brassicaceae with specific focus on seed coat color of Brassica napus

Editorial: Multi-omics and computational biology in horticultural plants: from genotype to phenotype, volume II

Dissection of AT-Hook Motif Nuclear-Localized Genes and Their Potential Functions in Peach Growth and Development

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