Genome-Wide Identification of the Alfin-like Gene Family in Cotton (Gossypium hirsutum) and the GhAL19 Gene Negatively Regulated Drought and Salt Tolerance.

Alfin-like (AL) is a small plant-specific gene family characterized by a PHD-finger-like structural domain at the C-terminus and a DUF3594 structural domain at the N-terminus, and these genes play prominent roles in plant development and abiotic stress response. In this study, we conducted genome-wide identification and analyzed the AL protein family in Gossypium hirsutum cv. NDM8 to assess their response to various abiotic stresses for the first time. A total of 26 AL genes were identified in NDM8 and classified into four groups based on a phylogenetic tree. Moreover, cis-acting element analysis revealed that multiple phytohormone response and abiotic stress response elements were highly prevalent in AL gene promoters. Further, we discovered that the GhAL19 gene could negatively regulate drought and salt stresses via physiological and biochemical changes, gene expression, and the VIGS assay. The study found there was a significant increase in POD and SOD activity, as well as a significant change in MDA in VIGS-NaCl and VIGS-PEG plants. Transcriptome analysis demonstrated that the expression levels of the ABA biosynthesis gene (GhNCED1), signaling genes (GhABI1, GhABI2, and GhABI5), responsive genes (GhCOR47, GhRD22, and GhERFs), and the stress-related marker gene GhLEA14 were regulated in VIGS lines under drought and NaCl treatment. In summary, GhAL19 as an AL TF may negatively regulate tolerance to drought and salt by regulating the antioxidant capacity and ABA-mediated pathway.

Genome-wide identification and characterization of the JAZ gene family in Gynostemma pentaphyllum reveals the COI1/JAZ/MYC2 complex potential involved in the regulation of the MeJA-induced gypenoside biosynthesis.

The Jasmonate ZIM domain (JAZ) proteins, functioning as critical suppressors for jasmonic acid (JA) signal transduction in plants, occupy crucial roles in multiple biological processes, particularly in the orchestration of secondary metabolic pathways. However, the mechanism underlying the JA-induced gypenosides accumulation in Gynostemma pentaphyllum remains poorly elucidated. Our research led to the identification of 11 distinct JAZ members in G. pentaphyllum (GpJAZs). According to the classification approach of AtJAZ, we allocated these members into five subgroups that shared similar conserved motif compositions. Subsequently, we identified the presence of various cis-acting elements associated with light stimuli, hormone responses, and stress signals within the promoter regions of the GpJAZ gene family. The expression levels of GpJAZ genes in different tissues were quite different, and the majority of GpJAZ genes exhibited varying degrees of response to methyl jasmonate (MeJA) induction. Yeast two-hybrid (Y2H) assays revealed interactions between GpJAZ1/2/4/5/7/9/10 and GpMYC2, whereas GpCOI1 protein was found to interact with GpJAZ1/2/4/5, thereby forming the COI1/JAZ/MYC2 complex. Furthermore, as an activator of gypenoside metabolic pathway, GpMYC2 could activate the promoter activity of the gypenoside metabolism-related genes to varying degrees by binding to their promoters, indicating that the COI1/JAZ/MYC2 module involved in the MeJA-induced regulation of gypenosides. In summary, our findings present an exhaustive examination of the JAZ gene family, furnishing a significant lead for delving deeper into the molecular mechanisms that drive the MeJA-induced enhancement of gypenosides accumulation in G. pentaphyllum.

Genome-Wide Analysis of VILLIN Gene Family Associated with Stress Responses in Cotton (Gossypium spp.).

The VILLIN (VLN) protein plays a crucial role in regulating the actin cytoskeleton, which is involved in numerous developmental processes, and is crucial for plant responses to both biotic and abiotic factors. Although various plants have been studied to understand the VLN gene family and its potential functions, there has been limited exploration of VLN genes in Gossypium and fiber crops. In the present study, we characterized 94 VLNs from Gossypium species and 101 VLNs from related higher plants such as Oryza sativa and Zea mays and some fungal, algal, and animal species. By combining these VLN sequences with other Gossypium spp., we classified the VLN gene family into three distinct groups, based on their phylogenetic relationships. A more in-depth examination of Gossypium hirsutum VLNs revealed that 14 GhVLNs were distributed across 12 of the 26 chromosomes. These genes exhibit specific structures and protein motifs corresponding to their respective groups. GhVLN promoters are enriched with cis-elements related to abiotic stress responses, hormonal signals, and developmental processes. Notably, a significant number of cis-elements were associated with the light responses. Additionally, our analysis of gene-expression patterns indicated that most GhVLNs were expressed in various tissues, with certain members exhibiting particularly high expression levels in sepals, stems, and tori, as well as in stress responses. The present study potentially provides fundamental insights into the VLN gene family and could serve as a valuable reference for further elucidating the diverse functions of VLN genes in cotton.

Genome-wide characterization of the bHLH gene family in Gynostemma pentaphyllum reveals its potential role in the regulation of gypenoside biosynthesis.

BACKGROUND: Gynostemma pentaphyllum, an ancient Chinese herbal medicine, serves as a natural source of gypenosides with significant medicinal properties. Basic helix-loop-helix (bHLH) transcription factors play pivotal roles in numerous biological processes, especially in the regulation of secondary metabolism in plants. However, the characteristics and functions of the bHLH genes in G. pentaphyllum remain unexplored, and their regulatory role in gypenoside biosynthesis remains poorly elucidated. RESULTS: This study identified a total of 111 bHLH members in G. pentaphyllum (GpbHLHs), categorizing them into 26 subgroups based on shared conserved motif compositions and gene structures. Collinearity analysis illustrated that segmental duplications predominately lead to the evolution of GpbHLHs, with most duplicated GpbHLH gene pairs undergoing purifying selection. Among the nine gypenoside-related GpbHLH genes, two GpbHLHs (GpbHLH15 and GpbHLH58) were selected for further investigation based on co-expression analysis and functional prediction. The expression of these two selected GpbHLHs was dramatically induced by methyl jasmonate, and their nuclear localization was confirmed. Furthermore, yeast one-hybrid and dual-luciferase assays demonstrated that GpbHLH15 and GpbHLH58 could bind to the promoters of the gypenoside biosynthesis pathway genes, such as GpFPS1, GpSS1, and GpOSC1, and activate their promoter activity to varying degrees. CONCLUSIONS: In conclusion, our findings provide a detailed analysis of the bHLH family and valuable insights into the potential use of GpbHLHs to enhance the accumulation of gypenosides in G. pentaphyllum.

Genome-Wide Analysis of R2R3-MYB Genes and Functional Characterization of SmMYB75 in Eggplant Fruit Implications for Crop Improvement and Nutritional Enhancement.

R2R3-MYB represents a substantial gene family that plays diverse roles in plant development. In this study, 102 SmR2R3-MYB genes were identified from eggplant fruit and classified into 31 subfamilies. Analysis indicated that segmental duplication events played a pivotal role in the expansion of the SmR2R3-MYB gene family. Furthermore, the prediction of miRNAs targeting SmR2R3-MYB genes revealed that 60 SmR2R3-MYBs are targeted by 57 miRNAs, with specific miRNAs displaying varying numbers of target genes, providing valuable insights into the regulatory functions of miRNAs in plant growth, development, and responses to stress conditions. Through expression profile analysis under various treatment conditions, including low temperature (4 °C), plant hormone (ABA, Abscisic acid), and drought stress (PEG, Polyethylene glycol), diverse and complex regulatory mechanisms governing SmR2R3-MYB gene expression were elucidated. Notably, EGP21875.1 and EGP21874.1 exhibited upregulation in expression under all treatment conditions. Transcriptome and metabolome analyses demonstrated that, apart from anthocyanins (delphinidin-3-O-glucoside, cyanidin-3-O-(6-O-p-coumaroyl)-glucoside, and malvidin-3-O-(6-O-p-coumaroyl)-glucoside), overexpression of SmMYB75 could also elevate the content of various beneficial compounds, such as flavonoids, phenolic acids, and terpenes, in eggplant pulp. This comprehensive study enhances our understanding of SmR2R3-MYB gene functions and provides a strong basis for further research on their roles in regulating anthocyanin synthesis and improving eggplant fruit quality.

Genome-Wide Analysis of the MADS-Box Gene Family in Hibiscus syriacus and Their Role in Floral Organ Development.

Hibiscus syriacus belongs to the Malvaceae family, and is a plant with medicinal, edible, and greening values. MADS-box transcription factor is a large family of regulatory factors involved in a variety of biological processes in plants. Here, we performed a genome-wide characterization of MADS-box proteins in H. syriacus and investigated gene structure, phylogenetics, cis-acting elements, three-dimensional structure, gene expression, and protein interaction to identify candidate MADS-box genes that mediate petal developmental regulation in H. syriacus. A total of 163 candidate MADS-box genes were found and classified into type I (Mα, Mß, and Mγ) and type II (MIKC and Mδ). Analysis of cis-acting elements in the promoter region showed that most elements were correlated to plant hormones. The analysis of nine HsMADS expressions of two different H. syriacus cultivars showed that they were differentially expressed between two type flowers. The analysis of protein interaction networks also indicated that MADS proteins played a crucial role in floral organ identification, inflorescence and fruit development, and flowering time. This research is the first to analyze the MADS-box family of H. syriacus and provides an important reference for further study of the biological functions of the MADS-box, especially in flower organ development.

Genome-wide characterization and expression analysis of MADS-box transcription factor gene family in Perilla frutescens.

MADS-box transcription factors are widely involved in the regulation of plant growth, developmental processes, and response to abiotic stresses. Perilla frutescens, a versatile plant, is not only used for food and medicine but also serves as an economical oil crop. However, the MADS-box transcription factor family in P. frutescens is still largely unexplored. In this study, a total of 93 PfMADS genes were identified in P. frutescens genome. These genes, including 37 Type I and 56 Type II members, were randomly distributed across 20 chromosomes and 2 scaffold regions. Type II PfMADS proteins were found to contain a greater number of motifs, indicating more complex structures and diverse functions. Expression analysis revealed that most PfMADS genes (more than 76 members) exhibited widely expression model in almost all tissues. The further analysis indicated that there was strong correlation between some MIKCC-type PfMADS genes and key genes involved in lipid synthesis and flavonoid metabolism, which implied that these PfMADS genes might play important regulatory role in the above two pathways. It was further verified that PfMADS47 can effectively mediate the regulation of lipid synthesis in Chlamydomonas reinhardtii transformants. Using cis-acting element analysis and qRT-PCR technology, the potential functions of six MIKCC-type PfMADS genes in response to abiotic stresses, especially cold and drought, were studied. Altogether, this study is the first genome-wide analysis of PfMADS. This result further supports functional and evolutionary studies of PfMADS gene family and serves as a benchmark for related P. frutescens breeding studies.