Genome-wide analysis of the MYB transcription factor superfamily in soybean

Genome-wide identification and expression profiling of MYB transcription factors in Artemisia argyi

Artemisia argyi, a significant medicinal plant in China, is known for its high content of essential oils, flavonoids, and other bioactive compounds. MYB transcription factors are the largest gene family in plants and are widely reported to play important roles in plant development, metabolism, defense, and stress resistance. However, the MYB family of A. argyi has not been systematically studied. The aim of this study was to comprehensively analyze the MYB gene family of A. argyi and explore its potential role in flavonoid biosynthesis. Here, the phylogeny, chromosome location, gene structure, cis-acting elements, expression patterns and Gene ontology (GO) annotation of MYB gene family members were investigated using bioinformatics methods based on the whole-genome and transcriptome data of A. argyi. In total, 227 AYMYB transcription factors were identified from A. argyi genome, including 22 1R-MYB, 165 R2R3-MYB, 16 3R-MYB, 5 4R-MYB and 19 atypical MYB members. These AYMYBs were unevenly distributed across the A. argyi genome. Subcellular localization prediction revealed that all the AYMYBs were localized in the nucleus. The protein motifs, conserved domains, and gene structures of AYMYBs were identified, and the results showed that AYMYBs from the same subfamily exhibited similar motifs and gene structures. Cis-acting elements and GO analysis suggested that AYMYBs may be involved in many biological processes related to plant development, metabolism, defense, and stress resistance. Moreover, quantitative real-time PCR (qRT-PCR) analysis showed that approximately 50 genes showed high expression levels in the leaves of A. argyi and AYMYBs showed specific expression patterns under MeJA treatment. Together, our research will offer useful information for future investigations into the functions of MYB genes in A. argyi, especially in regulating the process of flavonoid biosynthesis in leaves and in response to MeJA treatment.

Identification of the regulatory role of SsMYBS25-4 in salt stress from MYB-related transcription factors in sugarcane (Saccharum spontaneum)

Sugarcane is a highly valued crop known for its significant production of sugar and biomass. MYB transcription factors (TFs) are critical regulators in plant growth and stress tolerance, but MYB-related genes, an atypical subset of the MYB family, remain less explored. In this study, we identified 119 MYB-related genes in the genome of wild sugarcane (S. spontaneum). We thoroughly investigated their phylogenetic relationships, chromosomal locations, motif compositions, and three-dimensional (3D) protein structures by bioinformatic methods. Moreover, the expression patterns of these genes demonstrated significant diversity in plant growth and under salt stress. One of the genes, SsMYBS25-4, exhibited a significantly up-regulated expression in response to salt stress and was selected for further functional elucidation. It was found that the overexpression (OE) of SsMYBS25-4 in Arabidopsis can improve the salt stress tolerance of transgenic plants. Interestingly, the expression of some marker genes related to salt stress was significantly up-regulated in OE plants compared to wide-type plants. The SsMYB25-4 protein was localized in the nucleus and was proven to be directly bound to the promoter of the AtDR29B gene. We proposed a mechanism for SsMYB25-4 that enhances salt stress tolerance, contributing to the understanding and application of MYB-related genes in sugarcane breeding.

Omics-based identification of the broader effects of 2-hydroxyisoflavanone synthase gene editing on a gene regulatory network beyond isoflavonoid loss in soybean hairy roots

Soybean (Glycine max) is a leguminous crop cultivated worldwide that accumulates high levels of isoflavones. Although previous research has often focused on increasing the soybean isoflavone content because of the estrogen-like activity of dietary soy in humans, the rapidly increasing demand for soybean as a plant-based meat substitute has raised concerns about excessive isoflavone intake. Therefore, the production of isoflavone-free soybean has been anticipated. However, there have been no reports of an isoflavone-free soybean until now. Here, 2-hydroxyisoflavanone synthase (IFS), which is essential for isoflavone biosynthesis, was targeted for genome editing in soybean. A novel CRISPR/Cas9 system using Staphylococcus aureus Cas9 instead of the commonly used Streptococcus pyogenes Cas9 was established and customized. Through Agrobacterium rhizogenes-mediated transformation, IFS-edited hairy roots were generated in which all three IFS genes contained deletion mutations. Metabolome analyses of IFS-edited hairy roots revealed that isoflavone content significantly decreased, whereas levels of flavonoids, including a novel chalcone derivative, increased. A transcriptome analysis revealed changes in the expression levels of a large number of genes, including jasmonic acid-inducible genes. In addition, the functions of selected transcription factor genes (MYB14-L, GmbHLH112, and GmbHLH113), which were dramatically upregulated by IFS editing, were investigated by multiomics analyses of their over-expressing hairy root lines. They appear to be involved in flavonoid and triterpene saponin biosynthesis, salicylic acid metabolism, and central carbon metabolism. Overall, the results indicated that editing IFS genes caused the redirection of the metabolic flux from isoflavonoid biosynthesis to flavonoid accumulation, as well as dynamic changes in gene regulatory networks.

Identification and functional characterization of MYB genes regulating polyphenol biosynthesis in cabbage for resistance to Xanthomonas campestris pv. campestris

Cabbage (Brassica oleracea L. var. capitata) is a vital leafy vegetable, but its production is frequently impacted by Xanthomonas campestris pv. campestris (Xcc). The MYB family is one of the most abundant families involved in plant responses to biotic stresses. However, genome-wide identification of MYB and their roles in regulating phenolic synthesis during Xcc resistance have not been previously reported in cabbage. The present investigation reports a total of 322 BoMYB genes. Transcriptome data revealed that 37 BoMYBs were significantly upregulated upon Xcc infection. Concurrently, an increase in polyphenol content was observed, suggesting a pivotal role of polyphenols in Xcc resistance. Based on phylogenetic relationships and qRT-PCR analysis, BoMYB108 was identified as a candidate gene potentially involved in early resistance to Xcc by regulating polyphenol biosynthesis. Overexpression and silencing experiments were conducted to validate the function of BoMYB108. Overexpression of BoMYB108 significantly enhanced the accumulation of phenolic acids, while silencing resulted in the opposite effect. Furthermore, increased phenolic acid levels were associated with reduced reactive oxygen species (ROS) accumulation. These findings indicate that BoMYB108 promotes phenolic acid biosynthesis and mitigates ROS accumulation under Xcc stress, thereby alleviating Xcc-induced damage. In summary, this study provides a valuable data resource for the MYB gene family in cabbage and establishes a theoretical foundation for understanding the phenolic-based mechanisms of Xcc resistance in brassicaceous vegetables.

A wild-allele GsPP2C-51-a1 enhances tolerance to drought stress in soybean and Arabidopsis

KEY MESSAGE

A wild-allele GsPP2C-51-a1 of Glyma.14g162100 was identified in SojaCSSLP5, back to wild soybean, conferring drought tolerance. Its functions were verified in transgenic hairy root soybeans and Arabidopsis under water deficit and ABA treatment. A population of wild soybean chromosome segment substitution lines (CSSLs), SojaCSSLP5, with NN1138-2 as the cultivated recurrent parent and N24852 as the wild donor parent, was used to identify drought-tolerant loci/segments from the donor. Relative shoot dry weight, a tolerance indicator, varied significantly among the parents and CSSLs. Six drought tolerance loci/segments were detected in SojaCSSLP5, including Gm14_LDB_21 with GsPP2C-51 (Glyma.14g162100) as one of the four possible genes. This gene belongs to the F1 clade of protein phosphatase 2C based on gene ontology annotation, qPCR, and previous research results. Glyma.14g162100 was traced back to the Chinese germplasm population, in which four alleles existed on the locus, with soja holding all four, and max holding only two without any new alleles emerging. N24852 and NN1138-2 hold a1 and a2, respectively. The GsPP2C-51 protein was located inside the nucleus. In transgenic hairy root composite soybean, the GsPP2C-51-a1 overexpressed plants maintained a higher leaf fresh weight (tolerance) under 15% PEG stress compared to the empty vector plants. This was strongly supported by improved tolerance, chlorophyll content, and a series of physiological responses in GsPP2C-51-a1 overexpressed Arabidopsis plants under water deficit and abscisic acid treatments. Thus, the wild-type allele GsPP2C-51-a1 (Glyma.14g162100a1) from N24852 positively regulates plant drought tolerance.

Identification and functional characterization of the MYB transcription factor GmMYBLJ in soybean leaf senescence

Leaf senescence is an important agronomic trait that significantly influences the quality and yield of soybeans. v-Myb avian myeloblastosis viral oncogene homolog (MYB) transcription factors are considered crucial regulators governing leaf senescence, which can be utilized to improve agronomic traits in crops. However, our knowledge regarding the functional roles of soybean MYBs in leaf senescence is extremely limited. In this study, GmMYBLJ, a CCA1-like MYB, was identified and functionally characterized with respect to leaf senescence. The GmMYBLJ protein is localized in the nucleus, and a high accumulation of its transcripts was observed in nodules and embryos. Notably, GmMYBLJ was highly expressed in soybean senescent leaves and was transcriptionally induced by dark or NaCl treatment, as confirmed by histochemical GUS staining analysis. Ectopic overexpression of GmMYBLJ in Arabidopsis not only led to earlier leaf senescence, reduced chlorophyll content, and increased MDA accumulation but also promoted the expression of several WRKY family transcription factors and senescence-associated genes, such as SAG12 and ORE1. Further investigation showed that overexpression of GmMYBLJ accelerated Arabidopsis leaf senescence under darkness and in response to Pst DC3000 infection. Moreover, transgenic soybean plants overexpressing GmMYBLJ grew faster and exhibited accelerated senescence under salt stress. DAB staining analysis showed that GmMYBLJ induced ROS accumulation in soybean hairy roots and Arabidopsis leaves. Collectively, our results provided useful information into the functional roles of GmMYBLJ in both age-dependent and stress-induced senescence.

Genome-wide association mapping of bruchid resistance loci in soybean

Soybean is a globally important industrial, food, and cash crop. Despite its importance in present and future economies, its production is severely hampered by bruchids (Callosobruchus chinensis), a destructive storage insect pest, causing considerable yield losses. Therefore, the identification of genomic regions and candidate genes associated with bruchid resistance in soybean is crucial as it helps breeders to develop new soybean varieties with improved resistance and quality. In this study, 6 multi-locus methods of the mrMLM model for genome-wide association study were used to dissect the genetic architecture of bruchid resistance on 4traits: percentage adult bruchid emergence (PBE), percentage weight loss (PWL), median development period (MDP), and Dobie susceptibility index (DSI) on 100 diverse soybean genotypes, genotyped with 14,469 single-nucleotide polymorphism (SNP) markers. Using the best linear unbiased predictors (BLUPs), 13 quantitative trait nucleotides (QTNs) were identified by the mrMLM model, of which rs16_14976250 was associated with more than 1 bruchid resistance traits. As a result, the identified QTNs linked with resistance traits can be employed in marker-assisted breeding for the accurate and rapid screening of soybean genotypes for resistance to bruchids. Moreover, a gene search on the Phytozome soybean reference genome identified 27 potential candidate genes located within a window of 478.45 kb upstream and downstream of the most reliable QTNs. These candidate genes exhibit molecular and biological functionalities associated with various soybean resistance mechanisms and, therefore, could be incorporated into the farmers' preferred soybean varieties that are susceptible to bruchids.

Analysis of the MYB gene family in tartary buckwheat and functional investigation of FtPinG0005108900.01 in response to drought

Tartary buckwheat (Fagopyrum tataricum) is an important crop used for edible food and medicinal usage. Drought annually brings reduction in crop yield and quality, causing enormous economic losses. Transcription factors are often involved in the regulation of plant responses to environmental stresses. In this study, we identified 233 MYB transcription factors in tartary buckwheat and classified them into 13 groups, including 1R, R2R3, 3R, 4R types. Gene structure and conserved motifs of these 233 FtMYBs suggested the relative conservation of these FtMYBs within each group. There is strong collinearity within the genomes of F. tataricum, with identifying syntenic gene pairs of FtMYB. Further, the expansion of FtMYB genes was attributed to whole genome duplication. The enrichment analysis of cis-acting elements in the FtMYB genes indicated that FtMYBs may participate in abiotic stress responses. The transcriptional changes of FtMYB genes in tartary buckwheat were then investigated using public data and qPCR. A number of FtMYB genes exhibited apparent transcript levels in the detected tissues and most of them disturbed their expression after the treatment of PEG6000 or natural treatment of tartary buckwheat seedlings. Some of the FtMYB genes showed a similar expression trend with qPCR validation. FtMYB gene FtPinG0005108900.01 were shown to activated by PEG6000 and natural drought treatment, and its encoded protein localizes to nucleus, revealing it as a typical transcription factor. Overexpression of FtPinG0005108900.01 increase the drought tolerance, and transcriptome analysis indicated that lignin synthesis other than flavonoid biosynthesis pathway was activated in the overexpressing plants following drought treatment. Our results provided detailed evolution and comparative genomic information of FtMYBs in tartary buckwheat and dissected the function of a FtMYB gene FtPinG0005108900.01 in response to drought.

In-silico analysis and transformation of OsMYB48 transcription factor driven by CaMV35S promoter in model plant - Nicotiana tabacum L. conferring abiotic stress tolerance

Global crop yield has been affected by a number of abiotic stresses. Heat, salinity, and drought stress are at the top of the list as serious environmental growth-limiting factors. To enhance crop productivity, molecular approaches have been used to determine the key regulators affecting stress-related phenomena. MYB transcription factors (TF) have been reported as one of the promising defensive proteins against the unfavorable conditions that plants must face. Different roles of MYB TFs have been suggested such as regulation of cellular growth and differentiation, hormonal signaling, mediating abiotic stress responses, etc. To gain significant insights, a comprehensive in-silico analysis of OsMYB TF was carried out in comparison with 21 dicot MYB TFs and 10 monocot MYB TFs. Their chromosomal location, gene structure, protein domain, and motifs were analyzed. The phylogenetic relationship was also studied, which resulted in the classification of proteins into four basic groups: groups A, B, C, and D. The protein motif analysis identified several conserved sequences responsible for cellular activities. The gene structure analysis suggested that proteins that were present in the same class, showed similar intron-exon structures. Promoter analysis revealed major cis-acting elements that were found to be responsible for hormonal signaling and initiating a response to abiotic stress and light-induced mechanisms. The transformation of OsMYB TF into tobacco was carried out using the Agrobacterium-mediated transformation method, to further analyze the expression level of a gene in different plant parts, under stress conditions. To summarize, the current studies shed light on the evolution and role of OsMYB TF in plants. Future investigations should focus on elucidating the functional roles of MYB transcription factors in abiotic stress tolerance through targeted genetic modification and CRISPR/Cas9-mediated genome editing. The application of omics approaches and systems biology will be indispensable in delineating the regulatory networks orchestrated by MYB TFs, facilitating the development of crop genotypes with enhanced resilience to environmental stressors. Rigorous field validation of these genetically engineered or edited crops is imperative to ascertain their utility in promoting sustainable agricultural practices.

An integrated physiological indicator and transcriptomic analysis reveals the response of soybean buds to high-temperature stress

BACKGROUND

Under global warming, high temperature (HT) has become a major meteorological factor affecting soybean production. To explore the candidate genes and regulatory mechanism of the soybean bud response to HT stress, previously identified as HT-tolerant ('Handou14'; HD14) and HT-sensitive ('Jiadou36'; JD36) were treated for 5 days in an artificial climate incubator either with HT (43 °C (day)/ 33 °C (night), 16 h light/8 h darkness) or the non-stress growth condition (25 °C, 16 h light/8 h darkness) as the control at the bud stage were used as experimental materials in this study. After HT treatment, changes in physiological indicators including hypocotyl length, enzyme activity and hormone content were detected; at the same time, the cotyledons, hypocotyls, and main roots were collected for transcriptome sequencing analysis. Analyzing the mechanisms of HT stress response in the bud stage of HD14 and JD36 at physiological and transcription levels.

RESULTS

Analysis of physiological indicator showed that the activities of superoxide dismutase (SOD) were significantly increased 47.4% and 41.2% in the cotyledon of HD14 and the main root of JD36, and the contents of peroxidase (POD) were significantly increased 61.5% and 125% in the hypocotyl of HD14 and JD36; the contents of malonaldehyde (MDA) were significantly increased 44.8% and 22.2% in the main root of HD14 and JD36 after HT treatment. The content of abscisic acid (ABA) were significantly increased 1.9 fold and 1.2 fold in the root of HD14 and JD36 in response to HT treatment, whereas the content of gibberellin (GA) were decreased 2.2 fold and 1.3 fold in the cotyledon and root, and increased 1.6 fold in the hypocotyl in HD14 (P < 0.05). Thus, higher SOD and POD activities, higher ABA content, and a smaller increase in MDA content may improve tolerance to HT stress. The HT-tolerant cultivar may have stronger GA signal transduction in the hypocotyl to combat the negative effects of HT. RNA-sequencing was performed to analyze the differential expression of genes in buds of the two cultivars under the HT treatment and control condition. In total, 3,633, 1,964, 9,934, and 3,036 differentially expressed genes (DEGs) were identified in the CH (control group of HD14) vs. TH (HT-treatment group of HD14), CJ (control group of JD36) vs. TJ (HT-treatment group of JD36), TJ vs. TH, and CJ vs. CH comparison groups, respectively. Bioinformatic analysis revealed that most DEGs were mainly involved in metabolic processes, catalytic activity, carbohydrate, energy transduction, and signaling pathways. The results of qRT-PCR validation (86.67%) and changes in physiological indicators were consistent with the RNA-sequencing data. Five DEGs were selected as candidate genes in the response to HT stress at the bud stage.

CONCLUSION

In summary, soybean cells are protected from oxidative damage by an increase in antioxidant enzyme activities and accumulation of hormone content under HT stress. Concomitantly, changes in the expression of crucial genes and signal transmission processes are induced, thus initiating adaptive and protective mechanisms. This study provides a theoretical basis for clarification of the physiological and molecular mechanisms in the response to HT stress of soybean bud.

Genome-Wide Analysis of the Common Fig (Ficus carica L.) R2R3-MYB Genes Reveals Their Structure, Evolution, and Roles in Fruit Color Variation

The R2R3-MYB transcription factor (TF) family is crucial for regulating plant growth, stress response, and fruit ripening. Although this TF family has been examined in a multitude of plants, the R2R3-MYB TFs in Ficus carica, a Mediterranean fruit species, have yet to be characterized. This study identified and classified 63 R2R3-MYB genes (FcMYB1 to FcMYB63) in the F. carica genome. We analyzed these genes for physicochemical properties, conserved motifs, phylogenetic relationships, gene architecture, selection pressure, and gene expression profiles and networks. The genes were classified into 29 clades, with members of the same clade showing similar exon-intron structures and motif compositions. Of the 54 orthologous gene pairs shared with mulberry (Morus notabilis), 52 evolved under negative selection, while two pairs (FcMYB55/MnMYB20 and FcMYB59/MnMYB31) experienced diversifying selection. RNA-Seq analysis showed that FcMYB26, FcMYB33, and FcMYB34 were significantly overexpressed in fig fruit peel during maturation phase III. Weighted gene co-expression network analysis (WGCNA) indicated that these genes are part of an expression module associated with the anthocyanin pathway. RT-qPCR validation confirmed these findings and revealed that the Tunisian cultivars 'Zidi' and 'Soltani' have cultivar-specific R2R3-FcMYB genes highly overexpressed during the final stage of fruit maturation and color acquisition. These genes likely influence cultivar-specific pigment synthesis. This study provides a comprehensive overview of the R2R3-MYB TF family in fig, offering a framework for selecting genes related to fruit peel color in breeding programs.

Genome-wide investigation of MYB gene family in Areca catechu and potential roles of AcTDF in transgenic Arabidopsis

BACKGROUND

MYB protein, a crucial transcription factor, holds crucial importance in plant growth, development, stress responses, and secondary metabolite regulation. While MYB proteins have been extensively studied, research on MYBs within the palm family, particularly in Areca catechu, remains limited.

METHODS AND RESULTS

This study identified 259 MYB genes in Areca catechu, including 105 1R-MYBs, 150 R2R3-MYBs, 3 3R-MYBs, and 1 4R-MYBs. Physicochemical properties, collinearity, and gene structure of these genes were analyzed. The AcMYB is distributed across 16 chromosomes of A.catechu and has 119 and 195 homologs in Arabidopsis and rice, respectively. Cis-acting elements in the promoter region suggest roles in plant hormones, growth, development, and stress. R2R3-MYB genes were divided into eight groups based on tissue expression profiles. The flowering-related gene AcTDF is highly expressed in male flowers. Overexpression of AcTDF in Arabidopsis promotes early flowering, upregulates AtSOC1 and AtFUL, and enhances tolerance to drought and salt stress.

CONCLUSIONS

These results provide valuable insights for the identification and analysis of the MYB gene family in Areca catechu and offer a basis for the subsequent verification of its related functions and the role and significance of its role in the evolution of palms.

Genome-wide analysis of the R2R3-MYB gene family and identification of candidate genes that regulate isoflavone biosynthesis in red clover (Trifolium pratense)

Red clover (Trifolium pratense) is a perennial legume with high feeding and medicinal value attributed to its abundant isoflavone content. Previous studies reported that R2R3-MYB transcription factors are involved in the biosynthesis of isoflavones; however, their specific role in red clover remains poorly understood. Through comprehensive genome-wide and transcriptome analyses, a total of 138 TpR2R3-MYB genes were identified and classified into 30 distinct subgroups within a phylogenetic tree. Importantly, six of these subgroups showed associations with isoflavone biosynthesis in red clover. The majority of segmental duplication events (Ka/Ks < 1) indicated that the TpR2R3-MYB gene underwent strong purifying selection during evolution. The qRT-PCR analysis demonstrated high expression levels of TpMYB79 and TpMYB53 in Minshan red clover at full flowering stage, consistent with the trend for isoflavone content determination, suggesting that TpMYB79 and TpMYB53 might be important regulators of isoflavone biosynthesis in red clover. Additionally, we observed nucleus and vacuole membrane localization of TpMYB53 and TpMYB79, with TpMYB53 primarily exerting transcriptional activation through its C-terminal activation motifs while TpMYB79 exhibited no transcriptional activity. These findings provided a foundation for the study of the biological function of R2R3-MYB transcription factors in red clover.

Comprehensive studies of the serine carboxypeptidase-like (SCPL) gene family in Carya cathayensis revealed the roles of SCPL4 in epigallocatechin-3-gallate (EGCG) synthesis and drought tolerance

Hickory (Carya cathayensis) nuts are rich in epigallocatechin-3-gallate (EGCG) with multiple health functions. EGCG also regulates plant growth, development and stress responses. However, research on the synthesis mechanism of EGCG and its function in hickory is currently limited. Herein, 44 serine carboxypeptidase-like (SCPL) members were identified from the hickory genome and classified into three major categories: SCPL-I, SCPL-II, and SCPL-III. In the CcSCPLs-IA branch, CcSCPL3/4/5/8/9/11/13 showed differential expression patterns in various tissues, especially with relatively high expression levels in plant roots, female flowers and seed coat. These proteins have a catalytic triad composed of serine (Ser), aspartic acid (Asp) and histidine (His). Ser-His in the triad and arginine (Arg) mediated the docking of CcSCPL3/4/5/11 with 1-O-galloyl-β-d-glucose (βG) and epigallocatechin (EGC), whereas the Asp of the triad did not. CcSCPL4 was further confirmed to promote the synthesis of EGCG in tobacco leaves. CcSCPL4 may function as monomer and be mainly localized within cellular structures outside the nucleus. Notably, the expression level of CcSCPL4 significantly changed after drought, cold, and salt stress, with the highest expression level under drought stress. Meanwhile CcSCPL4 over-expression could enhance the drought resistance of Saccharomyces cerevisiae and Arabidopsis. This study elucidates key enzymes for EGCG synthesis and their role in drought resistance, providing insights into the EGCG synthesis pathway and molecular breeding of hickory in future.

MYB transcription factors, their regulation and interactions with non-coding RNAs during drought stress in Brassica juncea

BACKGROUND

Brassica juncea (L.) Czern is an important oilseed crop affected by various abiotic stresses like drought, heat, and salt. These stresses have detrimental effects on the crop's overall growth, development and yield. Various Transcription factors (TFs) are involved in regulation of plant stress response by modulating expression of stress-responsive genes. The myeloblastosis (MYB) TFs is one of the largest families of TFs associated with various developmental and biological processes such as plant growth, secondary metabolism, stress response etc. However, MYB TFs and their regulation by non-coding RNAs (ncRNAs) in response to stress have not been studied in B. juncea. Thus, we performed a detailed study on the MYB TF family and their interactions with miRNAs and Long non coding RNAs.

RESULTS

Computational investigation of genome and proteome data presented a comprehensive picture of the MYB genes and their protein architecture, including intron-exon organisation, conserved motif analysis, R2R3 MYB DNA-binding domains analysis, sub-cellular localization, protein-protein interaction and chromosomal locations. Phylogenetically, BjuMYBs were further classified into different subclades on the basis of topology and classification in Arabidopsis. A total of 751 MYBs were identified in B. juncea corresponding to 297 1R-BjuMYBs, 440 R2R3-BjuMYBs, 12 3R-BjuMYBs, and 2 4R-BjuMYBs types. We validated the transcriptional profiles of nine selected BjuMYBs under drought stress through RT-qPCR. Promoter analysis indicated the presence of drought-responsive cis-regulatory components. Additionally, the miRNA-MYB TF interactions was also studied, and most of the microRNAs (miRNAs) that target BjuMYBs were involved in abiotic stress response and developmental processes. Regulatory network analysis and expression patterns of lncRNA-miRNA-MYB indicated that selected long non-coding RNAs (lncRNAs) acted as strong endogenous target mimics (eTMs) of the miRNAs regulated expression of BjuMYBs under drought stress.

CONCLUSIONS

The present study has established preliminary groundwork of MYB TFs and their interaction with ncRNAs in B. juncea and it will help in developing drought- tolerant Brassica crops.

Genome-Wide Identification and Characterization of MYB Transcription Factors in Sudan Grass under Drought Stress

Sudan grass (Sorghum sudanense S.) is a warm-season annual grass with high yield, rich nutritional value, good regeneration, and tolerance to biotic and abiotic stresses. However, prolonged drought affects the yield and quality of Sudan grass. As one of the largest families of multifunctional transcription factors in plants, MYB is widely involved in regulating plant growth and development, hormonal signaling, and stress responses at the gene transcription level. However, the regulatory role of MYB genes has not been well characterized in Sudan grass under abiotic stress. In this study, 113 MYB genes were identified in the Sudan grass genome and categorized into three groups by phylogenetic analysis. The promoter regions of SsMYB genes contain different cis-regulatory elements, which are involved in developmental, hormonal, and stress responses, and may be closely related to their diverse regulatory functions. In addition, collinearity analysis showed that the expansion of the SsMYB gene family occurred mainly through segmental duplications. Under drought conditions, SsMYB genes showed diverse expression patterns, which varied at different time points. Interaction networks of 74 SsMYB genes were predicted based on motif binding sites, expression correlations, and protein interactions. Heterologous expression showed that SsMYB8, SsMYB15, and SsMYB64 all significantly enhanced the drought tolerance of yeast cells. Meanwhile, the subcellular localization of all three genes is in the nucleus. Overall, this study provides new insights into the evolution and function of MYB genes and provides valuable candidate genes for breeding efforts in Sudan grass.

Transcriptomic analysis unveils alterations in the genetic expression profile of tree peony (Paeonia suffruticosa Andrews) infected by Alternaria alternata

BACKGROUND

Black spot disease in tree peony caused by the fungal necrotroph A. alternata, is a primary limiting factor in the production of the tree peony. The intricate molecular mechanisms underlying the tree peony resistance to A. alternata have not been thoroughly investigated.

RESULTS

The present study utilized high-throughput RNA sequencing (RNA-seq) technology to conduct global expression profiling, revealing an intricate network of genes implicated in the interaction between tree peony and A. alternata. RNA-Seq libraries were constructed from leaf samples and high-throughput sequenced using the BGISEQ-500 sequencing platform. Six distinct libraries were characterized. M1, M2 and M3 were derived from leaves that had undergone mock inoculation, while I1, I2 and I3 originated from leaves that had been inoculated with the pathogen. A range of 10.22-11.80 gigabases (Gb) of clean bases were generated, comprising 68,131,232 - 78,633,602 clean bases and 56,677 - 68,996 Unigenes. A grand total of 99,721 Unigenes were acquired, boasting a mean length of 1,266 base pairs. All these 99,721 Unigenes were annotated in various databases, including NR (Non-Redundant, 61.99%), NT (Nucleotide, 45.50%), SwissProt (46.32%), KEGG (Kyoto Encyclopedia of Genes and Genomes, 49.33%), KOG (clusters of euKaryotic Orthologous Groups, 50.18%), Pfam (Protein family, 47.16%), and GO (Gene Ontology, 34.86%). In total, 66,641 (66.83%) Unigenes had matches in at least one database. By conducting a comparative transcriptome analysis of the mock- and A. alternata-infected sample libraries, we found differentially expressed genes (DEGs) that are related to phytohormone signalling, pathogen recognition, active oxygen generation, and circadian rhythm regulation. Furthermore, multiple different kinds of transcription factors were identified. The expression levels of 10 selected genes were validated employing qRT-PCR (quantitative real-time PCR) to confirm RNA-Seq data.

CONCLUSIONS

A multitude of transcriptome sequences have been generated, thus offering a valuable genetic repository for further scholarly exploration on the immune mechanisms underlying the tree peony infected by A. alternata. While the expression of most DEGs increased, a few DEGs showed decreased expression.

Identification of autophagy gene family in potato and the role of StATG8a in salt and drought stress

Autophagy is a highly conserved method of recycling cytoplasm components in eukaryotes. It plays an important role in plant growth and development, as well as in response to biotic and abiotic stresses. Although autophagy-related genes (ATGs) have been identified in several crop species, their particular role in potato (Solanum tuberosum L.) remains unclear. Several transcription factors and signaling genes in the transgenic lines of the model plant Arabidopsis thaliana, such as AtTSPO, AtBES1, AtPIP2;7, AtCOST1 as well as AtATI1/2, ATG8f, GFP-ATG8F-HA, AtDSK2, AtNBR1, AtHKT1 play crucial functions under drought and salt stresses, respectively. In this study, a total of 29 putative StATGs from 15 different ATG subfamilies in the potato genome were identified. Their physicochemical properties, evolutionary connections, chromosomal distribution, gene duplication, protein-protein interaction network, conserved motifs, gene structure, interspecific collinearity relationship, and cis-regulatory elements were analyzed. The results of qRT-PCR detection of StATG expression showed that 29 StATGs were differentially expressed in potato's leaves, flowers, petiole, stem, stolon, tuber, and root. StATGs were dynamically modulated by salt and drought stresses and up-regulated under salt and drought conditions. Our results showed that the StATG8a localized in the cytoplasm and the nucleus. Potato cultivar "Atlantic" overexpressing or downregulating StATG8a were constructed. Based on physiological, biochemical, and photosynthesis parameters, potato lines overexpressing StATG8a exhibited 9 times higher drought and salt tolerance compared to non-transgenic plants. In contrast, the potato plants with knockdown expression showed a downtrend in drought and salt tolerance compared to non-transgenic potato lines. These results could provide new insights into the function of StATG8a in salt and drought response and its possible mechanisms.

Genome-Wide Analysis of Transcription Factor R2R3-MYB Gene Family and Gene Expression Profiles during Anthocyanin Synthesis in Common Walnut (Juglans regia L.)

The R2R3-MYB gene family, encoding plant transcriptional regulators, participates in many metabolic pathways of plant physiology and development, including flavonoid metabolism and anthocyanin synthesis. This study proceeded as follows: the JrR2R3-MYB gene family was analyzed genome-wide, and the family members were identified and characterized using the high-quality walnut reference genome "Chandler 2.0". All 204 JrR2R3-MYBs were established and categorized into 30 subgroups via phylogenetic analysis. JrR2R3-MYBs were unevenly distributed over 16 chromosomes. Most JrR2R3-MYBs had similar structures and conservative motifs. The cis-acting elements exhibit multiple functions of JrR2R3-MYBs such as light response, metabolite response, and stress response. We found that the expansion of JrR2R3-MYBs was mainly caused by WGD or segmental duplication events. Ka/Ks analysis indicated that these genes were in a state of negative purifying selection. Transcriptome results suggested that JrR2R3-MYBs were widely entangled in the process of walnut organ development and differentially expressed in different colored varieties of walnuts. Subsequently, we identified 17 differentially expressed JrR2R3-MYBs, 9 of which may regulate anthocyanin biosynthesis based on the results of a phylogenetic analysis. These genes were present in greater expression levels in 'Zijing' leaves than in 'Lvling' leaves, as revealed by the results of qRT-PCR experiments. These results contributed to the elucidation of the functions of JrR2R3-MYBs in walnut coloration. Collectively, this work provides a foundation for exploring the functional characteristics of the JrR2R3-MYBs in walnuts and improving the nutritional value and appearance quality of walnuts.

GhMYB52 Like: A Key Factor That Enhances Lint Yield by Negatively Regulating the Lignin Biosynthesis Pathway in Fibers of Upland Cotton (Gossypium hirsutum L.)

In the context of sustainable agriculture and biomaterial development, understanding and enhancing plant secondary cell wall formation are crucial for improving crop fiber quality and biomass conversion efficiency. This is especially critical for economically important crops like upland cotton (Gossypium hirsutum L.), for which fiber quality and its processing properties are essential. Through comprehensive genome-wide screening and analysis of expression patterns, we identified a particularly high expression of an R2R3 MYB transcription factor, GhMYB52 Like, in the development of the secondary cell wall in cotton fiber cells. Utilizing gene-editing technology to generate a loss-of-function mutant to clarify the role of GhMYB52 Like, we revealed that GhMYB52 Like does not directly contribute to cellulose synthesis in cotton fibers but instead represses a subset of lignin biosynthesis genes, establishing it as a lignin biosynthesis inhibitor. Concurrently, a substantial decrease in the lint index, a critical measure of cotton yield, was noted in parallel with an elevation in lignin levels. This study not only deepens our understanding of the molecular mechanisms underlying cotton fiber development but also offers new perspectives for the molecular improvement of other economically important crops and the enhancement of biomass energy utilization.

Genome-Wide Analysis of MYB Gene Family in Chrysanthemum ×morifolium Provides Insights into Flower Color Regulation

MYBs constitute the second largest transcription factor (TF) superfamily in flowering plants with substantial structural and functional diversity, which have been brought into focus because they affect flower colors by regulating anthocyanin biosynthesis. Up to now, the genomic data of several Chrysanthemum species have been released, which provides us with abundant genomic resources for revealing the evolution of the MYB gene family in Chrysanthemum species. In the present study, comparative analyses of the MYB gene family in six representative species, including C. lavandulifolium, C. seticuspe, C. ×morifolium, Helianthus annuus, Lactuca sativa, and Arabidopsis thaliana, were performed. A total of 1104 MYBs, which were classified into four subfamilies and 35 lineages, were identified in the three Chrysanthemum species (C. lavandulifolium, C. seticuspe, and C. ×morifolium). We found that whole-genome duplication and tandem duplication are the main duplication mechanisms that drove the occurrence of duplicates in CmMYBs (particularly in the R2R3-MYB subfamily) during the evolution of the cultivated chrysanthemums. Sequence structure and selective pressure analyses of the MYB gene family revealed that some of R2R3-MYBs were subjected to positive selection, which are mostly located on the distal telomere segments of the chromosomes and contain motifs 7 and 8. In addition, the gene expression analysis of CmMYBs in different organs and at various capitulum developmental stages of C. ×morifolium indicated that CmMYBS2, CmMYB96, and CmMYB109 might be the negative regulators for anthocyanin biosynthesis. Our results provide the phylogenetic context for research on the genetic and functional evolution of the MYB gene family in Chrysanthemum species and deepen our understanding of the regulatory mechanism of MYB TFs on the flower color of C. ×morifolium.

Genome‑wide analysis of the MYB gene family in pumpkin

The MYB gene family exerts significant influence over various biological processes and stress responses in plants. Despite this, a comprehensive analysis of this gene family in pumpkin remains absent. In this study, the MYB genes of Cucurbita moschata were identified and clustered into 33 groups (C1-33), with members of each group being highly conserved in terms of their motif composition. Furthermore, the distribution of 175 CmoMYB genes across all 20 chromosomes was found to be non-uniform. Examination of the promoter regions of these genes revealed the presence of cis-acting elements associated with phytohormone responses and abiotic/biotic stress. Utilizing quantitative real-time polymerase chain reaction (qRT-PCR), the expression patterns of 13 selected CmoMYB genes were validated, particularly in response to exogenous phytohormone exposure and various abiotic stressors, including ABA, SA, MeJA, and drought treatments. Expression analysis in different tissues showed that CmoMYB genes are expressed at different levels in different tissues, suggesting that they are functionally divergent in regulating growth and abiotic stresses. These results provide a basis for future studies to characterize the function of the MYB gene family under abiotic stresses in pumpkins.

Overexpression of transcription factor FaMYB63 enhances salt tolerance by directly binding to the SOS1 promoter in Arabidopsis thaliana

Salinity is a pivotal abiotic stress factor with far-reaching consequences on global crop growth, yield, and quality and which includes strawberries. R2R3-MYB transcription factors encompass a range of roles in plant development and responses to abiotic stress. In this study, we identified that strawberry transcription factor FaMYB63 exhibited a significant upregulation in its expression under salt stress conditions. An analysis using yeast assay demonstrated that FaMYB63 exhibited the ability to activate transcriptional activity. Compared with those in the wild-type (WT) plants, the seed germination rate, root length, contents of chlorophyll and proline, and antioxidant activities (SOD, CAT, and POD) were significantly higher in FaMYB63-overexpressing Arabidopsis plants exposed to salt stress. Conversely, the levels of malondialdehyde (MDA) were considerably lower. Additionally, the FaMYB63-overexpressed Arabidopsis plants displayed a substantially improved capacity to scavenge active oxygen. Furthermore, the activation of stress-related genes by FaMYB63 bolstered the tolerance of transgenic Arabidopsis to salt stress. It was also established that FaMYB63 binds directly to the promoter of the salt overly sensitive gene SOS1, thereby activating its expression. These findings identified FaMYB63 as a possible and important regulator of salt stress tolerance in strawberries.

Genome-Wide Analysis of the Xyloglucan Endotransglucosylase/Hydrolase (XTH) Gene Family: Expression Pattern during Magnesium Stress Treatment in the Mulberry Plant (Morus alba L.) Leaves

Mulberry (Morus alba L.), a significant fruit tree crop, requires magnesium (Mg) for its optimal growth and productivity. Nonetheless, our understanding of the molecular basis underlying magnesium stress tolerance in mulberry plants remains unexplored. In our previous study, we identified several differential candidate genes associated with Mg homeostasis via transcriptome analysis, including the xyloglucan endotransglucosylase/hydrolase (XTH) gene family. The XTH gene family is crucial for plant cell wall reconstruction and stress responses. These genes have been identified and thoroughly investigated in various plant species. However, there is no research pertaining to XTH genes within the M. alba plant. This research systematically examined the M. alba XTH (MaXTH) gene family at the genomic level using a bioinformatic approach. In total, 22 MaXTH genes were discovered and contained the Glyco_hydro_16 and XET_C conserved domains. The MaXTHs were categorized into five distinct groups by their phylogenetic relationships. The gene structure possesses four exons and three introns. Furthermore, the MaXTH gene promoter analysis reveals a plethora of cis-regulatory elements, mainly stress responsiveness, phytohormone responsiveness, and growth and development. GO analysis indicated that MaXTHs encode proteins that exhibit xyloglucan xyloglucosyl transferase and hydrolase activities in addition to cell wall biogenesis as well as xyloglucan and carbohydrate metabolic processes. Moreover, a synteny analysis unveiled an evolutionary relationship between the XTH genes in M. alba and those in three other species: A. thaliana, P. trichocarpa, and Zea mays. Expression profiles from RNA-Seq data displayed distinct expression patterns of XTH genes in M. alba leaf tissue during Mg treatments. Real-time quantitative PCR analysis confirmed the expression of the MaXTH genes in Mg stress response. Overall, this research enhances our understanding of the characteristics of MaXTH gene family members and lays the foundation for future functional genomic study in M. alba.

Genome-wide identification and comparative analysis of the Amino Acid Transporter (AAT) gene family and their roles during Phaseolus vulgaris symbioses

Amino acid transporters (AATs) are essential integral membrane proteins that serve multiple roles, such as facilitating the transport of amino acids across cell membranes. They play a crucial role in the growth and development of plants. Phaseolus vulgaris, a significant legume crop, serves as a valuable model for studying root symbiosis. In this study, we have conducted an exploration of the AAT gene family in P. vulgaris. In this research, we identified 84 AAT genes within the P. vulgaris genome sequence and categorized them into 12 subfamilies based on their similarity and phylogenetic relationships with AATs found in Arabidopsis and rice. Interestingly, these AAT genes were not evenly distributed across the chromosomes of P. vulgaris . Instead, there was an unusual concentration of these genes located toward the outer edges of chromosomal arms. Upon conducting motif analysis and gene structural analysis, we observed a consistent presence of similar motifs and an intron-exon distribution pattern among the subfamilies. When we analyzed the expression profiles of PvAAT genes, we noted tissue-specific expression patterns. Furthermore, our investigation into AAT gene expression under rhizobial and mycorrhizal symbiotic conditions revealed that certain genes exhibited high levels of expression. Specifically, ATLa5 and LHT2 was notably upregulated under both symbiotic conditions. These findings point towards a potential role of AATs in the context of rhizobial and mycorrhizal symbiosis in P. vulgaris, in addition to their well-established regulatory functions.

Transcriptome-Based Identification of the SaR2R3-MYB Gene Family in Sophora alopecuroides and Function Analysis of SaR2R3-MYB15 in Salt Stress Tolerance

As one of the most prominent gene families, R2R3-MYB transcription factors significantly regulate biochemical and physiological processes under salt stress. However, in Sophora alopecuroides, a perennial herb known for its exceptional saline alkali resistance, the comprehensive identification and characterization of SaR2R3-MYB genes and their potential functions in response to salt stress have yet to be determined. We investigated the expression profiles and biological functions of SaR2R3-MYB transcription factors in response to salt stress, utilizing a transcriptome-wide mining method. Our analysis identified 28 SaR2R3-MYB transcription factors, all sharing a highly conserved R2R3 domain, which were further divided into 28 subgroups through phylogenetic analysis. Some SaR2R3-MYB transcription factors showed induction under salt stress, with SaR2R3-MYB15 emerging as a potential regulator based on analysis of the protein-protein interaction network. Validation revealed the transcriptional activity and nuclear localization of SaR2R3-MYB15. Remarkably, overexpression of SaR2R3-MYB15 in transgenic plants could increase the activity of antioxidant enzymes and the accumulation of proline but decrease the content of malondialdehyde (MDA), compared with wild-type plants. Moreover, several salt stress-related genes showed higher expression levels in transgenic plants, implying their potential to enhance salt tolerance. Our findings shed light on the role of SaR2R3-MYB genes in salt tolerance in S. alopecuroides.

Cloning, Expression, and Functional Analysis of the MYB Transcription Factor SlMYB86-like in Tomato

MYB transcription factors (TFs) have been shown to play a key role in plant growth and development and are in response to various types of biotic and abiotic stress. Here, we clarified the structure, expression patterns, and function of a MYB TF, SlMYB86-like (Solyc06g071690) in tomato using an inbred tomato line exhibiting high resistance to bacterial wilt (Hm 2-2 (R)) and one susceptible line (BY 1-2 (S)). The full-length cDNA sequence of this gene was 1226 bp, and the open reading frame was 966 bp, which encoded 321 amino acids; its relative molecular weight was 37.05055 kDa; its theoretical isoelectric point was 7.22; it was a hydrophilic nonsecreted protein; and it had no transmembrane structures. The protein also contains a highly conserved MYB DNA-binding domain and was predicted to be localized to the nucleus. Phylogenetic analysis revealed that SlMYB86-like is closely related to SpMYB86-like in Solanum pennellii and clustered with other members of the family Solanaceae. Quantitative real-time PCR (qRT-PCR) analysis revealed that the expression of the SlMYB86-like gene was tissue specific and could be induced by Ralstonia solanacearum, salicylic acid, and jasmonic acid. The results of virus-induced gene silencing (VIGS) revealed that SlMYB86-like silencing decreased the resistance of tomato plants to bacterial wilt, suggesting that it positively regulates the resistance of tomatoes to bacterial wilt. Overall, these findings indicate that SlMYB86-like plays a key role in regulating the resistance of tomatoes to bacterial wilt.

Genome-wide identification, phylogeny and expression analysis of the R2R3-MYB gene family in quinoa (Chenopodium quinoa) under abiotic stress

The MYB transcription factor (TF) are among the largest gene families of plants being responsible for several biological processes. The R2R3-MYB gene family are integral player regulating plant primary and secondary metabolism, growth and development, and responses to hormones and stresses. The phylogenetic analysis combined with gene structure analysis and motif determination resulted in division of R2R3-MYB gene family into 27 subgroups. Evidence generated from synteny analyses indicated that CqR2R3-MYBs gene family is featured by tandem and segmental duplication events. On the basis of RNA-Seq data, the expression patterns of different tissues under salt treatment were investigated resulting CqR2R3-MYB genes high expression both in roots and stem of quinoa (Chenopodium quinoa ) plants. More than half of CqR2R3-MYB genes showed expression under salt stress. Based on this result, CqR2R3-MYB s may regulate quinoa plant growth development and resistance to abiotic stresses. These findings provided comprehensive insights on role of CqR2R3-MYBs gene family members in quinoa and candidate MYB gene family members can be further studies on their role for abiotic stress tolerance in crop plants.

Genome-Wide Analysis of Cotton MYB Transcription Factors and the Functional Validation of GhMYB in Response to Drought Stress

MYB transcription factors play important roles during abiotic stress responses in plants. However, little is known about the accurate systematic analysis of MYB genes in the four cotton species, Gossypium hirsutum, G. barbadense, G. arboreum and G. raimondii. Herein, we performed phylogenetic analysis and showed that cotton MYBs and Arabidopsis MYBs were clustered in the same subfamilies for each species. The identified cotton MYBs were distributed unevenly on chromosomes in various densities for each species, wherein genome-wide tandem and segment duplications were the main driving force of MYB family expansion. Synteny analysis suggested that the abundant collinearity pairs of MYBs were identified between G. hirsutum and the other three species, and that they might have undergone strong purification selection. Characteristics of conserved motifs, along with their consensus sequence, promoter cis elements and gene structure, revealed that MYB proteins might be highly conserved in the same subgroups for each species. Subsequent analysis of differentially expressed genes and expression patterns indicated that most GhMYBs might be involved in response to drought (especially) and salt stress, which was supported by the expression levels of nine GhMYBs using real-time quantitative PCR. Finally, we performed a workflow that combined virus-induced gene silencing and the heterologous transformation of Arabidopsis, which confirmed the positive roles of GhMYBs under drought conditions, as validated by determining the drought-tolerant phenotypes, damage index and/or water loss rate. Collectively, our findings not only expand our understanding of the relationships between evolution and function of MYB genes, but they also provide candidate genes for cotton breeding.

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

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.

Genome-Wide Identification and Characterization of MYB Gene Family and Analysis of Its Sex-Biased Expression Pattern in Spinacia oleracea L

The members of the myeloblastosis (MYB) family of transcription factors (TFs) participate in a variety of biological regulatory processes in plants, such as circadian rhythm, metabolism, and flower development. However, the characterization of MYB genes across the genomes of spinach Spinacia oleracea L. has not been reported. Here, we identified 140 MYB genes in spinach and described their characteristics using bioinformatics approaches. Among the MYB genes, 54 were 1R-MYB, 80 were 2R-MYB, 5 were 3R-MYB, and 1 was 4R-MYB. Almost all MYB genes were located in the 0-30 Mb region of autosomes; however, the 20 MYB genes were enriched at both ends of the sex chromosome (chromosome 4). Based on phylogeny, conserved motifs, and the structure of genes, 2R-MYB exhibited higher conservation relative to 1R-MYB genes. Tandem duplication and collinearity of spinach MYB genes drive their evolution, enabling the functional diversification of spinach genes. Subcellular localization prediction indicated that spinach MYB genes were mainly located in the nucleus. Cis-acting element analysis confirmed that MYB genes were involved in various processes of spinach growth and development, such as circadian rhythm, cell differentiation, and reproduction through hormone synthesis. Furthermore, through the transcriptome data analysis of male and female flower organs at five different periods, ten candidate genes showed biased expression in spinach males, suggesting that these genes might be related to the development of spinach anthers. Collectively, this study provides useful information for further investigating the function of MYB TFs and novel insights into the regulation of sex determination in spinach.

Identification of MYB gene family in medicinal tea tree Melaleuca alternifolia (Maiden and Betche) cheel and analysis of members regulating terpene biosynthesis

BACKGROUND

The tea tree (Melaleuca alternifolia) is renowned for its production of tea tree oil, an essential oil primarily composed of terpenes extracted from its shoot. MYB transcription factors, which are one of the largest TF families, play a crucial role in regulating primary and secondary metabolite synthesis. However, knowledge of the MYB gene family in M. alternifolia is limited.

METHODS AND RESULTS

Here, we conducted a comprehensive genome-wide analysis of MYB genes in M. alternifolia, referred to as MaMYBs, including phylogenetic relationships, structures, promoter regions, and GO annotations. Our findings classified 219 MaMYBs into four subfamilies: one 5R-MYB, four 3R-MYBs, sixty-one MYB-related, and the remaining 153 are all 2R-MYBs. Seven genes (MYB189, MYB146, MYB44, MYB29, MYB175, MYB162, and MYB160) were linked to terpenoid synthesis based on GO annotation. Phylogenetic analysis with Arabidopsis homologous MYB genes suggested that MYB193 and MYB163 may also be involved in terpenoid synthesis. Additionally, through correlation analysis of gene expression and metabolite content, we identified 42 MYB genes associated with metabolite content.

CONCLUSION

The results provide valuable insights into the importance of MYB transcription factors in essential oil production in M. alternifolia. These findings lay the groundwork for a better understanding of the MYB regulatory network and the development of novel strategies to enhance essential oil synthesis in M. alternifolia.

Genome wide identification and characterization of the amino acid transporter (AAT) genes regulating seed protein content in chickpea (Cicer arietinum L.)

Amino acid transporters (AATs), besides, being a crucial component for nutrient partitioning system are also vital for growth and development of the plants and stress resilience. In order to understand the role of AAT genes in seed quality proteins, a comprehensive analysis of AAT gene family was carried out in chickpea leading to identification of 109 AAT genes, representing 10 subfamilies with random distribution across the chickpea genome. Several important stress responsive cis-regulatory elements like Myb, ABRE, ERE were detected in the promoter region of these CaAAT genes. Most of the genes belonging to the same sub-families shared the intron-exon distribution pattern owing to their conserved nature. Random distribution of these CaAAT genes was observed on plasma membrane, vacuolar membrane, Endoplasmic reticulum and Golgi membranes, which may be associated to distinct biochemical pathways. In total 92 out 109 CaAAT genes arise as result of duplication, among which segmental duplication was more prominent over tandem duplication. As expected, the phylogenetic tree was divided into 2 major clades, and further sub-divided into different sub-families. Among the 109 CaAAT genes, 25 were found to be interacting with 25 miRNAs, many miRNAs like miR156, miR159 and miR164 were interacting only with single AAT genes. Tissues specific expression pattern of many CaAAT genes was observed like CaAAP7 and CaAVT18 in nodules, CaAAP17, CaAVT5 and CaCAT9 in vegetative tissues while CaCAT10 and CaAAP23 in seed related tissues as per the expression analysis. Mature seed transcriptome data revealed that genotypes having high protein content (ICC 8397, ICC 13461) showed low CaAATs expression as compared to the genotypes having low protein content (FG 212, BG 3054). Amino acid profiling of these genotypes revealed a significant difference in amount of essential and non-essential amino acids, probably due to differential expression of CaAATs. Thus, the present study provides insights into the biological role of AAT genes in chickpea, which will facilitate their functional characterization and role in various developmental stages, stress responses and involvement in nutritional quality enhancement.

Genome-wide identification and expression analysis of the BURP domain-containing genes in Malus domestica

The conserved BURP-containing proteins are specific to plants and play a crucial role in plant growth, development, and response to abiotic stresses. However, less is known about the systematic characterization of BURP-containing proteins in apple. This study aimed to identify and analyze all BURP-containing genes in the apple genome, as well as to examine their expression patterns through various bioinformatics methods. Eighteen members of BURP-containing genes were identified in apple, six members lacked signal peptides, and the secondary structure was mainly a Random coil of BURP-containing genes. Gene structure and Motif analysis showed that proteins have similar structures and are conserved at the C-terminal. Cis-acting element analysis revealed that the proteins contain phytohormone and stress response elements, and chromosomal localization revealed that the family is unevenly distributed across eight chromosomes, with duplication of fragments leading to the expansion of family proteins. Tissue expression showed that MdPG3 and MdPG4 were expressed in different tissues and different varieties, MdRD2 and MdRD7 were highly expressed in 'M74' fruits and MdRD7 in 'M49' leaves, while MdUSP1 was highly expressed in 'GD' roots. The quantitative real-time PCR analysis showed that the expressions of six and seven genes were significantly up-regulated under NaCl and PEG treatments, respectively, whereas MdRD7 was significantly up-regulated under NaCl and PEG treatment over time. This study offers a comprehensive identification and expression analysis of BURP-containing proteins in apple. The findings provide a theoretical foundation for further exploration of the functions of this protein family.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01393-7.

Genome-Wide Identification and Analysis of MYB Transcription Factors in Pyropia yezoensis

MYB transcription factors are one of the largest transcription factor families in plants, and they regulate numerous biological processes. Red algae are an important taxonomic group and have important roles in economics and research. However, no comprehensive analysis of the MYB gene family in any red algae, including Pyropia yezoensis, has been conducted. To identify the MYB gene members of Py. yezoensis, and to investigate their family structural features and expression profile characteristics, a study was conducted. In this study, 3 R2R3-MYBs and 13 MYB-related members were identified in Py. yezoensis. Phylogenetic analysis indicated that most red algae MYB genes could be clustered with green plants or Glaucophyta MYB genes, inferring their ancient origins. Synteny analysis indicated that 13 and 5 PyMYB genes were orthologous to Pyropia haitanensis and Porphyra umbilicalis, respectively. Most Bangiaceae MYB genes contain several Gly-rich motifs, which may be the result of an adaptation to carbon limitations and maintenance of important regulatory functions. An expression profile analysis showed that PyMYB genes exhibited diverse expression profiles. However, the expression patterns of different members appeared to be diverse, and PyMYB5 was upregulated in response to dehydration, low temperature, and Pythium porphyrae infection. This is the first comprehensive study of the MYB gene family in Py. Yezoensis and it provides vital insights into the functional divergence of MYB genes.

MYB transcription factors and their roles in the male reproductive development of flowering plants

As one of the largest transcription factor families with complex functional differentiation in plants, the MYB transcription factors (MYB TFs) play important roles in the physiological and biochemical processes of plant growth and development. Male reproductive development, an essential part of sexual reproduction in flowering plants, is undoubtedly regulated by MYB TFs. In this review, we summarize the roles of the MYB TFs involved in the three stages of male reproductive development: pollen grains formation and maturation, filament elongation and anther dehiscence, and fertilization. Also, the potential downstream target genes and upstream regulators of these MYB TFs are discussed. Furthermore, we propose the underlying regulatory mechanisms of these MYB TFs: (1) A complex network of MYB TFs regulates various aspects of male reproductive development; (2) MYB homologous genes in different species may be functionally conserved or differentiated; (3) MYB TFs often form regulatory complexes with bHLH TFs.

Genome-wide identification of the longan R2R3-MYB gene family and its role in primary and lateral root

R2R3-MYB is an important transcription factor family that regulates plant growth and development. Root development directly affects the absorption of water and nutrients by plants. Therefore, to understand the regulatory role of R2R3-MYB transcription factor family in root development of longan, this study identified the R2R3-MYB gene family members at the genome-wide level, and analyzed their phylogenetic characteristics, physical and chemical properties, gene structure, chromosome location and tissue expression. The analysis identified 124 R2R3-MYB family members in the longan genome. Phylogenetic analysis divided these members into 22 subfamilies, and the members of the unified subfamily had similar motifs and gene structures. The result of qRT-PCR showed that expression levels of DlMYB33, DlMYB34, DlMYB59, and DlMYB77 were significantly higher in main roots than in lateral as opposed to those of DlMYB35, DlMYB69, DlMYB70, and DlMYB83, which were significantly lower. SapBase database prediction and miRNAs sequencing results showed that 34 longan miRNAs could cleave R2R3-MYB, including 17 novel miRNAs unique to longan. The qRT-PCR and subcellular localization experiments of DlMYB92 and DlMYB98 showed that DlMYB92 is a key factor that regulates transcription in the nucleus and participates in the regulation of longan lateral root development. Longan also has a conserved miRNA-MYB-lateral root development regulation mechanism. This study provides a reference for further research on the transcriptional regulation of the miRNA-R2R3-MYB module in the root development of longan.

Genome-Wide Identification and Expression Analysis of the RADIALIS-like Gene Family in Camellia sinensis

The RADIALIS-like (RL) proteins are v-myb avian myeloblastosis viral oncogene homolog (MYB)-related transcription factors (TFs), and are involved in many biological processes, including metabolism, development, and response to biotic and abiotic stresses. However, the studies on the RL genes of Camellia sinensis are not comprehensive enough. Therefore, we undertook this study and identified eight CsaRLs based on the typical conserved domain SANT Associated domain (SANT) of RL. These genes have low molecular weights and theoretical pI values ranging from 5.67 to 9.76. Gene structure analysis revealed that six CsaRL genes comprise two exons and one intron, while the other two contain a single exon encompassing motifs 1 and 2, and part of motif 3. The phylogenetic analysis divided one hundred and fifty-eight RL proteins into five primary classes, in which CsaRLs clustered in Group V and were homologous with CssRLs of the Shuchazao variety. In addition, we selected different tissue parts to analyze the expression profile of CsaRLs, and the results show that almost all genes displayed variable expression levels across tissues, with CsaRL1a relatively abundant in all tissues. qRT-PCR (real-time fluorescence quantitative PCR) was used to detect the relative expression levels of the CsaRL genes under various abiotic stimuli, and it was found that CsaRL1a expression levels were substantially higher than other genes, with abscisic acid (ABA) causing the highest expression. The self-activation assay with yeast two-hybrid system showed that CsaRL1a has no transcriptional activity. According to protein functional interaction networks, CsaRL1a was well connected with WIN1-like, lysine histidine transporter-1-like, β-amylase 3 chloroplastic-like, carbonic anhydrase-2-like (CA2), and carbonic anhydrase dnaJC76 (DJC76). This study adds to our understanding of the RL family and lays the groundwork for further research into the function and regulatory mechanisms of the CsaRLs gene family in Camellia sinensis.

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

Spatholobus suberectus Dunn (S. suberectus), a plant species within the Leguminosae family, has a long history of use in traditional medicines. The dried stem of S. suberectus exhibits various pharmacological activities because it contains various flavonoids. Diverse functions in plants are associated with the R2R3-MYB gene family, including the biosynthesis of flavonoids. Nonetheless, its role remains unelucidated in S. suberectus. Therefore, the newly sequenced S. suberectus genome was utilized to conduct a systematic genome-wide analysis of the R2R3-MYB gene family. The resulting data identified 181 R2R3-SsMYB genes in total, which were then categorized by phylogenetic analysis into 35 subgroups. Among the R2R3-SsMYB genes, 174 were mapped to 9 different chromosomes, and 7 genes were not located on any chromosome. Moreover, similarity in terms of exon-intron structures and motifs was exhibited by most genes in the same subgroup. The expansion of the gene family was primarily driven by segmental duplication events, as demonstrated by collinearity analysis. Notably, most of the duplicated genes underwent purifying selection, which was depicted through the Ka/Ks analysis. In this study, 22 R2R3-SsMYB genes were shown to strongly influence the level of flavonoids. The elevated expression level of these genes was depicted in the tissues with flavonoid accumulation in contrast with other tissues through qRT-PCR data. The resulting data elucidate the structural and functional elements of R2R3-SsMYB genes and present genes that could potentially be utilized for enhancing flavonoid biosynthesis in S. suberectus.

Function of the R2R3-MYB Transcription Factors in Dalbergia odorifera and Their Relationship with Heartwood Formation

R2R3-MYB transcription factors (TFs) form one of the most important TF families involved in regulating various physiological functions in plants. The heartwood of Dalbergia odorifera is a kind of high-grade mahogany and valuable herbal medicine with wide application. However, the role of R2R3-MYB genes in the growth and development of D. odorifera, especially their relevance to heartwood formation, has not been revealed. A total of 126 R2R3-MYBs were screened from the D. odorifera genome and named DodMYB1-126 based on their location on 10 chromosomes. The collinearity results showed that purification selection was the main driving force for the evolution of the R2R3-MYB TFs family, and whole genome/fragment replication event was the main form for expanding the R2R3-MYB family, generating a divergence of gene structure and function. Comparative phylogenetic analysis classified the R2R3-MYB TFs into 33 subfamilies. S3-7,10,12-13,21 and N4-7 were extensively involved in the metabolic process; S9,13,16-19,24-25 and N1-3,8 were associated with the growth and development of D. odorifera. Based on the differential transcriptional expression levels of R2R3-MYBs in different tissues, DodMYB32, DodMYB55, and DodMYB89 were tentatively screened for involvement in the regulatory process of heartwood. Further studies have shown that the DodMYB89, localized in the nucleus, has transcriptional activation activity and is involved in regulating the biosynthesis of the secondary metabolites of heartwood by activating the promoters of the structural genes DodI2'H and DodCOMT. This study aimed to comprehensively analyze the functions of the R2R3-MYB TFs and screen for candidate genes that might be involved in heartwood formation of D. odorifera.

Two R2R3-MYB transcription factors from Chinese cedar (Cryptomeria fortunei Hooibrenk) are involved in the regulation of secondary cell wall formation

As the most abundant renewable energy source, wood comprises the secondary cell wall (SCW). SCW biosynthesis involves lignin and cellulose deposition. Increasing studies have illustrated that R2R3-MYB transcription factors (TFs) play pivotal roles in affecting lignin accumulation and SCW formation. Nevertheless, the regulatory roles of R2R3-MYBs are still unresolved in Cryptomeria fortunei Hooibrenk cambium and wood formation. To dissect the potentials of CfMYBs, we successfully cloned and intensively studied the functions of CfMYB4 and CfMYB5 in SCW formation and abiotic stress response. They both contained the conserved MYB domain capable of forming a special structure that could bind to the core motifs of downstream genes. The phylogenetic tree implied that two CfMYBs clustered into different evolutionary branches. They were predominantly expressed in the stem and were localized to the nucleus. Furthermore, CfMYB4 functioned as an activator to enhance lignin and cellulose accumulation, and increase the SCW thickness by elevating the expression levels of SCW-related genes. By contrast, CfMYB5 negatively regulated lignin and cellulose biosynthesis, and decreased SCW formation by reducing the expression of SCW biosynthetic genes. Our data not only highlight the regulatory functions of CfMYBs in lignin deposition but also provide critical insights into the development of strategies for the genetic improvement of Cryptomeria fortunei wood biomass.

Persulfidation of transcription factor MYB10 inhibits anthocyanin synthesis in red-skinned pear

Hydrogen sulfide (H2S) is a gaseous signaling molecule that delays color change during fruit ripening. Whether H2S affects anthocyanin biosynthesis in red-skinned pears (Pyrus L.) remains unclear. Here, we found that H2S substantially inhibits anthocyanin accumulation in red-skinned pears and the expression of several genes encoding transcription factors is affected in response to H2S signaling. For example, PyMYB10 and PyMYB73 were down-regulated, whereas PyMYB114 and PyMYB6 were up-regulated. Bioinformatics analysis showed that PyMYB73 and PyMYB6, each containing an EAR motif, may negatively regulate anthocyanin accumulation. Transient expression analysis showed that PyMYB73 substantially promotes anthocyanin biosynthesis by co-transforming with PyMYB10/PyMYB114 + PybHLH3; however, PyMYB6 inhibited anthocyanin biosynthesis in strawberry (Fragaria vesca) receptacles and pear fruits, and PyMYB73 interacted with PyMYB10 and PyMYB6 but not PyMYB114 or PybHLH3. Further investigation showed that Cys194 and Cys218 of PyMYB10 were modified by persulfidation and that PyMYB10Cys218Ala substantially increased anthocyanin accumulation by a transient transformation system. Co-transformation of PyMYB10Cys218Ala + PyMYB73/PyMYB6 also promoted anthocyanin accumulation in pear fruits. Yeast two-hybrid assays showed that the mutation of PyMYB10 did not affect the interaction between PyMYB10 and PyMYB73, but it inhibited interaction with PyMYB6. Moreover, H2S weakened the interaction between PyMYB10 and PyMYB73 but enhanced the interaction with PyMYB6. Thus, we provided a model in which PyMYB10 undergoes persulfidation at Cys218, enhancing the interaction with PyMYB6 and reducing the interaction with PyMYB73. These subsequently results in lower expression of the anthocyanin biosynthesis-related genes Pyrus dihydroflavonol 4-reductase (PyDFR), Pyrus anthocyanidin synthase (PyANS), Pyrus UDP-glucose: flavonoid 3-glucosyl transferase (PyUFGT) and Pyrus glutathione S-transferase (PyGST), thereby inhibiting anthocyanin accumulation in red-skinned pears. Our findings provided a molecular mechanism for H2S-mediated anthocyanin biosynthesis in red-skinned pears.

Global dissection of R2R3-MYB in Pogostemon cablin uncovers a species-specific R2R3-MYB clade

MYB family is one of the largest transcription factor families in plants and plays a crucial role in regulating plant biochemical and physiological processes. However, R2R3-MYBs in patchouli have not been systematically investigated. Here, based on the gene annotation of patchouli genome sequence, 484 R2R3-MYB transcripts were detected. Further in-depth analysis of the gene structure and expression of R2R3-MYBs supported the tetraploid hybrid origin of patchouli. When combined with R2R3-MYBs from Arabidopsis, a phylogenetic tree of patchouli R2R3-MYBs was constructed and divided into 31 clades. Interestingly, a patchouli-specific R2R3-MYB clade was found and confirmed by homologous from other Lamiaceae species. The syntenic analysis demonstrated that tandem duplication contributed to its evolution. This study systematically analysed the R2R3-MYB family in patchouli, providing information on its gene characterization, functional prediction, and species evolution.

Function and molecular mechanism of a poplar placenta limited MIXTA gene in regulating differentiation of plant epidermal cells

The placenta in fruits of most plants either desiccate and shrink as the fruits mature or develop further to form the fleshy tissues. In poplars, placental epidermal cells protrude collectively to produce catkin fibers. In this study, three carpel limited MIXTA genes, PdeMIXTA02, PdeMIXTA03, PdeMIXTA04, were find to specifically expressed in carpel immediately after pollination. Heterologous expression of the three genes in Arabidopsis demonstrated that PdeMIXTA04 significantly promoted trichomes density and could restore trichomes in the trichomeless mutant. By contrast, such functions were not observed with PdeMIXTA02, PdeMIXTA03. In situ hybridization revealed that PdeMIXTA04 was explicitly expressed in poplar placental epidermal cells. We also confirmed trichome-specific expression of the PdeMIXTA04 promoter. Multiple experimental proofs have confirmed the interaction between PdeMIXTA04, PdeMYC and PdeWD40, indicating PdeMIXTA04 functioned through the MYB-bHLH-WD40 ternary complex. Our work provided distinctive understanding of the molecular mechanism triggering differentiation of poplar catkins.

Genome-wide identification and expression analysis of MYB gene family in Cajanus cajan and CcMYB107 improves plant drought tolerance

MYB transcription factor (TF) is one of the largest superfamilies that play a vital role in multiple plant biological processes. However, the MYB family has not been comprehensively identified and functionally verified in Cajanus cajan, which is the sixth most important legume crop. Here, 170 CcR2R3-MYBs were identified and divided into 43 functional subgroups. Segmental and tandem duplications and alternative splicing events were found and promoted the expansion of the CcR2R3-MYB gene family. Functional prediction results showed that CcR2R3-MYBs were mainly involved in secondary metabolism, cell fate and identity, developmental processes, and responses to abiotic stress. Cis-acting element analysis of promoters revealed that stress response elements were widespread in the above four functional branches, further suggesting CcR2R3-MYBs were extensively involved in abiotic stress response. The transcriptome data and qRT-PCR results indicated that most of the CcR2R3-MYB genes responded to various stresses, of which the expression of CcMYB107 was significantly induced by drought stress. Overexpression of CcMYB107 enhanced antioxidant enzyme activity and increased proline and lignin accumulation, thus improving the drought resistance of C. cajan. Furthermore, Overexpression of CcMYB107 up-regulated the expression of stress-related genes and lignin biosynthesis genes after drought stress. Our findings established a strong foundation for the investigation of biological function of CcR2R3-MYB TFs in C. cajan.

In-silico mining and characterization of MYB family genes in wilt-resistant hybrid guava (Psidium guajava × Psidium molle)

BACKGROUND

The MYB family is one of the most significant groups of transcription factors in plants. However, several MYBs have been linked to secondary metabolism and are important for determining the color of fruit's peel and pulp. Despite being a substantial fruit crop in tropical and subtropical areas of the world, wilt-resistant hybrid guava (Psidium guajava × Psidium molle; PGPM) has not yet been the subject of a thorough examination. This study's goal was to assess the expression of MYB in guava fruit pulp, roots, and seeds to predict its function by in silico analysis of the guava root transcriptome data.

RESULTS

In the current study, we have mined the MYBs family of MYB genes from the transcriptome of the PGPM guava root. We have mined 15 distinct MYB transcription factor genes/transcripts viz MYB3, MYB4, MYB23, MYB86, MYB90, MYB308, MYB5, MYB82, MYB114, MYB6, MYB305, MYB44, MYB51, MYB46, and MYB330. From the analyses, it was found that R2-MYB and R3-MYB domains are conserved in all known guava MYB proteins. The expression of six different MYB TFs was examined using semi-quantitative RT-PCR in "Shweta" pulp (white colour pulp), "Lalit" pulp (red color pulp), "Lalit" root, and "Lalit" seed.

CONCLUSION

There were 15 MYB family members observed in guava. They were unequally distributed across the chromosomes, most likely as a result of gene duplication. Additionally, the expression patterns of the particular MYBs showed that MYB may be involved in the control of wilt, fruit ripening, seed development, and root development. Our results allow for a more thorough functional characterization of the guava MYB family genes and open the door to additional research into one essential MYB transcription factor family of genes and its involvement in the growth and ripening of guava fruit.

Living yeast-based biostimulants: different genes for the same results?

Nowadays, many products are available in the plant biostimulants market. Among them, living yeast-based biostimulants are also commercialized. Given the living aspect of these last products, the reproducibility of their effects should be investigated to ensure end-users' confidence. Therefore, this study aimed to compare the effects of a living yeast-based biostimulant between two different soybean cultures. These two cultures named C1 and C2 were conducted on the same variety and soil but in different locations and dates until the VC developmental stage (unifoliate leaves unrolled), with Bradyrhizobium japonicum (control and Bs condition) and with and without biostimulant coating seed treatment. The foliar transcriptomic analysis done first showed a high gene expression difference between the two cultures. Despite this first result, a secondary analysis seemed to show that this biostimulant led to a similar pathway enhancement in plants and with common genes even if the expressed genes were different between the two cultures. The pathways which seem to be reproducibly impacted by this living yeast-based biostimulant are abiotic stress tolerance and cell wall/carbohydrate synthesis. Impacting these pathways may protect the plant from abiotic stresses and maintain a higher level of sugars in plant.

Systematic investigation of the R2R3-MYB gene family in Aquilaria sinensis reveals a transcriptional repressor AsMYB054 involved in 2-(2-phenylethyl)chromone biosynthesis

Trees in the genus Aquilaria produce agarwood, a valuable resin used in medicine, perfumes, and incense. 2-(2-Phenethyl)chromones (PECs) are characteristic components of agarwood; however, molecular mechanisms underlying PEC biosynthesis and regulation remain largely unknown. The R2R3-MYB transcription factors play important regulatory roles in the biosynthesis of various secondary metabolites. In this study, 101 R2R3-MYB genes in Aquilaria sinensis were systematically identified and analyzed at the genome-wide level. Transcriptomic analysis revealed that 19 R2R3-MYB genes were significantly regulated by an agarwood inducer, and showed significant correlations with PEC accumulation. Expression and evolutionary analyses revealed that AsMYB054, a subgroup 4 R2R3-MYB, was negatively correlated with PEC accumulation. AsMYB054 was located in the nucleus and functioned as a transcriptional repressor. Moreover, AsMYB054 could bind to the promoters of the PEC biosynthesis related genes AsPKS02 and AsPKS09, and inhibit their transcriptional activity. These findings suggested that AsMYB054 functions as a negative regulator of PEC biosynthesis via the inhibition of AsPKS02 and AsPKS09 in A. sinensis. Our results provide a comprehensive understanding of the R2R3-MYB subfamily in A. sinensis and lay a foundation for further functional analyses of R2R3-MYB genes in PEC biosynthesis.

Genomic survey of MYB gene family in six pearl millet (Pennisetum glaucum) varieties and their response to abiotic stresses

In addition to their roles in developmental and metabolic processes, MYB transcription factors play crucial roles in plant defense mechanisms and stress responses. A comprehensive analysis of six pearl millet genomes revealed the presence of 1133 MYB genes, which can be classified into four phylogenetically distinct subgroups. The duplication pattern of MYB genes across the pearl millet genomes demonstrates their conserved and similar evolutionary history. Overall, MYB genes were observed to be involved in drought and heat stress responses, with stronger differential expressed observed in root tissues. Multiple analyses indicated that MYB genes mediate abiotic stress responses by modulating abscisic acid-related pathways, circadian rhythms, and histone modification processes. A substantial number of duplicated genes were determined to exhibit differential expression under abiotic stress. The consistent positive expression trend observed in duplicated gene pairs, such as PMA5G04432.1 and PMA2G00728.1, across various abiotic stresses suggests that duplicated MYB genes plays a key role in the evolution of adaptive responses of pearl millet to abiotic stresses.

Identification of Vitis vinifera MYB transcription factors and their response against grapevine berry inner necrosis virus

BACKGROUND

The myeloblastosis (MYB) superfamily is the largest transcription factor family in plants that play diverse roles during stress responses. However, the biotic stress-responsive MYB transcription factors of the grapevine have not been systematically studied. In China, grapevine berries are often infected with the grapevine berry inner necrosis virus (GINV), which eventually reduces the nutritional quality and commodity value.

RESULTS

The present study identified and characterized 265 VvMYB or VvMYB-related genes of the "Crimson seedless" grapevine. Based on DNA-binding domain analysis, these VvMYB proteins were classified into four subfamilies, including MYB-related, 2R-MYB, 3R-MYB, and 4R-MYB. Phylogenetic analysis divided the MYB transcription factors into 26 subgroups. Overexpression of VvMYB58 suppressed GINV abundance in the grapevine. Further qPCR indicated that among 41 randomly selected VvMYB genes, 12 were induced during GINV infection, while 28 were downregulated. These findings suggest that VvMYB genes actively regulate defense response in the grapevine.

CONCLUSION

A deeper understanding of the MYB TFs engaged in GINV defense response will help devise better management strategies. The present study also provides a foundation for further research on the functions of the MYB transcription factors.