A genomic perspective on plant transcription factors

AtMYB72 aggravates photosynthetic inhibition and oxidative damage in Arabidopsis thaliana leaves caused by salt stress

MYB transcription factor is one of the largest families in plants. There are more and more studies on plants responding to abiotic stress through MYB transcription factors, but the mechanism of some family members responding to salt stress is unclear. In this study, physiological and transcriptome techniques were used to analyze the effects of the R2R3-MYB transcription factor AtMYB72 on the growth and development, physiological function, and key gene response of Arabidopsis thaliana. Phenotypic observation showed that the damage of overexpression strain was more serious than that of Col-0 after salt treatment, while the mutant strain showed less salt injury symptoms. Under salt stress, the decrease of chlorophyll content, the degree of photoinhibition of photosystem II (PSII) and photosystem I (PSI) and the degree of oxidative damage of overexpressed lines were significantly higher than those of Col-0. Transcriptome data showed that the number of differentially expressed genes (DEGs) induced by salt stress in overexpressed lines was significantly higher than that in Col-0. GO enrichment analysis showed that the response of AtMYB72 to salt stress was mainly by affecting gene expression in cell wall ectoplast, photosystem I and photosystem II, and other biological processes related to photosynthesis. Compared with Col-0, the overexpression of AtMYB72 under salt stress further inhibited the synthesis of chlorophyll a (Chla) and down-regulated most of the genes related to photosynthesis, which made the photosynthetic system more sensitive to salt stress. AtMYB72 also caused the outbreak of reactive oxygen species and the accumulation of malondialdehyde under salt stress, which decreased the activity and gene expression of key enzymes in SOD, POD, and AsA-GSH cycle, thus destroying the ability of antioxidant system to maintain redox balance. AtMYB72 negatively regulates the accumulation of osmotic regulatory substances such as soluble sugar (SS) and soluble protein (SP) in A. thaliana leaves under salt stress, which enhances the sensitivity of Arabidopsis leaves to salt. To sum up, MYB72 negatively regulates the salt tolerance of A. thaliana by destroying the light energy capture, electron transport, and antioxidant capacity of Arabidopsis.

Selection of Stable Reference Genes for QRT-PCR in Tree Peony 'Doulv' and Functional Analysis of PsCUC3

(1) Background: Tree peonies display extensive cultivar diversity due to widespread hybridization, resulting in a complex genetic architecture. This complexity complicates the selection of universal reference genes across different cultivars for qRT-PCR analyses. Paeonia suffruticosa 'Doulv', notable for its unique green blooms in China, exhibits chlorosis post-flowering and features petaloid stamens and pistils. (2) Methods: Based on published literature and RNA-seq data from 'Doulv', nine candidate reference genes-ACT (Actin), TUB (β-Tubulin), UBC (Ubiquitin Conjugating Enzyme), UBQ (Ubiquitin), UPL (Ubiquitin Protein Ligase), PP2A (Protein Phosphatase 2A), PP2C (Protein Phosphatase 2C), MBF1A (Multiprotein Bridging Factor 1A), and GAPDH (Glyceraldehyde-3-Phosphate Dehydrogenase)-were selected. Their expression stability was assessed across various tissues and developmental stages of 'Doulv' flowers using qRT-PCR, with evaluations conducted via GeNorm_v3.5, NormFinder_v20, and BestKeeper_v1.0. Gene cloning and expression analyses of PsCUC3, including its subcellular localization, were performed. (3) Results: GAPDH and ACT were identified as the most stable reference genes in petaloid stamens across various developmental stages of 'Doulv', whereas UBC and MBF1A were optimal across different tissues. Notably, specific conserved amino acids in PsCUC3 from 'Doulv' diverged from those in NAM/CUC3 proteins of other species, impacting its protein structure. PsCUC3 expression analysis revealed no correlation with chlorophyll content in petaloid stamens but an association with petaloid organ development. Furthermore, PsCUC3 was predominantly localized in the nucleus. (4) Conclusions: This study comprehensively evaluated suitable reference genes using GeNorm_v3.5, NormFinder_v20, and BestKeeper_v1.0 software, establishing a robust qRT-PCR detection system for 'Doulv' peony. These results provide a solid experimental foundation for further research on 'Doulv' peony. Building on this experimental foundation, the functional analysis of the PsCUC3 gene was conducted. The findings suggest a potential association between the PsCUC3 gene and floral morphology alterations in 'Doulv', identifying PsCUC3 as crucial for understanding the molecular mechanisms influencing floral structure in tree peonies.

Salicylic Acid-mediated Alleviation of Salt Stress: Insights from Physiological and Transcriptomic Analysis in Asarum sieboldii Miq

As global agriculture faces the pressing threat of salt stress, innovative solutions are imperative for sustainable agriculture. The remarkable potential of salicylic acid (SA) in enhancing plant resilience against environmental stressors has recently gained attention. However, the specific molecular mechanisms by which SA mitigates salt stress in Asarum sieboldii Miq., a valuable medicinal plant, remain poorly understood. Here, we evaluated the physiological and transcriptomic regulatory responses of A. sieboldii under salt stress (100 mM NaCl), both in the presence (1 mM SA) and absence of exogenous SA. The results highlighted that SA significantly alleviates salt stress, primarily through enhancing antioxidant activities as evidenced by increased superoxide dismutase, and peroxidase activities. Additionally, we observed an increment in chlorophyll (a and b), proline, total soluble sugar, and plant fresh weight, along with a decrease in malondialdehyde contents. Transcriptome analysis suggested consistency in the regulation of many differentially expressed genes and transcription factors (TFs); however, genes targets (GSTs, TIR1, and NPR1), and TFs (MYB, WRKY, TCP, and bHLH) possessed expressional uniqueness, and majority had significantly up-regulated trends in SA-coupled salt stress treatments. Further, bioinformatics and KEGG enrichment analysis indicated several SA-induced significantly enriched biological pathways. Specifically, plant hormone signal transduction was identified as being populated with key genes distinctive to auxin, cytokinin, ethylene, and salicylic acid signaling, suggesting their important role in salt stress alleviation. Inclusively, this report presents a comprehensive analysis encompassing gene targets, TFs, and biological pathways, and these insights may offer a valuable contribution to our knowledge of SA-mediated regulation and its crucial role in enhancing plant defense against diverse abiotic stressors.

Genome-wide identification of bHLH gene family and its response to cadmium stress in Populus × canescens

The basic helix-loop-helix (bHLH) gene family is integral to various aspects of plant development and the orchestration of stress response. This study focuses on the bHLH genes within Populus × canescens, a poplar species noted for its significant tolerance to cadmium (Cd) stress. Through our comprehensive genomic analysis, we have identified and characterized 170 bHLH genes within the P. canescens genome. These genes have been systematically classified into 22 distant subfamilies based on their evolutionary relationships. A notable conservation in gene structure and motif compositions were conserved across these subfamilies. Further analysis of the promoter regions of these genes revealed an abundance of essential cis-acting element, which are associated with plant hormonal regulation, development processes, and stress response pathway. Utilizing quantitative PCR (qPCR), we have documented the differential regulation of PcbHLHs in response to elevated Cd concentrations, with distinct expression patterns observed across various tissues. This study is poised to unravel the molecular mechanism underpinning Cd tolerance in P. canescens, offering valuable insights for the development of new cultivars with enhanced Cd accumulation capacity and tolerance. Such advancements are crucial for implementing effective phytoremediation strategies to mitigate soil pollution caused by Cd.

ACRE, a class of AP2/ERF transcription factors, activates the expression of sweet potato ß-amylase and sporamin genes through the sugar-responsible element CMSRE-1

Sugars, synthesized by photosynthesis in source organs, are loaded and utilized as an energy source and carbon skeleton in sink organs, and also known to be important signal molecules regulating gene expression in higher plants. The expression of genes coding for sporamin and β-amylase, the two most abundant proteins in storage roots of sweet potato, is coordinately induced by sugars. We previously reported on the identification of the carbohydrate metabolic signal-responsible element-1 (CMSRE-1) essential for the sugar-responsible expression of two genes. However, transcription factors that bind to this sequence have not been identified. In this study, we performed yeast one-hybrid screening using the sugar-responsible minimal promoter region of the ß-amylase gene as bait and a library composed only transcription factor cDNAs of Arabidopsis. Two clones, named Activator protein binding to CMSRE-1 (ACRE), encoding AP2/ERF transcription factors were isolated. ACRE showed transactivation activity of the sugar-responsible minimal promoter in a CMSRE-1-dependent manner in Arabidopsis protoplasts. Electric mobility shift assay (EMSA) using recombinant proteins and transient co-expression assay in Arabidopsis protoplasts revealed that ACRE could actually act to the CMSRE-1. Among the DEHYDRATION -RESPONSIVE ELEMENT BINDING FACTOR (DREB) subfamily, almost all homologs including ACRE, could act on the DRE, while only three ACREs could act to the CMSRE-1. Moreover, ACRE-homologs of Japanese morning glory also have the same property of DNA-binding preference and transactivation activity through the CMSRE-1. These findings suggested that ACRE plays an important role in the mechanism regulating the sugar-responsible gene expression through the CMSRE-1 conserved across plant species.

TARGET OF MONOPTEROS: key transcription factors orchestrating plant development and environmental response

Plants have an incredible ability to sustain root and vascular growth after initiation of the embryonic root and the specification of vascular tissue in early embryos. Microarray assays have revealed that a group of transcription factors, TARGET OF MONOPTEROS (TMO), are important for embryonic root initiation in Arabidopsis. Despite the discovery of their auxin responsiveness early on, their function and mode of action remained unknown for many years. The advent of genome editing has accelerated the study of TMO transcription factors, revealing novel functions for biological processes such as vascular development, root system architecture, and response to environmental cues. This review covers recent achievements in understanding the developmental function and the genetic mode of action of TMO transcription factors in Arabidopsis and other plant species. We highlight the transcriptional and post-transcriptional regulation of TMO transcription factors in relation to their function, mainly in Arabidopsis. Finally, we provide suggestions for further research and potential applications in plant genetic engineering.

A Comprehensive Analysis of the Peanut SQUAMOSA Promoter Binding Protein-like Gene Family and How AhSPL5 Enhances Salt Tolerance in Transgenic Arabidopsis

SPL (SQUAMOSA promoter binding protein-like), as one family of plant transcription factors, plays an important function in plant growth and development and in response to environmental stresses. Despite SPL gene families having been identified in various plant species, the understanding of this gene family in peanuts remains insufficient. In this study, thirty-eight genes (AhSPL1-AhSPL38) were identified and classified into seven groups based on a phylogenetic analysis. In addition, a thorough analysis indicated that the AhSPL genes experienced segmental duplications. The analysis of the gene structure and protein motif patterns revealed similarities in the structure of exons and introns, as well as the organization of the motifs within the same group, thereby providing additional support to the conclusions drawn from the phylogenetic analysis. The analysis of the regulatory elements and RNA-seq data suggested that the AhSPL genes might be widely involved in peanut growth and development, as well as in response to environmental stresses. Furthermore, the expression of some AhSPL genes, including AhSPL5, AhSPL16, AhSPL25, and AhSPL36, were induced by drought and salt stresses. Notably, the expression of the AhSPL genes might potentially be regulated by regulatory factors with distinct functionalities, such as transcription factors ERF, WRKY, MYB, and Dof, and microRNAs, like ahy-miR156. Notably, the overexpression of AhSPL5 can enhance salt tolerance in transgenic Arabidopsis by enhancing its ROS-scavenging capability and positively regulating the expression of stress-responsive genes. These results provide insight into the evolutionary origin of plant SPL genes and how they enhance plant tolerance to salt stress.

Genome-wide analysis of the C2H2-ZFP gene family in Stevia rebaudiana reveals involvement in abiotic stress response

Stevia (Stevia rebaudiana Bertoni) is a natural sweetener plant that accumulates highly sweet steviol glycosides (SGs) especially in leaves. Stevia is native to humid areas and does not have a high tolerance to drought which is the most serious abiotic stress restricting its production worldwide. C2H2 zinc finger proteins (C2H2-ZFPs) are a group of well-known transcription factors that involves in various developmental, physiological and biochemical activities as well as in response to abiotic stresses. Here we analyzed C2H2-ZFP gene family in stevia and identified a total of 185 putative SrC2H2-ZF proteins from the genome sequence of S. rebaudiana. We further characterized the identified C2H2-ZF domains and their organization, additional domains and motifs and analyzed their physicochemical properties, localization and gene expression patterns. The cis-element analysis suggested multiple roles of SrC2H2-ZFPs in response to light, phytohormone, and abiotic stresses. In silico analysis revealed that the stevia C2H2-ZFP genes are interactively expressed in different tissues and developmental stages and some C2H2-ZFP genes are involved in response to drought stress. This study provides a background for future exploration of the functional, and regulatory aspects of the C2H2-ZFP gene family in S. rebaudiana.

Genome-Wide Identification and Characterization of the WRKY Gene Family in Cucurbita maxima

In higher plants, WRKY transcription factors are broadly involved in a variety of life activities and play an important role in both biotic and abiotic stress responses. However, little is known about the functions of WRKY genes in the popular species, such as Cucurbita maxima (pumpkin), which is planted worldwide. In the present study, 102 CmWRKY genes were identified in the C. maxima genome. Chromosome location, multiple sequence alignment, phylogenetic analysis, and synteny analysis of the CmWRKYs were performed. Notably, we found that silencing CmWRKY22 promoted cucumber mosaic virus (CMV) infection, whereas overexpression of CmWRKY22 inhibited the CMV infection. Subsequently, an electrophoretic mobility shift assay (EMSA) confirmed that CmWRKY22 was able to bind to the W-box at the promoter of CmPR1b, which is a responsive gene of the salicylic acid (SA) signaling pathway. In summary, this study has provided a foundation for the antiviral functions of WRKY transcription factors in C. maxima.

WRKY transcription factors and OBERON histone-binding proteins form complexes to balance plant growth and stress tolerance

WRKY transcription factors in plants are known to be able to mediate either transcriptional activation or repression, but the mechanism regulating their transcriptional activity is largely unclear. We found that group IId WRKY transcription factors interact with OBERON (OBE) proteins, forming redundant WRKY-OBE complexes in Arabidopsis thaliana. The coiled-coil domain of WRKY transcription factors binds to OBE proteins and is responsible for target gene selection and transcriptional repression. The PHD finger of OBE proteins binds to both histones and WRKY transcription factors. WRKY-OBE complexes repress the transcription of numerous stress-responsive genes and are required for maintaining normal plant growth. Several WRKY and OBE mutants show reduced plant size and increased drought tolerance, accompanied by increased expression of stress-responsive genes. Moreover, expression levels of most of these WRKY and OBE genes are reduced in response to drought stress, revealing a previously uncharacterized regulatory mechanism of the drought stress response. These results suggest that WRKY-OBE complexes repress transcription of stress-responsive genes, and thereby balance plant growth and stress tolerance.

Genome-Wide Analysis of the bHLH Gene Family in Loropetalum chinense var. rubrum: Identification, Classification, Evolution, and Diversity of Expression Patterns under Cultivation

The basic helix-loop-helix (bHLH) transcription factor family is the second-largest transcription factor family in plants. Members of this family are involved in the processes of growth and development, secondary metabolic biosynthesis, signal transduction, and plant resistance. Loropetalum chinense var. rubrum is a critical woody plant with higher ornamental and economic values, which has been used as ornamental architecture and traditional Chinese herbal medicine plants. However, the bHLH transcription factors in Loropetalum chinense var. rubrum (L. chinense var. rubrum) have not yet been systematically demonstrated, and their role in the biosynthesis of anthocyanin is still unclear. Here, we identified 165 potential LcbHLHs genes by using two methods, and they were unequally distributed on chromosomes 1 to 12 of the genome of L. chinense var. rubrum. Based on an evolutionary comparison with proteins from Arabidopsis and Oryza sativa, these bHLH proteins were categorized into 21 subfamilies. Most LcbHLHs in a particular subfamily had similar gene structures and conserved motifs. The Gene Ontology annotation and Cis-elements predicted that LcbHLHs had many molecular functions and were involved in processes of plant growth, including the biosynthesis of flavonoids and anthocyanins. Transcriptomic analysis revealed different expression patterns among different tissues and cultivars of L. chinense var. rubrum. Many LcbHLHs were expressed in the leaves, and only a few genes were highly expressed in the flowers. Six LcbHLHs candidate genes were identified by bioinformatics analysis and expression analysis. Further Real-time quantitative PCR analysis and protein interaction network analysis showed that LcbHLH156, which is one of the candidate proteins belonging to the IIIf subfamily, could interact with proteins related to anthocyanin synthesis. Therefore, LcbHLH156 was transiently expressed in L. chinense var. rubrum to verify its function in regulating anthocyanin synthesis. Compared with the control group, red pigment accumulation appeared at the wound after injection, and the total anthocyanin content increased at the wound of leaves. These results lay a foundation for the research of the regulation mechanism of leaf colors in L. chinense var. rubrum and also provide a basis for the function of the LcbHLH family.

Physiological Changes and Transcriptomic Analysis throughout On-Tree Fruit Ripening Process in Persimmon (Diospyros kaki L.)

The involvement of effectors and transcriptional regulators in persimmon fruit maturation has been mostly approached by the literature under postharvest conditions. In order to elucidate the participation of these genes in the on-tree fruit maturation development, we have collected samples from seven persimmon germplasm accessions at different developmental stages until physiological maturation. This study has focused on the expression analysis of 13 genes involved in ethylene biosynthesis and response pathways, as well as the evolution of important agronomical traits such as skin colour, weight, and firmness. Results revealed different gene expression patterns, with genes up- and down-regulated during fruit development progression. A principal component analysis was performed to correlate gene expression with agronomical traits. The decreasing expression of the ethylene biosynthetic genes DkACO1, DkACO2, and DkACS2, in concordance with other sensing (DkERS1) and transduction genes (DkERF18), provides a molecular mechanism for the previously described high production of ethylene in immature detached fruits. On the other side, DkERF8 and DkERF16 are postulated to induce fruit softening and skin colour change during natural persimmon fruit ripening via DkXTH9 and DkPSY activation, respectively. This study provides valuable information for a better understanding of the ethylene signalling pathway and its regulation during on-tree fruit ripening in persimmon.

Evolution and diversification of the ACT-like domain associated with plant basic helix-loop-helix transcription factors

Basic helix-loop-helix (bHLH) proteins are one of the largest families of transcription factor (TF) in eukaryotes, and ~30% of all flowering plants' bHLH TFs contain the aspartate kinase, chorismate mutase, and TyrA (ACT)-like domain at variable distances C-terminal from the bHLH. However, the evolutionary history and functional consequences of the bHLH/ACT-like domain association remain unknown. Here, we show that this domain association is unique to the plantae kingdom with green algae (chlorophytes) harboring a small number of bHLH genes with variable frequency of ACT-like domain's presence. bHLH-associated ACT-like domains form a monophyletic group, indicating a common origin. Indeed, phylogenetic analysis results suggest that the association of ACT-like and bHLH domains occurred early in Plantae by recruitment of an ACT-like domain in a common ancestor with widely distributed ACT DOMAIN REPEAT (ACR) genes by an ancestral bHLH gene. We determined the functional significance of this association by showing that Chlamydomonas reinhardtii ACT-like domains mediate homodimer formation and negatively affect DNA binding of the associated bHLH domains. We show that, while ACT-like domains have experienced faster selection than the associated bHLH domain, their rates of evolution are strongly and positively correlated, suggesting that the evolution of the ACT-like domains was constrained by the bHLH domains. This study proposes an evolutionary trajectory for the association of ACT-like and bHLH domains with the experimental characterization of the functional consequence in the regulation of plant-specific processes, highlighting the impacts of functional domain coevolution.

Transcriptome Characterization and Gene Changes Induced by Fusarium solani in Sweetpotato Roots

Sweetpotato (Ipomoea batatas) is an important root crop that is infected by Fusarium solani in both seedling and root stages, causing irregular black or brown disease spots and root rot and canker. This study aims to use RNA sequencing technology to investigate the dynamic changes in root transcriptome profiles between control check and roots at 6 h, 24 h, 3 days, and 5 days post-inoculation (hpi/dpi) with F. solani. The results showed that the defense reaction of sweetpotato could be divided into an early step (6 and 24 hpi) without symptoms and a late step to respond to F. solani infection (3 and 5 dpi). The differentially expressed genes (DEGs) in response to F. solani infection were enriched in the cellular component, biological process, and molecular function, with more DEGs in the biological process and molecular function than in the cellular component. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the main pathways were metabolic pathways, the biosynthesis of secondary metabolites, and carbon metabolism. More downregulated genes were identified than upregulated genes in the plant-pathogen interaction and transcription factors, which might be related to the degree of host resistance to F. solani. The findings of this study provide an important basis to further characterize the complex mechanisms of sweetpotato resistance against biotic stress and identify new candidate genes for increasing the resistance of sweetpotato.

Transcriptome and metabolome analyses reveal molecular mechanisms of anthocyanin-related leaf color variation in poplar (Populus deltoides) cultivars

INTRODUCTION

Colored-leaf plants are increasingly popular for their aesthetic, ecological, and social value, which are important materials for research on the regulation of plant pigments. However, anthocyanin components and the molecular mechanisms of anthocyanin biosynthesis in colored-leaf poplar remain unclear. Consequently, an integrative analysis of transcriptome and metabolome is performed to identify the key metabolic pathways and key genes, which could contribute to the molecular mechanism of anthocyanin biosynthesis in the colored-leaf cultivars poplar.

METHODS

In this study, integrated metabolite and transcriptome analysis was performed to explore the anthocyanin composition and the specific regulatory network of anthocyanin biosynthesis in the purple leaves of the cultivars 'Quanhong' (QHP) and 'Zhongshanyuan' (ZSY). Correlation analysis between RNA-seq data and metabolite profiles were also performed to explore the candidate genes associated with anthocyanin biosynthesis. R2R3-MYB and bHLH TFs with differential expression levels were used to perform a correlation analysis with differentially accumulated anthocyanins.

RESULTS AND DISCUSSION

A total of 39 anthocyanin compounds were detected by LC-MS/MS analysis. Twelve cyanidins, seven pelargonidins, five delphinidins, and five procyanidins were identified as the major anthocyanin compounds, which were differentially accumulated in purple leaves of QHP and ZSY. The major genes associated with anthocyanin biosynthesis, including structural genes and transcription factors, were differentially expressed in purple leaves of QHP and ZSY through RNA-sequencing (RNA-seq) data analysis, which was consistent with quantitative real-time PCR analysis results. Correlation analysis between RNA-seq data and metabolite profiles showed that the expression patterns of certain differentially expressed genes in the anthocyanin biosynthesis pathway were strongly correlated with the differential accumulation of anthocyanins. One R2R3-MYB subfamily member in the SG5 subgroup, Podel.04G021100, showed a similar expression pattern to some structural genes. This gene was strongly correlated with 16 anthocyanin compounds, indicating that Podel.04G021100 might be involved in the regulation of anthocyanin biosynthesis. These results contribute to a systematic and comprehensive understanding of anthocyanin accumulation and to the molecular mechanisms of anthocyanin biosynthesis in QHP and ZSY.

Genome-Wide Identification of the SQUAMOSA Promoter-Binding Protein-like (SPL) Transcription Factor Family in Sweet Cherry Fruit

Plant-specific SQUAMOSA promoter-binding protein-like (SPL) transcription factors play important regulatory roles during plant growth and development, fruit ripening, inflorescence branching, and biotic and abiotic stresses. However, there have been no identification or systematic studies of the SPL gene family in the sweet cherry. In this study, 12 SPL genes were identified in the sweet cherry reference genome, which were distributed over 6 chromosomes and classified into six groups according to phylogenetic relationships with other SPL gene families. Nine PavSPLs were highly expressed at green fruit stages and dramatically decreased at the onset of fruit ripening, which implied that they were important regulators during fruit development and ripening. The expression patterns of PavSPL genes under ABA, GA, and MeJA treatments showed that the PavSPLs were involved in the process of fruit ripening. A subcellular localization experiment proved that PavSPL4 and PavSPL7 proteins were localized in the nucleus. The genome-wide identification of the SPL gene family provided new insights while establishing an important foundation for sweet cherry studies.

Basic Helix-Loop-Helix Transcription Factors: Regulators for Plant Growth Development and Abiotic Stress Responses

Plant basic helix-loop-helix (bHLH) transcription factors are involved in many physiological processes, and they play important roles in the abiotic stress responses. The literature related to genome sequences has increased, with genome-wide studies on the bHLH transcription factors in plants. Researchers have detailed the functionally characterized bHLH transcription factors from different aspects in the model plant Arabidopsis thaliana, such as iron homeostasis and abiotic stresses; however, other important economic crops, such as rice, have not been summarized and highlighted. The bHLH members in the same subfamily have similar functions; therefore, unraveling their regulatory mechanisms will help us to identify and understand the roles of some of the unknown bHLH transcription factors in the same subfamily. In this review, we summarize the available knowledge on functionally characterized bHLH transcription factors according to four categories: plant growth and development; metabolism synthesis; plant signaling, and abiotic stress responses. We also highlight the roles of the bHLH transcription factors in some economic crops, especially in rice, and discuss future research directions for possible genetic applications in crop breeding.

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

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

Transcriptome-wide identification of WRKY transcription factors and their expression profiles in response to methyl jasmonate in Platycodon grandiflorus

Platycodon grandiflorus, a perennial flowering plant widely distributed in China and South Korea, is an excellent resource for both food and medicine. The main active compounds of P. grandiflorus are triterpenoid saponins. WRKY transcription factors (TFs) are among the largest gene families in plants and play an important role in regulating plant terpenoid accumulation, physiological metabolism, and stress response. Numerous studies have been reported on other medicinal plants; however, little is known about WRKY genes in P. grandiflorus. In this study, 27 PgWRKYs were identified in the P. grandiflorus transcriptome. Phylogenetic analysis showed that PgWRKY genes were clustered into three main groups and five subgroups. Transcriptome analysis showed that the PgWRKY gene expression patterns in different tissues differed between those in Tongcheng City (Southern Anhui) and Taihe County (Northern Anhui). Gene expression analysis based on RNA sequencing and qRT-PCR analysis showed that most PgWRKY genes were expressed after induction with methyl jasmonate (MeJA). Co-expressing PgWRKY genes with triterpenoid biosynthesis pathway genes revealed four PgWRKY genes that may have functions in triterpenoid biosynthesis. Additionally, functional annotation and protein-protein interaction analysis of PgWRKY proteins were performed to predict their roles in potential regulatory networks. Thus, we systematically analyzed the structure, evolution, and expression patterns of PgWRKY genes to provide an important theoretical basis for further exploring the molecular basis and regulatory mechanism of WRKY TFs in triterpenoid biosynthesis.

Genome-Wide Analysis of Wheat GATA Transcription Factor Genes Reveals Their Molecular Evolutionary Characteristics and Involvement in Salt and Drought Tolerance

GATA transcription factor genes participate in plant growth, development, morphogenesis, and stress response. In this study, we carried out a comprehensive genome-wide analysis of wheat GATA transcription factor genes to reveal their molecular evolutionary characteristics and involvement in salt and drought tolerance. In total, 79 TaGATA genes containing a conserved GATA domain were identified in the wheat genome, which were classified into four subfamilies. Collinear analysis indicated that fragment duplication plays an important role in the amplification of the wheat GATA gene family. Functional disproportionation analysis between subfamilies found that both type I and type II functional divergence simultaneously occurs in wheat GATA genes, which might result in functional differentiation of the TaGATA gene family. Transcriptional expression analysis showed that TaGATA genes generally have a high expression level in leaves and in response to drought and salt stresses. Overexpression of TaGATA62 and TaGATA73 genes significantly enhanced the drought and salt tolerance of yeast and Arabidopsis. Protein-protein docking indicated that TaGATAs can enhance drought and salt tolerance by interacting between the DNA-binding motif of GATA transcription factors and photomorphogenesis-related protein TaCOP9-5A. Our results provided a base for further understanding the molecular evolution and functional characterization of the plant GATA gene family in response to abiotic stresses.

Transcriptome-wide identification of NAC (no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon) transcription factors potentially involved in salt stress response in garlic

Soil salinity has been an increasing problem worldwide endangering crop production and human food security. It is an ideal strategy to excavate stress resistant genes and develop salt tolerant crops. NAC (no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon) transcription factors have been demonstrated to be involved in salt stress response. However, relevant studies have not been observed in garlic, an important vegetable consumed in the world. In this study, a total of 46 AsNAC genes encoding NAC proteins were identified in garlic plant by transcriptome data. Phylogenetic analysis showed that the examined AsNAC proteins were clustered into 14 subgroups. Motif discovery revealed that the conserved domain region was mainly composed of five conserved subdomains. Most of the genes selected could be induced by salt stress in different tissues, indicating a potential role in salt stress response. Further studies may focus on the molecular mechanisms of the AsNAC genes in salt stress response. The results of the current work provided valuable resources for researchers aimed at developing salt tolerant crops.

Evolution and functional analysis of the GRAS family genes in six Rosaceae species

BACKGROUND

GRAS genes formed one of the important transcription factor gene families in plants, had been identified in several plant species. The family genes were involved in plant growth, development, and stress resistance. However, the comparative analysis of GRAS genes in Rosaceae species was insufficient.

RESULTS

In this study, a total of 333 GRAS genes were identified in six Rosaceae species, including 51 in strawberry (Fragaria vesca), 78 in apple (Malus domestica), 41 in black raspberry (Rubus occidentalis), 59 in European pear (Pyrus communis), 56 in Chinese rose (Rosa chinensis), and 48 in peach (Prunus persica). Motif analysis showed the VHIID domain, SAW motif, LR I region, and PFYRE motif were considerably conserved in the six Rosaceae species. All GRAS genes were divided into 10 subgroups according to phylogenetic analysis. A total of 15 species-specific duplicated clades and 3 lineage-specific duplicated clades were identified in six Rosaceae species. Chromosomal localization presented the uneven distribution of GRAS genes in six Rosaceae species. Duplication events contributed to the expression of the GRAS genes, and Ka/Ks analysis suggested the purification selection as a major force during the evolution process in six Rosaceae species. Cis-acting elements and GO analysis revealed that most of the GRAS genes were associated with various environmental stress in six Rosaceae species. Coexpression network analysis showed the mutual regulatory relationship between GRAS and bZIP genes, suggesting the ability of the GRAS gene to regulate abiotic stress in woodland strawberry. The expression pattern elucidated the transcriptional levels of FvGRAS genes in various tissues and the drought and salt stress in woodland strawberry, which were verified by RT-qPCR analysis.

CONCLUSIONS

The evolution and functional analysis of GRAS genes provided insights into the further understanding of GRAS genes on the abiotic stress of Rosaceae species.

Genome-Scale Identification, Classification, and Expression Profiling of MYB Transcription Factor Genes in Cinnamomum camphora

The camphor tree (Cinnamomum camphora (L.) Presl.) is the representative species of subtropical evergreen broadleaved forests in eastern Asia and an important raw material for essential oil production worldwide. Although MYBs have been comprehensively characterized and their functions have been partially resolved in many plants, it has not been explored in C. camphora. In this study, 121 CcMYBs were identified on 12 chromosomes in the whole genome of C. camphora and found that CcMYBs were mainly expanded by segmental duplication. They were divided into 28 subgroups based on phylogenetic analysis and gene structural characteristics. In the promoter regions, numerous cis-acting elements were related to biological processes. Analysis of RNA sequencing data from seven tissues showed that CcMYBs exhibited different expression profiles, suggesting that they have various roles in camphor tree development. In addition, combined with the correlation analysis of structural genes in the flavonoid synthesis pathway, we identified CcMYBs from three subgroups that might be related to the flavonoid biosynthesis pathway. This study systematically analyzed CcMYBs in C. camphora, which will set the stage for subsequent research on the functions of CcMYBs during their lifetime and provide valuable insights for the genetic improvement of camphor trees.

Genome-wide identification and characterization of AP2/ERF gene superfamily during flower development in Actinidia eriantha

Background

As one of the largest transcription factor families in plants, AP2/ERF gene superfamily plays important roles in plant growth, development, fruit ripening and biotic and abiotic stress responses. Despite the great progress has been made in kiwifruit genomic studies, little research has been conducted on the AP2/ERF genes of kiwifruit. The increasing kiwifruit genome resources allowed us to reveal the tissue expression profiles of AP2/ERF genes in kiwifruit on a genome-wide basis.

Results

In present study, a total of 158 AP2/ERF genes in A. eriantha were identified. All genes can be mapped on the 29 chromosomes. Phylogenetic analysis divided them into four main subfamilies based on the complete protein sequences. Additionally, our results revealed that the same subfamilies contained similar gene structures and conserved motifs. Ka/Ks calculation indicated that AP2/ERF gene family was undergoing a strong purifying selection and the evolutionary rates were slow. RNA-seq showed that the AP2/ERF genes were expressed differently in different flower development stages and 56 genes were considered as DEGs among three contrasts. Moreover, qRT-PCR suggested partial genes showed significant expressions as well, suggesting they could be key regulators in flower development in A. eriantha. In addition, two genes (AeAP2/ERF061, AeAP2/ERF067) had abundant transcription level based on transcriptomes, implying that they may play a crucial role in plant flower development regulation and flower tissue forming.

Conclusions

We identified AP2/ERF genes and demonstrated their gene structures, conserved motifs, and phylogeny relationships of AP2/ERF genes in two related species of kiwifruit, A. eriantha and A. chinensis, and their potential roles in flower development in A. eriantha. Such information would lay the foundation for further functional identification of AP2/ERF genes involved in kiwifruit flower development.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08871-4.

Comprehensive Biochemical, Physiological, and Transcriptomic Analyses Provide Insights Into Floral Bud Dormancy in Rhododendron delavayi Franch

Due to a scarcity of relevant data, the ornamental woody flower Rhododendron delavayi Franch. is examined in the current study for its low temperature-induced floral bud dormancy (late October-end December) aspect. This study used transcriptome data profiling and co-expression network analyses to identify the interplay between endogenous hormones and bud dormancy phases such as pre-dormancy, para-dormancy, endo-dormancy, eco-dormancy, and dormancy release. The biochemical and physiological assays revealed the significance of the abundance of phytohormones (abscisic acid, auxin, zeatin, and gibberellins), carbohydrate metabolism, oxidative species, and proteins (soluble proteins, proline, and malondialdehyde) in the regulatory mechanism of floral bud dormancy. The transcriptome sequencing generated 65,531 transcripts, out of which 504, 514, 307, and 240 expressed transcripts were mapped uniquely to pre-, para-, endo-, and eco-phases of dormancy, showing their roles in the stimulation of dormancy. The transcripts related to LEA29, PGM, SAUR family, RPL9e, ATRX, FLOWERING LOCUS T, SERK1, ABFs, ASR2, and GID1 were identified as potential structural genes involved in floral bud dormancy. The transcription factors, including Zinc fingers, CAD, MADS-box family, MYB, and MYC2, revealed their potential regulatory roles concerning floral bud dormancy. The gene co-expression analysis highlighted essential hub genes involved in cold stress adaptations encoding proteins, viz, SERPIN, HMA, PMEI, LEA_2, TRX, PSBT, and AMAT. We exposed the connection among low temperature-induced dormancy in floral buds, differentially expressed genes, and hub genes via strict screening steps to escalate the confidence in selected genes as being truly putative in the pathways regulating bud dormancy mechanism. The identified candidate genes may prove worthy of further in-depth studies on molecular mechanisms involved in floral bud dormancy of Rhododendron species.

Genome-wide identification and characterization of mungbean CIRCADIAN CLOCK ASSOCIATED 1 like genes reveals an important role of VrCCA1L26 in flowering time regulation

Background

CIRCADIAN CLOCK ASSOCIATED 1 like (CCA1L) proteins are important components that participate in plant growth and development, and now have been characterized in multiple plant species. However, information on mungbean CCA1L genes is limited.

Results

In this study, we identified 27 VrCCA1L genes from the mungbean genome. VrCCA1L genes were unevenly distributed on 10 of the 11 chromosomes and showed one tandem and two interchromosomal duplication events. Two distinct kinds of conserved MYB domains, MYB 1 and MYB 2, were found, and the conserved SHAQK(Y/F) F sequence was found at the C terminus of each MYB 2 domain. The VrCCA1Ls displayed a variety of exon-intron organizations, and 24 distinct motifs were found among these genes. Based on phylogenetic analysis, VrCCA1L proteins were classified into five groups; group I contained the most members, with 11 VrCCA1Ls. VrCCA1L promoters contained different types and numbers of cis-acting elements, and VrCCA1Ls showed different expression levels in different tissues. The VrCCA1Ls also displayed distinct expression patterns under different photoperiod conditions throughout the day in leaves. VrCCA1L26 shared greatest homology to Arabidopsis CCA1 and LATE ELONGATED HYPOCOTYL (LHY). It delayed the flowering time in Arabidopsis by affecting the expression levels of CONSTANS (CO), FLOWERING LOCUS T (FT), and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1).

Conclusion

We identified and characterized 27 VrCCA1L genes from mungbean genome, and investigated their spatio-temporal expression patterns. Further analysis revealed that VrCCA1L26 delayed flowering time in transgenic Arabidopsis plants. Our results provide useful information for further functional characterization of the VrCCA1L genes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08620-7.

Two Dof transcription factors promote flavonoid synthesis in kumquat fruit by activating C-glucosyltransferase

Although DNA binding with one finger (Dof) constitutes a crucial plant-specific family of transcription factors (TFs) that plays important roles in a wide range of biological processes, the molecular mechanisms underlying Dof regulation of flavonoid biosynthesis in plants remain largely unknown. Here, we characterized 28 Dof genes (FhDof1-FhDof28) from the 'Hongkong' kumquat (Fortunella hindsii) cultivar genome. Promoter analysis and transcriptome profiling revealed that four FhDofs - FhDof4, FhDof9, FhDof15, and FhDof16 - may be involved in flavonoid biosynthesis through binding to the flavonoid C-glycosyltransferase (FhCGT) promoter. We cloned homologous genes of four FhDofs, designated as FcDof4, FcDof9, FcDof15, FcDof16, and a homologous gene of FhCGT, designated as FcCGT, from the widely cultivated 'HuaPi' kumquat (F. crassifolia). Quantitative reverse transcription-polymerase chain reaction analysis revealed that FcDof4 and FcDof16 were significantly correlated with FcCGT expression during development stages in the 'HuaPi' fruit (Pearson's correlation coefficient > 0.7) and were localized to the nucleus. Results of yeast one-hybrid, electrophoretic mobility shift, and dual-luciferase assays indicated that the two FcDofs trigger FcCGT expression by specifically binding to its promoters. Moreover, transient overexpression of FcDof4 and FcDof16 enhances the transcription of structural genes in the flavonoid biosynthetic pathway and increases C-glycosylflavonoid content. Our results provide strong evidence that the TFs FcDof4 and FcDof16 promote flavonoid synthesis in kumquat fruit by activating FcCGT expression.

Analyses of Botrytis cinerea-responsive LrWRKY genes from Lilium regale reveal distinct roles of two LrWRKY transcription factors in mediating responses to B. cinerea

Botrytis cinerea induced expression of 15 LrWRKY genes; overexpression of LrWRKY39 and LrWRKY41a increased resistance and susceptibility, respectively, to B. cinerea in a manner related to SA and JA signaling. WRKY transcription factors (TFs), a large family, play important roles in coping with biotic stresses. Lilium regale Wilson is a lily species with strong resistance to fungi and viruses; however, functional characterization of LrWRKY TFs remains very limited. Here, a total of 25 LrWRKY members were identified from the L. regale transcriptome, and 15 LrWRKY genes were significantly induced by Botrytis cinerea. Based on their structural features, B. cinerea-responsive LrWRKY genes could be classified into six subgroups (Groups I, IIa-d, and III), and sequence alignment showed that 12 LrWRKY proteins have a well-conserved WRKYGQK domain, while 3 LrWRKYs have a variant sequence (WRKYGKK or WRMYEQK). Quantitative RT-PCR analysis revealed tissue-specific expression of B. cinerea-responsive LrWRKY genes and their expression profiles in response to defense-related hormones salicylic acid (SA), methyl jasmonate (MeJA) and hydrogen peroxide. LrWRKY39 and LrWRKY41a, which encode two LrWRKY TFs with different three-dimensional (3D) models of the WRKY domain, were cloned, and both proteins were targeted to the nucleus. Overexpression of LrWRKY39 and LrWRKY41a in Arabidopsis thaliana increased the resistance and susceptibility to B. cinerea, respectively, compared to the wild type. Similar results were also observed in tobacco and lily (L. longiflorum 'Snow Queen') by transient transformation analyses. Their distinct roles may be related to changes in the transcript levels of SA-/JA-responsive genes. Our results provide new insights into B. cinerea-responsive LrWRKY members and the biological functions of two different 3D models of LrWRKY TFs in defense responses to B. cinerea infection.

Insights Into the MYB-Related Transcription Factors Involved in Regulating Floral Aroma Synthesis in Sweet Osmanthus

As an important member of the MYB transcription factor (TF) family, the MYB-related TFs play multiple roles in regulating the synthesis of secondary metabolites and developmental processes, as well as in response to numerous biotic and abiotic stressors in plants. However, little is known regarding their roles in regulating the formation of floral volatile organic compounds (VOCs). In this study, we conducted a genome-wide analysis of MYB-related proteins in sweet osmanthus; 212 OfMYB-related TFs were divided into three distinct subgroups based on the phylogenetic analysis. Additionally, we found that the expansion of the OfMYB-related genes occurred primarily through segmental duplication events, and purifying selection occurred in all duplicated gene pairs. RNA-seq data revealed that the OfMYB-related genes were widely expressed in different organs of sweet osmanthus, and some showed flower organ/development stage-preferential expression patterns. Here, three OfMYB-related genes (OfMYB1R70/114/201), which were expressed nuclearly in floral organs, were found to be significantly involved in regulating the synthesis of floral VOCs. Only, OfMYB1R201 had transcriptional activity, thus implying that this gene participates in regulating the expression of VOC synthesis related genes. Remarkably, the transient expression results suggested that OfMYB1R70, OfMYB1R114, and OfMYB1R201 are involved in the regulation of VOC synthesis; OfMYB1R114 and OfMYB1R70 are involved in accelerating β-ionone formation. In contrast, OfMYB1R201 decreases the synthesis of β-ionone. Our results deepen our knowledge of the functions of MYB-related TFs and provide critical candidate genes for the floral aroma breeding of sweet osmanthus in the future.

Cis-regulatory sequences in plants: Their importance, discovery, and future challenges

The identification and characterization of cis-regulatory DNA sequences and how they function to coordinate responses to developmental and environmental cues is of paramount importance to plant biology. Key to these regulatory processes are cis-regulatory modules (CRMs), which include enhancers and silencers. Despite the extraordinary advances in high-quality sequence assemblies and genome annotations, the identification and understanding of CRMs, and how they regulate gene expression, lag significantly behind. This is especially true for their distinguishing characteristics and activity states. Here, we review the current knowledge on CRMs and breakthrough technologies enabling identification, characterization, and validation of CRMs; we compare the genomic distributions of CRMs with respect to their target genes between different plant species, and discuss the role of transposable elements harboring CRMs in the evolution of gene expression. This is an exciting time to study cis-regulomes in plants; however, significant existing challenges need to be overcome to fully understand and appreciate the role of CRMs in plant biology and in crop improvement.

Transcriptomic Insight into Underground Floral Differentiation in Erythronium japonicum

Erythronium japonicum Decne (Liliaceae) flowers in early spring after overwintering. Its sexual reproduction process includes an underground development process of floral organs, but the underlying molecular mechanisms are obscure. The present study is aimed at exploring the transcriptional changes and key genes involved at underground floral developmental stages, including flower primordium differentiation, perianth differentiation, stamen differentiation, and pistil differentiation in E. japonicum. Multistage high-quality transcriptomic data resulted in identifying putative candidate genes for underground floral differentiation in E. japonicum. A total of 174,408 unigenes were identified, 28,508 of which were differentially expressed genes (DEGs) at different floral developmental stages, while only 44 genes were identified with conserved regulation between different stages. Further annotation of DEGs resulted in the identification of 270 DEGs specific to floral differentiation. In addition, ELF3, PHD, cullin 1, SE14, ZSWIM3, GIGNATEA, and SERPIN B were identified as potential candidate genes involved in the regulation of floral differentiation. Besides, we explored transcription factors with differential regulation at different developmental stages and identified bHLH, FAR1, mTERF, MYB-related, NAC, Tify, and WRKY TFs for their potential involvement in the underground floral differentiation process. Together, these results laid the foundation for future molecular works to improve our understanding of the underground floral differentiation process and its genetic regulation in E. japonicum.

Identification and expression analysis of the sucrose synthase gene family in pomegranate (Punica granatum L.)

BACKGROUND

Sucrose synthase (SUS, EC 2.4.1.13) is one of the major enzymes of sucrose metabolism in higher plants. It has been associated with C allocation, biomass accumulation, and sink strength. The SUS gene families have been broadly explored and characterized in a number of plants. The pomegranate (Punica granatum) genome is known, however, it lacks a comprehensive study on its SUS genes family.

METHODS

PgSUS genes were identified from the pomegranate genome using a genome-wide search method. The PgSUS gene family was comprehensively analyzed by physicochemical properties, evolutionary relationship, gene structure, conserved motifs and domains, protein structure, syntenic relationships, and cis-acting elements using bioinformatics methods. The expression pattern of the PgSUS gene in different organs and fruit development stages were assayed with RNA-seq obtained from the NCBI SRA database as well as real-time quantitative polymerase chain reaction (qPCR).

RESULTS

Five pomegranate SUS genes, located on four different chromosomes, were divided into three subgroupsaccording to the classification of other seven species. The PgSUS family was found to be highly conserved during evolution after studying the gene structure, motifs, and domain analysis. Furthermore, the predicted PgSUS proteins showed similar secondary and tertiary structures. Syntenic analysis demonstrated that four PgSUS genes showed syntenic relationships with four species, with the exception of PgSUS2. Predictive promoter analysis indicated that PgSUS genes may be responsive to light, hormone signaling, and stress stimulation. RNA-seq analysis revealed that PgSUS1/3/4 were highly expressed in sink organs, including the root, flower, and fruit, and particularly in the outer seed coats. qPCR analysis showed also that PgSUS1, PgSUS3, and PgSUS4 were remarkably expressed during fruit seed coat development. Our results provide a systematic overview of the PgSUS gene family in pomegranate, developing the framework for further research and use of functional PgSUS genes.

MeWRKY IIas, Subfamily Genes of WRKY Transcription Factors From Cassava, Play an Important Role in Disease Resistance

Cassava (Manihot esculenta Crantz) is an important tropical crop for food, fodder, and energy. Cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) occurs in all cassava growing regions and threatens global cassava production. WRKY transcription factor family plays the essential roles during plant growth, development, and abiotic or biotic stress. Particularly, previous studies have revealed the important role of the group IIa WRKY genes in plant disease resistance. However, a comprehensive analysis of group IIa subfamily in cassava is still missing. Here, we identified 102 WRKY members, which were classified into three groups, I, II, and III. Transient expression showed that six MeWRKY IIas were localized in the nucleus. MeWRKY IIas transcripts accumulated significantly in response to SA, JA, and Xam. Overexpression of MeWRKY27 and MeWRKY33 in Arabidopsis enhanced its resistance to Pst DC3000. In contrast, silencing of MeWRKY27 and MeWRKY33 in cassava enhanced its susceptibility to Xam. Co-expression network analysis showed that different downstream genes are regulated by different MeWRKY IIa members. The functional analysis of downstream genes will provide clues for clarifying molecular mechanism of cassava disease resistance. Collectively, our results suggest that MeWRKY IIas are regulated by SA, JA signaling, and coordinate response to Xam infection.

The GmXTH1 gene improves drought stress resistance of soybean seedlings

In order to study the role of GmXTH1 gene in alleviating drought stress, soybean seeds with GmXTH1 gene were transferred by T4 treated with PEG6000 concentration of 0%, 5%, 10%, and 15% respectively. The germination potential, germination rate, germination index, and other indicators were measured. The results showed that the germination potential, germination rate, and germination index of OEA1 and OEA2 strains overexpressed in T4 generation were significantly higher than those of the control material M18. After 0-day, 7-day, and 15-day drought stress, the analysis of seedling phenotypes and root-shoot of different T4 generation transgenic soybean lines showed that under stress conditions, the growth of GmXTH1 overexpression material was generally better than that of the control material M18. The growth of GmXTH1 interference expression material was generally worse than that of the control material M18, with significant differences in plant phenotypes. The root system of GmXTH1 overexpressed material was significantly developed compared with that of the control material M18. The analysis of physiological and biochemical indexes showed that the relative water content and the activity of antioxidant enzymes (superoxide dismutase and peroxidase) of GmXTH1 transgenic soybean material were significantly higher than those of the control material M18, and the accumulation of malondialdehyde was lower under the same stress conditions at seedling stage. Fluorescence quantitative PCR assay showed that the relative expression of GmXTH1 gene in transgenic soybean was significantly increased after drought stress. The results showed that the overexpression of GmXTH1 could increase the total root length, surface area, total projection area, root volume, average diameter, total cross number, and total root tip number, thereby increasing the water intake and reducing the transpiration of water content in leaves, thus reducing the accumulation of MDA and producing more protective enzymes in a more effective and prompt way, reducing cell membrane damage to improve drought resistance of soybean.

Identification of bHLH genes through genome-wide association study and antisense expression of ZjbHLH076/ZjICE1 influence tolerance to low temperature and salinity in Zoysia japonica

Abiotic stress greatly affects plant growth and developmental processes, resulting in poor productivity. A variety of basic helix-loop-helix (bHLH) transcription factors (TFs) that play important roles in plant abiotic stress response pathways have been identified. However, bHLH proteins of Zoysia japonica, one of the warm-season turfgrasses, have not been widely studied. In this study, 141 bHLH genes (ZjbHLHs) were identified and classified into 22 subfamilies. The ZjbHLHs were mapped on 19 chromosomes except for Chr17 and one pair of the tandemly arrayed genes was identified on Chr06. Also, the co-linearity of ZjbHLHs was found to have been driven mostly by segmental duplication events. The subfamily IIIb genes of our present interest, possessed various stress responsive cis-elements in their promoters. ZjbHLH076/ZjICE1, a MYC-type bHLH TF in subfamily IIIb was analyzed by overexpression and its loss-of-function via overexpressing a short ZjbHLH076/ZjICE1 fragment in the antisense direction. The overexpression of ZjbHLH076/ZjICE1 enhanced the tolerance to cold and salinity stress in the transgenic Z. japonica plants. However, the anti-sense expression of ZjbHLH076/ZjICE1 showed sensitive to these abiotic stresses. These results suggest that ZjbHLH076/ZjICE1 would be a promising candidate for the molecular breeding program to improve the abiotic stress tolerance of Z. japonica.

High-quality evergreen azalea genome reveals tandem duplication-facilitated low-altitude adaptability and floral scent evolution

Azalea belongs to Rhododendron, which is one of the largest genera of flowering plants and is well known for the diversity and beauty in its more than 1000 woody species. Rhododendron contains two distinct groups: the most high-altitude and a few low-altitude species; however, the former group is difficult to be domesticated for urban landscaping, and their evolution and adaptation are little known. Rhododendron ovatum has broad adaptation in low-altitude regions but possesses evergreen characteristics like high-altitude species, and it has floral fragrance that is deficient in most cultivars. Here we report the chromosome-level genome assembly of R. ovatum, which has a total length of 549 Mb with scaffold N50 of 41 Mb and contains 41 264 predicted genes. Genomic micro-evolutionary analysis of R. ovatum in comparison with two high-altitude Rhododendron species indicated that the expansion genes in R. ovatum were significantly enriched in defence responses, which may account for its adaptability in low altitudes. The R. ovatum genome contains much more terpene synthase genes (TPSs) compared with the species that lost floral fragrance. The subfamily b members of TPS are involved in the synthesis of sesquiterpenes as well as monoterpenes and play a major role in flora scent biosynthesis and defence responses. Tandem duplication is the primary force driving expansion of defence-responsive genes for extensive adaptability to the low-altitude environments. The R. ovatum genome provides insights into low-altitude adaptation and gain or loss of floral fragrance for Rhododendron species, which are valuable for alpine plant domestication and floral scent breeding.

Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng

BACKGROUND

Panax ginseng is a well-known medicinal plant worldwide. As an herbal medicine, ginseng is also known for its long lifecycle, which can reach several decades. WRKY proteins play regulatory roles in many aspects of biological processes in plants, such as responses to biotic or abiotic stress, plant development, and adaptation to environmental challenges. Genome-wide analyses of WRKY genes in P. ginseng have not been reported.

RESULTS

In this study, 137 PgWRKY genes were identified from the ginseng genome. Phylogenetic analysis showed that the PgWRKYs could be clustered into three primary groups and five subgroups. Most of the PgWRKY gene promoters contained several kinds of hormone- and stress-related cis-regulatory elements. The expression patterns of PgWRKY genes in 14 different tissues were analyzed based on the available public RNA-seq data. The responses of the PgWRKY genes to heat, cold, salt and drought treatment were also investigated. Most of the PgWRKY genes were expressed differently after heat treatment, and expression trends changed significantly under drought and cold treatment but only slightly under salt treatment. The coexpression analysis of PgWRKY genes with the ginsenoside biosynthesis pathway genes identified 11 PgWRKYs that may have a potential regulatory role in the biosynthesis process of ginsenoside.

CONCLUSIONS

This work provides insights into the evolution, modulation and distribution of the WRKY gene family in ginseng and extends our knowledge of the molecular basis along with modulatory mechanisms of WRKY transcription factors in ginsenoside biosynthesis.

Expression analyses in Ginkgo biloba provide new insights into the evolution and development of the seed

Although the seed is a key morphological innovation, its origin remains unknown and molecular data outside angiosperms is still limited. Ginkgo biloba, with a unique place in plant evolution, being one of the first extant gymnosperms where seeds evolved, can testify to the evolution and development of the seed. Initially, to better understand the development of the ovules in Ginkgo biloba ovules, we performed spatio-temporal expression analyses in seeds at early developing stages, of six candidate gene homologues known in angiosperms: WUSCHEL, AINTEGUMENTA, BELL1, KANADI, UNICORN, and C3HDZip. Surprisingly, the expression patterns of most these ovule homologues indicate that they are not wholly conserved between angiosperms and Ginkgo biloba. Consistent with previous studies on early diverging seedless plant lineages, ferns, lycophytes, and bryophytes, many of these candidate genes are mainly expressed in mega- and micro-sporangia. Through in-depth comparative transcriptome analyses of Ginkgo biloba developing ovules, pollen cones, and megagametophytes we have been able to identify novel genes, likely involved in ovule development. Finally, our expression analyses support the synangial or neo-synangial hypotheses for the origin of the seed, where the sporangium developmental network was likely co-opted and restricted during integument evolution.

Integument-Specific Transcriptional Regulation in the Mid-Stage of Flax Seed Development Influences the Release of Mucilage and the Seed Oil Content

Flax (Linum usitatissimum L.) seed oil, which accumulates in the embryo, and mucilage, which is synthesized in the seed coat, are of great economic importance for food, pharmaceutical as well as chemical industries. Theories on the link between oil and mucilage production in seeds consist in the spatio-temporal competition of both compounds for photosynthates during the very early stages of seed development. In this study, we demonstrate a positive relationship between seed oil production and seed coat mucilage extrusion in the agronomic model, flax. Three recombinant inbred lines were selected for low, medium and high mucilage and seed oil contents. Metabolite and transcript profiling (1H NMR and DNA oligo-microarrays) was performed on the seeds during seed development. These analyses showed main changes in the seed coat transcriptome during the mid-phase of seed development (25 Days Post-Anthesis), once the mucilage biosynthesis and modification processes are thought to be finished. These transcriptome changes comprised genes that are putatively involved in mucilage chemical modification and oil synthesis, as well as gibberellic acid (GA) metabolism. The results of this integrative biology approach suggest that transcriptional regulations of seed oil and fatty acid (FA) metabolism could occur in the seed coat during the mid-stage of seed development, once the seed coat carbon supplies have been used for mucilage biosynthesis and mechanochemical properties of the mucilage secretory cells.

WRKY46 promotes ammonium tolerance in Arabidopsis by repressing NUDX9 and indole-3-acetic acid-conjugating genes and by inhibiting ammonium efflux in the root elongation zone

Ammonium (NH₄⁺ ) is toxic to root growth in most plants, even at moderate concentrations. Transcriptional regulation is one of the most important mechanisms in the response of plants to NH₄⁺ toxicity, but the nature of the involvement of transcription factors (TFs) in this regulation remains unclear. Here, RNA-seq analysis was performed on Arabidopsis roots to screen for ammonium-responsive TFs. WRKY46, the member of the WRKY transcription factor family most responsive to NH₄⁺ , was selected. We defined the role of WRKY46 using mutation and overexpression assays, and characterized the regulation of NUDX9 and indole-3-acetic acid (IAA)-conjugating genes by WRKY46 via yeast one-hybrid and electrophoretic mobility shift assays and chromatin immunoprecipitation-quantitative real-time polymerase chain reaction (ChIP-qPCR). Knockout of WRKY46 increased, while overexpression of WRKY46 decreased, NH₄⁺ -suppression of the primary root. WRKY46 is shown to directly bind to the promoters of the NUDX9 and IAA-conjugating genes (GH3.1, GH3.6, UGT75D1, UGT84B2) and to inhibit their transcription, thus positively regulating free IAA content and stabilizing protein N-glycosylation, leading to an inhibition of NH₄⁺ efflux in the root elongation zone (EZ). We identify TF involvement in the regulation of NH₄⁺ efflux in the EZ, and show that WRKY46 inhibits NH₄⁺ efflux by negative regulation of NUDX9 and IAA-conjugating genes.

Glyoxalase I-4 functions downstream of NAC72 to modulate downy mildew resistance in grapevine

Glyoxalase I (GLYI) is part of the glyoxalase system; its major function is the detoxification of α-ketoaldehydes, including the potent and cytotoxic methylglyoxal (MG). Methylglyoxal disrupts mitochondrial respiration and increases production of reactive oxygen species (ROS), which also increase during pathogen infection of plant tissues; however, there have been few studies relating the glyoxalase system to the plant pathogen response. We used the promoter of VvGLYI-4 to screen the upstream transcription factors and report a NAC (NAM/ATAF/CUC) domain-containing transcription factor VvNAC72 in grapevine, which is localized to the nucleus. Our results show that VvNAC72 expression is induced by downy mildew, Plasmopara viticola, while the transcript level of VvGLYI-4 decreases. Further analysis revealed that VvNAC72 can bind directly to the promoter region of VvGLYI-4 via the CACGTG element, leading to inhibition of VvGLYI-4 transcription. Stable overexpression of VvNAC72 in grapevine and tobacco showed a decreased expression level of VvGLYI-4 and increased content of MG and ROS, as well as stronger resistance to pathogen stress. Taken together, these results demonstrate that grapevine VvNAC72 negatively modulates detoxification of MG through repression of VvGLYI-4, and finally enhances resistance to downy mildew, at least in part, via the modulation of MG-associated ROS homeostasis through a salicylic acid-mediated defense pathway.

Genome-wide analysis of BpDof genes and the tolerance to drought stress in birch (Betula platyphylla)

Background

DNA binding with one finger (Dof) proteins are plant-specific transcription factors playing vital roles in developmental processes and stress responses in plants. Nevertheless, the characterizations, expression patterns, and functions of the Dof family under drought stress (a key determinant of plant physiology and metabolic homeostasis) in woody plants remain unclear.

Methods

The birch (Betula platyphylla var. mandshuric) genome and plant TFDB database were used to identify Dof gene family members in birch plants. ClustalW2 of BioEdit v7.2.1, MEGA v7.0, ExPASy ProtParam tool, Subloc, TMHMM v2.0, GSDS v2.0, MEME, TBtools, KaKs Calculator v2.0, and PlantCARE were respectively used to align the BpDof sequences, build a phylogenetic tree, identify the physicochemical properties, analyze the chromosomal distribution and synteny, and identify the cis-elements in the promoter regions of the 26 BpDof genes. Additionally, the birch seedlings were exposed to PEG6000-simulated drought stress, and the expression patterns of the BpDof genes in different tissues were analyzed by qRT-PCR. The histochemical staining and the evaluation of physiological indexes were performed to assess the plant tolerance to drought with transient overexpression of BpDof4, BpDof11, and BpDof17 genes. SPSS software and ANOVA were used to conduct all statistical analyses and determine statistically significant differences between results.

Results

A total of 26 BpDof genes were identified in birch via whole-genome analysis. The conserved Dof domain with a C(x)2C(x)21C(x)2C zinc finger motif was present in all BpDof proteins. These birch BpDofs were classified into four groups (A to D) according to the phylogenetic analysis of Arabidopsis thaliana Dof genes. BpDof proteins within the same group mostly possessed similar motifs, as detected by conserved motif analysis. The exon–intron analysis revealed that the structures of BpDof genes differed, indicating probable gene gain and lose during the BpDof evolution. The chromosomal distribution and synteny analysis showed that the 26 BpDofs were unevenly distributed on 14 chromosomes, and seven duplication events among six chromosomes were found. Cis-acting elements were abundant in the promoter regions of the 26 BpDof genes. qRT-PCR revealed that the expression of the 26 BpDof genes was differentially regulated by drought stress among roots, stems, and leaves. Most BpDof genes responded to drought stress, and BpDof4, BpDof11, and BpDof17­ were significantly up-regulated. Therefore, plants overexpressing these three genes were generated to investigate drought stress tolerance. The BpDof4-, BpDof11-, and BpDof17­-overexpressing plants showed promoted reactive oxygen species (ROS) scavenging capabilities and less severe cell damage, suggesting that they conferred enhanced drought tolerance in birch. This study provided an in-depth insight into the structure, evolution, expression, and function of the Dof gene family in plants.

CsMYB96 enhances citrus fruit resistance against fungal pathogen by activating salicylic acid biosynthesis and facilitating defense metabolite accumulation

Citrus fruit are generally confronted with various fungal diseases that cause fruit deterioration and economic loss. Salicylic acid (SA), a plant hormone, is an important signal molecule required for stimulating the disease resistance of plants. However, there has been limited information about the molecular mechanism of SA biosynthesis involving biotic stress response in citrus fruit. In the present study, an R2R3 MYB transcription factor (CsMYB96) was identified to mediate SA signaling in response to fungal diseases. The transient overexpression assay revealed that CsMYB96 contributed to the strong tolerance of citrus fruit to Penicillium italicum along with an increase in SA content; meanwhile, CsMYB96 conferred resistance to Botrytis cinerea in Arabidopsis plants. Further metabolomic profiling of stable transgenic Arabidopsis revealed that CsMYB96 participated in the regulation of various metabolism pathways and enhanced the accumulation of phenolic acids. RNA-seq analysis confirmed that overexpression of CsMYB96 activated the expression of genes involved in plant-pathogen interaction, phenylpropanoid biosynthesis, and SA signaling. Besides, CsMBY96 directly activated the transcription of calmodulin binding protein 60g (CsCBP60g), a predominant transcription factor required for the activation of SA signaling. In summary, our results reveal that CsMYB96 promotes SA biosynthesis and the accumulation of defense metabolites to enhance the fungal pathogen resistance of citrus fruit and Arabidopsis and provide new insights into the regulation of disease response.

MicroRNAs and Transcripts Associated with an Early Ripening Mutant of Pomelo (Citrus grandis Osbeck)

'Liuyuezaoyou' is an early-ripening cultivar selected from a bud mutation of Citrus grandis Osbeck 'Guanximiyou'. They were designated here as MT and WT, respectively. The fruit of MT matures about 45 days earlier than WT, which was accompanied by significant changes in key phytohormones, sugar compounds and organic acids. Recent studies have showed that microRNAs (miRNAs) play an important role in regulation of fruit ripening process. The aim of this study was to compare MT fruits with WT ones to uncover if miRNAs were implicated in the ripening of C. grandis. Fruits of both WT and MT at four developmental stages were analyzed using high-throughput sequencing and RT-PCR. Several independent miRNA libraries were constructed and sequenced. A total of 747 known miRNAs were identified and 99 novel miRNAs were predicted across all libraries. The novel miRNAs were found to have hairpin structures and possess star sequences. These results showed that transcriptome and miRNAs are substantially involved in a complex and comprehensive network in regulation of fruit ripening of this species. Further analysis of the network model revealed intricate interactions of miRNAs with mRNAs during the fleshy fruit ripening process. Several identified miRNAs have potential targets. These include auxin-responsive protein IAA9, sucrose synthase 3, V-type proton ATPase, NCED1 (ABA biosynthesis) and PL1/5 (pectate lyase genes), as well as NAC100 putative coordinated regulation networks, whose interactions with respective miRNAs may contribute significantly to fruit ripening of C. grandis.

Genome-wide characterization and expression profiling of B3 superfamily during ethylene-induced flowering in pineapple (Ananas comosus L.)

BACKGROUND

The B3 superfamily (B3s) represents a class of large plant-specific transcription factors, which play diverse roles in plant growth and development process including flowering induction. However, identification and functional surveys of B3 superfamily have not been reported in ethylene-induced pineapple flowering (Ananas comosus).

RESULTS

57 B3 genes containing B3 domain were identified and phylogenetically classified into five subfamilies. Chromosomal localization analysis revealed that 54 of 57 AcB3s were located on 21 Linkage Groups (LG). Collinearity analysis demonstrated that the segmental duplication was the main event in the evolution of B3 gene superfamily, and most of them were under purifying selection. The analysis of cis-element composition suggested that most of these genes may have function in response to abscisic acid, ethylene, MeJA, light, and abiotic stress. qRT-PCR analysis of 40 AcB3s containing ethylene responsive elements exhibited that the expression levels of 35 genes were up-regulated within 1 d after ethephon treatment and some were highly expressed in flower bud differentiation period in stem apex, such as Aco012003, Aco019552 and Aco014401.

CONCLUSION

This study provides a basic information of AcB3s and clues for involvement of some AcB3s in ethylene-induced flowering in pineapple.

Genome-Wide Analysis of MADS-Box Genes in Foxtail Millet (Setaria italica L.) and Functional Assessment of the Role of SiMADS51 in the Drought Stress Response

MADS-box transcription factors play vital roles in multiple biological processes in plants. At present, a comprehensive investigation into the genome-wide identification and classification of MADS-box genes in foxtail millet (Setaria italica L.) has not been reported. In this study, we identified 72 MADS-box genes in the foxtail millet genome and give an overview of the phylogeny, chromosomal location, gene structures, and potential functions of the proteins encoded by these genes. We also found that the expression of 10 MIKC-type MADS-box genes was induced by abiotic stresses (PEG-6000 and NaCl) and exogenous hormones (ABA and GA), which suggests that these genes may play important regulatory roles in response to different stresses. Further studies showed that transgenic Arabidopsis and rice (Oryza sativa L.) plants overexpressing SiMADS51 had reduced drought stress tolerance as revealed by lower survival rates and poorer growth performance under drought stress conditions, which demonstrated that SiMADS51 is a negative regulator of drought stress tolerance in plants. Moreover, expression of some stress-related genes were down-regulated in the SiMADS51-overexpressing plants. The results of our study provide an overall picture of the MADS-box gene family in foxtail millet and establish a foundation for further research on the mechanisms of action of MADS-box proteins with respect to abiotic stresses.

Genome-Wide Identification and Expression Analysis of MYB Transcription Factors and Their Responses to Abiotic Stresses in Woodland Strawberry (Fragaria vesca)

Woodland strawberry (Fragaria vesca) is a diploid strawberry that is widely used as a model of cultivated octoploid strawberry (Fragaria × ananassa). It has also been used as a model for Rosaceae fruits, non-climacteric fruits, and stolons. The MYB superfamily is the largest transcription factor family in plants, and its members play important roles in plant growth and development. However, the complete MYB superfamily in woodland strawberry has not been studied. In this study, a total of 217 MYB genes were identified in woodland strawberry and classified into four groups: one 4R-MYB protein, five 3R-MYB proteins, 113 2R-MYB proteins, and 98 1R-MYB proteins. The phylogenetic relationship of each MYB subgroup was consistent in terms of intron/exon structure and conserved motif composition. The MYB genes in woodland strawberry underwent loss and expansion events during evolution. The transcriptome data revealed that most FveMYB genes are expressed in several organs, whereas 15 FveMYB genes exhibit organ-specific expression, including five genes (FveMYB101, -112, -44, and -8; FveMYB1R81) in roots, two genes (FveMYB62 and -77) in stolon tips, three genes (FveMYB99 and -35; FveMYB1R96) in open flowers, and five genes (FveMYB76 and -100; FveMYB1R4, -5, and -86) in immature fruits. During fruit ripening of woodland strawberry, the expression levels of 84 FveMYB genes were decreased, of which five genes (FveMYB4, -22, -50, and -66; FveMYB1R57) decreased more than 10-fold, whereas those 18 FveMYB genes were increased, especially FveMYB10 and FveMYB74 increased more than 30-fold. In addition, the expression levels of 36, 68, 52, and 62 FveMYB genes were altered by gibberellic acid, abscisic acid, cold, and heat treatments, respectively, and among them, several genes exhibited similar expression patterns for multiple treatments, suggesting possible roles in the crosstalk of multiple signaling pathways. This study provides candidate genes for the study of stolon formation, fruit development and ripening, and abiotic stress responses.

The transcription factors of tall fescue in response to temperature stress

Tall fescue (Festuca arundinacea) is an important grass species worldwide, but temperature stress severely affects its distribution and yield. Transcription factors (TFs), as the master switches in sophisticated regulatory networks, play essential roles in plant growth development and abiotic stress responses. In this study, the comparative transcriptome analysis was performed to explore the commonalities and differences in the response of TFs to the heat (40 °C), cold (10 °C) and control (22 °C) conditions. A total of 877 TF genes belonging to 35 families were identified. Most of them (784) were differentially expressed genes (DEG), indicating TF genes actively responded to temperature stress. The expression of bZIP and GTF family members was up-regulated when exposed to both heat and cold, but conversely, the expression of the most WRKY and NAC families members decreased. The HSF and GTE families and DREB2B were up-regulated upon heat, while bHLH, MYB, HD-ZIP and ERF families were elevated under cold stress. The TFs involved in 'Plant hormone signal transduction', 'Plant-pathogen interaction', 'Circadian rhythm' play major roles in responding to temperature stresses. The results showed the temperature threats up-regulated the expression of stress tolerance-related genes, and down-regulated those genes associated with growth and disease resistance, indicating TFs exert crucial roles in plant adaptation to an adverse environment. This study profiled the responsive pattern of TFs to temperature stresses, partially explained the mechanism of adaptations of cold-season forage crops and screened many candidate stress-tolerant TF genes.

Genome-wide identification of the GATA transcription factor family and their expression patterns under temperature and salt stress in Aspergillus oryzae

GATA transcription factors (TFs) are involved in the regulation of growth processes and various environmental stresses. Although GATA TFs involved in abiotic stress in plants and some fungi have been analyzed, information regarding GATA TFs in Aspergillusoryzae is extremely poor. In this study, we identified and functionally characterized seven GATA proteins from A.oryzae 3.042 genome, including a novel AoSnf5 GATA TF with 20-residue between the Cys-X₂-Cys motifs which was found in Aspergillus GATA TFs for the first time. Phylogenetic analysis indicated that these seven A. oryzae GATA TFs could be classified into six subgroups. Analysis of conserved motifs demonstrated that Aspergillus GATA TFs with similar motif compositions clustered in one subgroup, suggesting that they might possess similar genetic functions, further confirming the accuracy of the phylogenetic relationship. Furthermore, the expression patterns of seven A.oryzae GATA TFs under temperature and salt stresses indicated that A. oryzae GATA TFs were mainly responsive to high temperature and high salt stress. The protein–protein interaction network of A.oryzae GATA TFs revealed certain potentially interacting proteins. The comprehensive analysis of A. oryzae GATA TFs will be beneficial for understanding their biological function and evolutionary features and provide an important starting point to further understand the role of GATA TFs in the regulation of distinct environmental conditions in A.oryzae.