DOF AFFECTING GERMINATION 2 is a positive regulator of light-mediated seed germination and is repressed by DOF AFFECTING GERMINATION 1

The N6-methyladenosine reader ECT1 regulates seed germination via gibberellic acid- and phytochrome B-mediated signaling

Seed germination, a pivotal stage in plant growth, is governed by phytohormones such as gibberellic acid (GA) and influenced by phytochromes, which are key photoreceptors in plants. The N6-methyladenosine (m6A) RNA modification is fundamental to plant growth and development. However, the molecular mechanisms underlying the regulation of PHYTOCHROME B (phyB) and the function of m6A signaling in GA-mediated seed germination remain elusive. Here, we discovered EVOLUTIONARILY CONSERVED C-TERMINAL REGION 1 (ECT1) as an m6A reader protein that directly binds to m6A and forms homodimers to enhance its stability in Arabidopsis (Arabidopsis thaliana). We observed that the ect1-1 mutant exhibits attenuated GA3 responsiveness in seed germination. Restoration of ECT1 function in ect1-1 confirmed the role of ECT1 in promoting seed germination. Our findings indicate that ECT1 promotes seed germination by destabilizing m6A-modified REPRESSOR OF GA1-3 1 (RGA1), a key inhibitor of GA-mediated seed germination. Moreover, ECT1 establishes a regulatory circuit with DOF AFFECTING GERMINATION 2 (DAG2), another regulator of GA-mediated seed germination. DAG2 directly binds to the ECT1 promoter and controls its transcription, and ECT1 modulates DAG2 mRNA stability through m6A binding. Furthermore, we identified PHYB as a common downstream target of DAG2 and ECT1. ECT1 binds directly to m6A-modified PHYB and influences its stability, and DAG2 binds to the PHYB promoter to regulate its transcription. Our findings demonstrate that ECT1 fine-tunes m6A-regulated seed germination via complex and multifaceted molecular mechanisms, particularly through interactions with GA and phyB, broadening our understanding of m6A-regulated processes in Arabidopsis.

Identification of the Dof Gene Family in Quinoa and Its Potential Role in Regulating Flavonoid Synthesis Under Different Stress Conditions

Quinoa (Chenopodium quinoa Willd.), often referred to as the "golden grain", is a highly nutritious crop that has garnered significant global attention due to its exceptional nutritional profile and health benefits. Flavonoids present in quinoa have been shown to possess antioxidant, anti-inflammatory, antiviral, anticancer, and antidepressant properties. The DNA binding with one finger (Dof) transcription factor is crucial for regulating growth, development, and stress responses. However, the identification of the Dof family using the latest quinoa genomic data and its function in abiotic stress response have not been fully elucidated. Here, 36 CqDof genes were identified from the quinoa genome and classified into ten subfamilies through phylogenetic analysis. Physicochemical property analysis predicted that CqDofs predominantly encode basic, hydrophilic, and unstable nuclear proteins. CqDofs were distributed across 15 chromosomes, with segmental duplication being the primary driver of their expansion. Subsequently, basic information on CqDofs was systematically analyzed, including conserved motifs, gene structure, cis-acting elements, and expression patterns. Notably, the promoter regions of all CqDof genes were enriched with cis-acting elements related to light responsiveness. Further analysis revealed that red and blue light significantly affected CqDof expression and flavonoid accumulation (epigallocatechin, rutin, naringenin, morin, pinocembrin, quercetin-7-O-rutinoside, quercetin-3-O-glucoside, and naringenin), in which 5 CqDofs exhibited a pronounced response to both light conditions and showed a significant correlation with flavonoid levels. Finally, RT-PCR analysis indicated that the expression levels of CqDofs (except CqDof21) were significantly upregulated under drought, salt, and saline-alkali stresses. These findings lay the groundwork for future studies on how CqDofs regulate flavonoid biosynthesis under different light qualities and function in abiotic stress.

The transcription factors DOF4.6 and XND1 jointly regulate root hydraulics and drought responses in Arabidopsis

Water uptake by roots is essential for plant growth and stress acclimation. We previously showed that the XYLEM NAC DOMAIN 1 (XND1) transcription factor negatively regulates root hydraulic conductivity (Lpr) in Arabidopsis (Arabidopsis thaliana). Here, we show that XND1 physically interacts with the transcription factor DNA-binding with One Finger 4.6 (DOF4.6). Analyses of loss-of-function mutants and overexpression lines revealed that, similar to XND1, DOF4.6 negatively regulates Lpr. DOF4.6 and XND1 jointly modulate downstream gene expression, inhibiting root xylem formation. Notably, DOF4.6 facilitates XND1 binding to the promoter of XYLEM CYSTEINE PROTEASE 1, the product of which controls programmed cell death during xylem development. DOF4.6 also independently binds to the promoters of the aquaporins PIP2;5 and PIP2;6, thereby suppressing their expression and exerting potential direct regulatory effects on membrane water transport. Importantly, the dof4.6 loss-of-function alleles showed significantly enhanced resistance to drought stress. Collectively, our findings demonstrate that DOF4.6 plays a crucial role in root hydraulics and drought stress responses, partially in concert with XND1 and through combined effects on xylem formation and aquaporin functions.

Genome-Wide Identification and Functional Characterization of the Dof Family in Dendrobium officinale

The Dof gene family represents a class of plant-specific transcription factors that play crucial regulatory roles in various biological processes, including plant growth, development, and responses to abiotic stress. However, genome-wide identification and functional characterization of the Dof gene family remain unexplored in Dendrobium officinale. In this study, we performed a genome-wide identification and functional analysis of the DoDof gene family. A total of 28 Dof family members were identified and named DoDof1-28 based on genome annotation data. Phylogenetic analysis classified these genes into four major groups (A-D) and further subdivided them into nine subfamilies. Gene structure analysis revealed that most DoDofs lack introns, with no distinct specificity observed among different subfamilies and considerable diversity within the same subfamily. Sequence alignment analysis demonstrated that all DoDof proteins contain a conserved Dof domain consisting of 52 amino acids, which includes a C2-C2 zinc finger motif and a DNA-binding domain. MEME analysis revealed that the conserved motif composition exhibits a certain degree of conservation among DoDof proteins, but significant differences exist across subfamilies. Expression pattern analysis demonstrated that DoDofs have exhibited diverse expression profiles across different developmental stages, tissues, and under abiotic stresses (such as low temperature, salinity, and drought) in D. officinale, suggesting their potential roles in plant development and stress responses. Subcellular localization analysis indicated that DoDof15, DoDof22, and DoDof24 are localized exclusively in the nucleus. Yeast one-hybrid assays revealed that DoDof22 binds to the promoter of the ABA receptor DoPYL9, while DoDof15 and DoDof24 bind to the promoter of the bHLH transcription factor DobHLH68. These results suggest that DoDof proteins may regulate the growth, development, and stress response processes of D. officinale by binding to the promoters of target genes. This study provides critical insights into the functional roles of Dof transcription factors in Orchidaceae family and establishes a theoretical foundation for molecular breeding and stress resistance improvement in D. officinale.

Establishment of single-cell transcriptional states during seed germination

Germination involves highly dynamic transcriptional programs as the cells of seeds reactivate and express the functions necessary for establishment in the environment. Individual cell types have distinct roles within the embryo, so must therefore have cell type-specific gene expression and gene regulatory networks. We can better understand how the functions of different cell types are established and contribute to the embryo by determining how cell type-specific transcription begins and changes through germination. Here we describe a temporal analysis of the germinating Arabidopsis thaliana embryo at single-cell resolution. We define the highly dynamic cell type-specific patterns of gene expression and how these relate to changing cellular function as germination progresses. Underlying these are unique gene regulatory networks and transcription factor activity. We unexpectedly discover that most embryo cells transition through the same initial transcriptional state early in germination, even though cell identity has already been established during embryogenesis. Cells later transition to cell type-specific gene expression patterns. Furthermore, our analyses support previous findings that the earliest events leading to the induction of seed germination take place in the vasculature. Overall, our study constitutes a general framework with which to characterize Arabidopsis cell transcriptional states through seed germination, allowing investigation of different genotypes and other plant species whose seed strategies may differ.

Genome-Wide Identification of the DOF Gene Family in Kiwifruit (Actinidia chinensis) and Functional Validation of AcDOF22 in Response to Drought Stress

DNA-binding one zinc finger (DOF) transcription factors are crucial plant-specific regulators involved in growth, development, signal transduction, and abiotic stress response generation. However, the genome-wide identification and characterization of AcDOF genes and their regulatory elements in kiwifruit (Actinidia chinensis) has not been thoroughly investigated. In this study, we screened the kiwifruit genome database and identified 42 AcDOF genes (AcDOF1 to AcDOF42). Phylogenetic analysis facilitated the categorization of these genes into five subfamilies (DOF-a, DOF-b, DOF-c, DOF-d, and DOF-e). We further analyzed the motifs, conserved domains, gene structures, and collinearity of the AcDOFgene family. Gene ontology (GO) enrichment analysis indicated significant enrichment in the "flower development" term and the "response to abiotic stress" category. Promoter prediction analysis revealed numerous cis-regulatory elements related to responses to light, hormones, and low-temperature and drought stress in AcDOF promoters. RNA-seq expression profiles demonstrated the tissue-specific expression of AcDOF genes. Quantitative real-time PCR results showed that six selected genes (AcDOF04, AcDOF09, AcDOF11, AcDOF13, AcDOF21, and AcDOF22) were differentially induced by abscisic acid (ABA), methyl jasmonate (MeJA), and cold, salt, and drought stresses, with AcDOF22 specifically expressed at high levels in drought-tolerant cultivars. Further experiments indicated that transient AcDOF22 overexpression in kiwifruit leaf disks reduced water loss and chlorophyll degradation. Additionally, AcDOF22 was localized to the nucleus and exhibited transcriptional activation, enhancing drought resistance by activating the downstream drought marker gene AcDREB2A. These findings lay the foundation for elucidating the molecular mechanisms of drought resistance in kiwifruit and offer new insights into drought-resistant breeding.

The Role of Liriodendron Dof Gene Family in Abiotic Stress Response

The DOF (DNA-binding with one finger) transcription factors are exclusive to plants and play crucial roles in plant growth, development, and environmental adaptation. Although extensive research has been conducted on the Dof gene family in Arabidopsis, maize, and Solanum, investigations concerning the role of this gene family in Liriodendron remain unreported, leaving its biological function largely unknown. In this study, we performed a comprehensive genome-wide identification of the Dof gene family based on the Liriodendron genome, resulting in the discovery of a total of 17 LcDof gene members. Based on the results of phylogenetic analysis, the 17 LcDof proteins were classified into eight subfamilies. The motif analysis revealed the diverse nature of motifs within the D1 subfamily, which includes a distinct type of Dof transcription factor known as CDF (Cycling Dof Factor). We further characterized the chromosomal distribution, gene structure, conserved protein motifs, and cis-elements in the promoter regions. Additionally, utilizing transcriptome data from Liriodendron hybrids and conducting RT-qPCR experiments, we investigated the expression patterns of LhDofs under various abiotic stresses such as drought, cold, and heat stress. Notably, we found that several LhDofs, particularly LhDof4 and LhDof6, were significantly upregulated in response to abiotic stress. Furthermore, we cloned LhDof4 and LhDof6 genes and found that its encoding protein was mainly located in the nucleus by transient transformation in Liriodendron hybrids protoplast. Subsequently, we used LhDof6-overexpressing Liriodendron hybrid seedlings. We found that overexpression of LhDof6 enhanced the cold tolerance of the plants, increasing their survival rate at -20 °C. This result was further validated by changes in physiological indicators.

DOF gene family expansion and diversification

DOF (DNA binding with one finger) proteins are part of a plant-specific transcription factor (TF) gene family widely involved in plant development and stress responses. Many studies have uncovered their structural and functional characteristics in recent years, leading to a rising number of genome-wide identification study approaches, unveiling the DOF family expansion in angiosperm species. Nonetheless, these studies primarily concentrate on particular taxonomic groups. Identifying DOF TFs within less-represented groups is equally crucial, as it enhances our comprehension of their evolutionary history, contributions to plant phenotypic diversity, and role in adaptation. This review summarizes the main findings and progress of genome-wide identification and characterization studies of DOF TFs in Viridiplantae, exposing their roles as players in plant adaptation and a glimpse of their evolutionary history. We also present updated data on the identification and number of DOF genes in native and wild species. Altogether, these data, comprising a phylogenetic analysis of 2124 DOF homologs spanning 83 different species, will contribute to identifying new functional DOF groups, adding to our understanding of the mechanisms driving plant evolution and offering valuable insights into their potential applications.

Genome-Wide Identification and Expression Analysis of the Dof Transcription Factor in Annual Alfalfa Medicago polymorpha

The Dof transcription factor is a plant-specific transcription gene family that plays various biological functions in plant development and stress response. However, no relevant research has been conducted on Medicago polymorpha. Here, 36 MpDof genes were identified in the M. polymorpha genome and further divided into 10 groups based on the comparative phylogenetic analysis. The essential information of MpDof genes, such as chromosomal localization, gene structure, conserved motifs, and selective pressures were systematically analyzed. All 36 MpDof genes were predicted to contain more cis-acting elements related to hormone response. MpDof24 and MpDof25 were predicted to interact with MpDof11 and MpDof26 to involve in the photoperiod blooms process. The MpDof genes showed a diverse expression pattern in different tissues. Notably, MpDof29 and MpDof31 were specifically expressed in the large pod and root, respectively, suggesting their crucial role in the pod and root development. qRT-PCR analysis indicated that the expression levels of MpDof10, MpDof25, MpDof26, and MpDof29 were obviously up-regulated under drought, salt, and cold stress. Collectively, genome-wide identification, evolutionary, and expression analysis of the Dof transcription gene family in M. polymorpha will provide new information to further understand and utilize the function of these Dof genes in Medicago plants.

DOF transcription factors: Specific regulators of plant biological processes

Plant biological processes, such as growth and metabolism, hormone signal transduction, and stress responses, are affected by gene transcriptional regulation. As gene expression regulators, transcription factors activate or inhibit target gene transcription by directly binding to downstream promoter elements. DOF (DNA binding with One Finger) is a classic transcription factor family exclusive to plants that is characterized by its single zinc finger structure. With breakthroughs in taxonomic studies of different species in recent years, many DOF members have been reported to play vital roles throughout the plant life cycle. They are not only involved in regulating hormone signals and various biotic or abiotic stress responses but are also reported to regulate many plant biological processes, such as dormancy, tissue differentiation, carbon and nitrogen assimilation, and carbohydrate metabolism. Nevertheless, some outstanding issues remain. This article mainly reviews the origin and evolution, protein structure, and functions of DOF members reported in studies published in many fields to clarify the direction for future research on DOF transcription factors.

Genome-Wide Identification and Analysis of DOF Gene Family in Eugenia uniflora L. (Myrtaceae)

Eugenia uniflora is a Brazilian native plant species with great ecological and economic importance. It is distributed throughout the Atlantic forest, where two distinct populations show local adaptation to the contrasting conditions of restinga and riparian forest. Among various TFs described in plants, the DOF TF family has been reported to affect flowering and vascular development, making them promising candidates for characterization in E. uniflora. In this study, 28 DOF genes were identified by a genome-wide analysis, of which 20 were grouped into 11 MCOGs by Bayesian phylogeny, suggesting a shared functionallity between members. Based on RNA-seq experiments, we have detected eight drought responsive genes, and SNPs identification revealed population unique polymorphisms, implying a role in local adapatation mechanisms. Finally, analysis of conserved motifs through MEME revealed 15 different protein motifs, and a promoter region analysis returned 40 enriched TF binding motifs, both reporting novel biological functions circa the DOF gene family. In general, the DOF family is found to be conserved both in sequence and expression. Furthermore, this study contributes to both DOF literature and the genetic exploration of native species, elucidating their genetic potential and bringing to light new research topics, paving the way to future studies.

Network of the transcriptome and metabolomics reveals a novel regulation of drought resistance during germination in wheat

BACKGROUND AND AIMS

The North China Plain, the highest winter-wheat-producing region of China, is seriously threatened by drought. Traditional irrigation wastes a significant amount of water during the sowing season. Therefore, it is necessary to study the drought resistance of wheat during germination to maintain agricultural ecological security. From several main cultivars in the North China Plain, we screened the drought-resistant cultivar JM47 and drought-sensitive cultivar AK58 during germination using the polyethylene glycol (PEG) drought simulation method. An integrated analysis of the transcriptome and metabolomics was performed to understand the regulatory networks related to drought resistance in wheat germination and verify key regulatory genes.

METHODS

Transcriptional and metabolic changes were investigated using statistical analyses and gene-metabolite correlation networks. Transcript and metabolite profiles were obtained through high-throughput RNA-sequencing data analysis and ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry, respectively.

KEY RESULTS

A total of 8083 and 2911 differentially expressed genes (DEGs) and 173 and 148 differential metabolites were identified in AK58 and JM47, respectively, under drought stress. According to the integrated analysis results, mammalian target of rapamycin (mTOR) signalling was prominently enriched in JM47. A decrease in α-linolenic acid content was consistent with the performance of DEGs involved in jasmonic acid biosynthesis in the two cultivars under drought stress. Abscisic acid (ABA) content decreased more in JM47 than in AK58, and linoleic acid content decreased in AK58 but increased in JM47. α-Tocotrienol was upregulated and strongly correlated with α-linolenic acid metabolism.

CONCLUSIONS

The DEGs that participated in the mTOR and α-linolenic acid metabolism pathways were considered candidate DEGs related to drought resistance and the key metabolites α-tocotrienol, linoleic acid and l-leucine, which could trigger a comprehensive and systemic effect on drought resistance during germination by activating mTOR-ABA signalling and the interaction of various hormones.

Transcription factor TERF1 promotes seed germination under osmotic conditions by activating gibberellin acid signaling

Seed germination is the first step of seedling establishment, which is particularly sensitive to drought stress. Elucidating the mechanism regulating seed germination under drought stress is of great importance. We showed that overexpressing Tomato Ethylene Responsive Factor 1 (TERF1), an ERF transcription factor in the ethylene signaling pathway, significantly reduced seed sensitivity to mannitol treatment during seed germination. Germination assay demonstrated that TERF1 could activate gibberellin acid (GA) signaling pathway independent on GA metabolism during germination. By comparative transcriptome analysis (mannitol vs normal germination condition, mannitol vs mannitol plus paclobutrazol (PAC, an inhibitor of GA biosynthesis)) we identified the genes regulated by TERF1 specifically under mannitol treatment and confirmed that TERF1 could activate GA signaling pathway independent on GA metabolism, which were consistent with the germination assay with mannitol and mannitol plus PAC treatment. Based on sugar, gene expression and germination analysis we proved that TERF1 promoted seed germination through glucose signaling pathway mediated by GA. Thus our study provides an underlying mechanism for activating GA signaling pathway by TERF1 during seed germination under osmotic conditions.

Effects of the Rhizosphere Fungus Cunninghamella bertholletiae on the Solanum lycopersicum Response to Diverse Abiotic Stresses

This study examined the efficiency of fungal strain (Cunninghamella bertholletiae) isolated from the rhizosphere of Solanum lycopersicum to reduce symptoms of salinity, drought and heavy metal stresses in tomato plants. In vitro evaluation of C. bertholletiae demonstrated its ability to produce indole-3-Acetic Acid (IAA), ammonia and tolerate varied abiotic stresses on solid media. Tomato plants at 33 days’ old, inoculated with or without C. bertholletiae, were treated with 1.5% sodium chloride, 25% polyethylene glycol, 3 mM cadmium and 3 mM lead for 10 days, and the impact of C. bertholletiae on plant performance was investigated. Inoculation with C. bertholletiae enhanced plant biomass and growth attributes in stressed plants. In addition, C. bertholletiae modulated the physiochemical apparatus of stressed plants by raising chlorophyll, carotenoid, glucose, fructose, and sucrose contents, and reducing hydrogen peroxide, protein, lipid metabolism, amino acid, antioxidant activities, and abscisic acid. Gene expression analysis showed enhanced expression of SlCDF3 and SlICS genes and reduced expression of SlACCase, SlAOS, SlGRAS6, SlRBOHD, SlRING1, SlTAF1, and SlZH13 genes following C. bertholletiae application. In conclusion, our study supports the potential of C. bertholletiae as a biofertilizer to reduce plant damage, improve crop endurance and remediation under stress conditions.

Cloning and activity analysis of the highly expressed gene VviABCG20 promoter in seed and its activity is negatively regulated by the transcription factor VviDof14

Half-size ATP binding cassette G (ABCG) transporters participate in the growth and development of plants by transporting substrates. The VviABCG20 gene is highly expressed in seed and plays an important role in seed development/abortion. However, little is known about the function of the VviABCG20 promoter (pVviABCG20) and its regulatory factors. In our study, we obtained pVviABCG20s from 15 seeded and seedless grape varieties and there were two types of 'a' and 'b' with 41 bp non-deletion or deletion, respectively. The pVviABCG20 activity was higher in seeds, siliques, flowers and roots of pVviABCG20-GUS Arabidopsis. The GUS activity analysis revealed that the activities of P4 (-586 bp) to P7 (-155 bp) were becoming increasingly weaker, and the P7 activity almost disappears compared with the pVviABCG20 (P0, -1604). Yeast one-hybrid and GUS activity analysis indicated that VviDof14 binds to the AAAG element in the P7' (-586 bp) fragment of the pVviABCG20 and regulated the activity negatively. The quantitative real-time PCR analysis suggested that the expression of VviDof14 in Thompson seedless seeds was higher than that in Pinot noir. Our study laid the foundation for further analysis of the functions of the pVviABCG20 and its regulator VviDof14 in grape seed development/abortion.

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.

Expression profiling of the Dof gene family under abiotic stresses in spinach

DNA-binding with one finger (Dof) are plant-specific transcription factors involved in numerous pathways of plant development, such as abiotic stresses responses. Although genome-wide analysis of Dof genes has been performed in many species, but these genes in spinach have not been analyzed yet. We performed a genome-wide analysis and characterization of Dof gene family in spinach (Spinacia oleracea L.). Twenty-two Dof genes were identified and classified into four groups with nine subgroups, which was further corroborated by gene structure and motif analyses. Ka/Ks analysis revealed that SoDofs were subjected to purifying selection. Using cis-acting elements analysis, SoDofs were involved in plant growth and development, plant hormones, and stress responses. Expression profiling demonstrated that SoDofs expressed in leaf and inflorescence, and responded to cold, heat, and drought stresses. SoDof22 expressed the highest level in male flowers and under cold stress. These results provided a genome-wide analysis of SoDof genes, their gender- and tissue-specific expression, and response to abiotic stresses. The knowledge and resources gained from these analyses will benefit spinach improvement.

Long Non-Coding RNA and Its Regulatory Network Response to Cold Stress in Eucalyptus urophylla S.T.Blake

Long non-coding RNA (lncRNA) plays an important regulatory role in plant growth and development, but its systematic identification and analysis in Eucalyptus has not yet been reported. Cold stress has a huge impact on the survival and yield of Eucalyptus seedlings, but the regulatory mechanism of lncRNA in Eucalyptus in response to cold stress is still unclear. In this study, the transcriptomes of young leaves of Eucalyptus urophylla S.T.Blake under low-temperature treatment and restoration were analyzed by RNA-seq. A total of 11,394 lncRNAs and 46,276 mRNAs were identified, of which 300 were differentially expressed lncRNAs (DE_lncRNAs) and 5606 were differentially expressed target genes of lncRNAs under cold stress, with the total number of target genes of DE_lncRNAs being 1681. A total of 677 differentially expressed transcription factors (TFs) were also identified, mainly including ERF, MYB and the NAC transcription factor family. Gene ontology (GO) analysis of the differentially expressed genes (DEGs) and target genes of DE_lncRNAs was mostly related to the response to cold stress and external stimuli. Furthermore, lncRNA–miRNA–mRNA regulatory networks were constructed, and 22 DE_lncRNAs were predicted to be targets or targeting mimics of 20 miRNAs. A qRT-PCR was used to verify the relative expression of genes in the regulatory EuGBF3-EUC_00002677-MSTRG.7690 network, and it matched the transcriptome data, indicating that it may play an important role in the response to cold stress in E. urophylla. This study provides a new insight into lncRNA and its regulatory network under abiotic stress, especially cold stress in E. urophylla.

Genome-Wide In Silico Identification and Comparative Analysis of Dof Gene Family in Brassica napus

DNA binding with one finger (DOF) proteins are plant-specific transcription factors that play roles in diverse plant functions. However, little is known about the DOF protein repertoire of the allopolyploid crop, Brassica napus. This in silico study identified 117 Brassica napus Dof genes (BnaDofs) and classified them into nine groups (A, B1, B2, C1, C2.1, C2.2, C3, D1, and D2), based on phylogenetic analysis. Most members belonging to a particular group displayed conserved gene structural organisation and protein motif distribution. Evolutionary analysis exemplified that the divergence of the Brassica genus from Arabidopsis, the whole-genome triplication event, and the hybridisation of Brassica oleracea and Brassica rapa to form B. napus, followed by gene loss and rearrangements, led to the expansion and divergence of the Dof transcription factor (TF) gene family in B. napus. So far, this is the largest number of Dof genes reported in a single eudicot species. Functional annotation of BnaDof proteins, cis-element analysis of their promoters, and transcriptomic analysis suggested potential roles in organ development, the transition from the vegetative to the reproductive stage, light responsiveness, phytohormone responsiveness, as well as potential regulatory roles in abiotic stress. Overall, our results provide a comprehensive understanding of the molecular structure, evolution, and possible functional roles of Dof genes in plant development and abiotic stress response.

Unravelling the Complex Interplay of Transcription Factors Orchestrating Seed Oil Content in Brassica napus L

Transcription factors (TFs) and their complex interplay are essential for directing specific genetic programs, such as responses to environmental stresses, tissue development, or cell differentiation by regulating gene expression. Knowledge regarding TF-TF cooperations could be promising in gaining insight into the developmental switches between the cultivars of Brassica napus L., namely Zhongshuang11 (ZS11), a double-low accession with high-oil- content, and Zhongyou821 (ZY821), a double-high accession with low-oil-content. In this regard, we analysed a time series RNA-seq data set of seed tissue from both of the cultivars by mainly focusing on the monotonically expressed genes (MEGs). The consideration of the MEGs enables the capturing of multi-stage progression processes that are orchestrated by the cooperative TFs and, thus, facilitates the understanding of the molecular mechanisms determining seed oil content. Our findings show that TF families, such as NAC, MYB, DOF, GATA, and HD-ZIP are highly involved in the seed developmental process. Particularly, their preferential partner choices as well as changes in their gene expression profiles seem to be strongly associated with the differentiation of the oil content between the two cultivars. These findings are essential in enhancing our understanding of the genetic programs in both cultivars and developing novel hypotheses for further experimental studies.

DOF, MYB and TCP transcription factors: Their possible roles on barley germination and seedling establishment

Seed germination is a multi-staged complex process during seed plant life cycle, and it is tightly regulated through a coordinated expression of diverse genes in diverse tissues. As regulatory molecules of gene expression, determination of transcription factors is crucial to understanding molecular basis and regulatory network of germination process and seedling establishment. However, limited data on the contributions of these transcription factors to the germination of crop barley (Hordeum vulgare L.) are available. Here, we investigated the expression profiles of selected transcription factors from different families (DOF, MYB and TCP) with qRT-PCR analysis in various tissues including coleoptiles, leaves and roots following the germination. Analysis of MYB and DOF gene expression profiles indicated that there were differing expressions in different aged tissues, HvMYB5 and HvDOF2 being the most outstanding one in the oldest tissue, 15-day-old root. On the other hand, investigated TCP genes were lowly expressed compared to selected MYB and DOF genes, except HvTCP3, where the highest expression was observed in 15-day-old root tissue. The obtained expression profiles illustrate the importance of potential regulatory roles of transcription factors in early developmental stages of barley germination and seedling establishment.

Characterizing rhizome bud dormancy in Polygonatum kingianum: Development of novel chill models and determination of dormancy release mechanisms by weighted correlation network analysis

This study was conducted to explore specific chill models and the mechanisms underlying rhizome bud dormancy break in Polygonatum kingianum. Rhizome buds were subjected to various chilling temperatures for different duration and then transferred to warm conditions for germination and subsequent evaluation of their response to temperature and chilling requirements. A CUkingianum model was constructed to describe the contribution of low temperature to the chill unit, and it was suggested that 2.97°C was the optimum temperature and that 11.54°C was the upper limit for bud release. The CASkingianum model showed the relationship between chilling accumulation and sprouting percentage; therefore, rhizome bud development could be predicted through the model. Weighted correlation network analysis (WGCNA) of transcriptomic data of endo-, eco- and nondormant rhizome buds generated 33 gene modules, 6 of which were significantly related to bud sprouting percentage. In addition, 7 significantly matched transcription factors (TFs) were identified from the promoters of 17 "real" hub genes, and DAG2 was the best matched TF that bound to AAAG element to regulate gene expression. The current study is valuable for developing a highly efficient strategy for seedling cultivation and provides strong candidates for key genes related to rhizome bud dormancy in P. kingianum.

Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and stress responses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon-intron structure. Synteny analysis indicated the presence of a large number of syntenic relationship events between watermelon and cucumber. In promoter analysis, five kinds of stress-related and nine kinds of hormone-related cis-elements were identified in the promoter regions of ClDof genes. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of 12 selected ClDof genes under salt stress and ABA treatments using qRT-PCR. As a result, they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

The DOF Transcription Factors in Seed and Seedling Development

The DOF (DNA binding with one finger) family of plant-specific transcription factors (TF) was first identified in maize in 1995. Since then, DOF proteins have been shown to be present in the whole plant kingdom, including the unicellular alga Chlamydomonas reinhardtii. The DOF TF family is characterised by a highly conserved DNA binding domain (DOF domain), consisting of a CX₂C-X₂₁-CX₂C motif, which is able to form a zinc finger structure. Early in the study of DOF proteins, their relevance for seed biology became clear. Indeed, the PROLAMIN BINDING FACTOR (PBF), one of the first DOF proteins characterised, controls the endosperm-specific expression of the zein genes in maize. Subsequently, several DOF proteins from both monocots and dicots have been shown to be primarily involved in seed development, dormancy and germination, as well as in seedling development and other light-mediated processes. In the last two decades, the molecular network underlying these processes have been outlined, and the main molecular players and their interactions have been identified. In this review, we will focus on the DOF TFs involved in these molecular networks, and on their interaction with other proteins.

Love on wings, a Dof family protein regulates floral vasculature in Vigna radiata

BACKGROUND

The interaction among plants and their pollinators has been a major factor which enriched floral traits known as pollination syndromes and promoted the diversification of flowering plants. One of the bee-pollination syndromes in Faboideae with keel blossoms is the formation of a landing platform by wing and keel petals. However, the molecular mechanisms of elaborating a keel blossom remain unclear.

RESULTS

By performing large scale mutagenesis, we isolated and characterized a mutant in Vigna radiata, love on wings (low), which shows developmental defects in petal asymmetry and vasculature, leading to a failure in landing platform formation. We cloned the locus through map-based cloning together with RNA-sequencing (RNA-seq) analysis. We found that LOW encoded a nucleus-localized Dof-like protein and was expressed in the flower provascular and vascular tissues. A single copy of LOW was detected in legumes, in contrast with other taxa where there seems to be at least 2 copies. Thirty one Dof proteins have been identified from the V. radiata's genome, which can be further divided into four Major Cluster of Orthologous Groups (MCOGs). We also showed that ectopic expression of LOW in Arabidopsis driven by its native promoter caused changes in petal vasculature pattern.

CONCLUSIONS

To summarize, our study isolated a legume Dof-like factor LOW from V. radiata, which affects vasculature development in this species and this change can, in turn, impact petal development and overall morphology of keel blossom.

Aethionema arabicum: a novel model plant to study the light control of seed germination

The timing of seed germination is crucial for seed plants and is coordinated by internal and external cues, reflecting adaptations to different habitats. Physiological and molecular studies with lettuce and Arabidopsis thaliana have documented a strict requirement for light to initiate germination and identified many receptors, signaling cascades, and hormonal control elements. In contrast, seed germination in several other plants is inhibited by light, but the molecular basis of this alternative response is unknown. We describe Aethionema arabicum (Brassicaceae) as a suitable model plant to investigate the mechanism of germination inhibition by light, as this species has accessions with natural variation between light-sensitive and light-neutral responses. Inhibition of germination occurs in red, blue, or far-red light and increases with light intensity and duration. Gibberellins and abscisic acid are involved in the control of germination, as in Arabidopsis, but transcriptome comparisons of light- and dark-exposed A. arabicum seeds revealed that, upon light exposure, the expression of genes for key regulators undergo converse changes, resulting in antipodal hormone regulation. These findings illustrate that similar modular components of a pathway in light-inhibited, light-neutral, and light-requiring germination among the Brassicaceae have been assembled in the course of evolution to produce divergent pathways, likely as adaptive traits.

Banana (Musa acuminata) transcriptome profiling in response to rhizobacteria: Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006

Background

Banana is one of the most important crops in tropical and sub-tropical regions. To meet the demands of international markets, banana plantations require high amounts of chemical fertilizers which translate into high farming costs and are hazardous to the environment when used excessively. Beneficial free-living soil bacteria that colonize the rhizosphere are known as plant growth-promoting rhizobacteria (PGPR). PGPR affect plant growth in direct or indirect ways and hold great promise for sustainable agriculture.

Results

PGPR of the genera Bacillus and Pseudomonas in banana cv. Williams were evaluated. These plants were produced through in vitro culture and inoculated individually with two rhizobacteria, Bacillus amyloliquefaciens strain Bs006 and Pseudomonas fluorescens strain Ps006. Control plants without microbial inoculum were also evaluated. These plants were kept in a controlled climate growth room with conditions required to favor plant-microorganism interactions. These interactions were evaluated at 1-, 48- and 96-h using transcriptome sequencing after inoculation to establish differentially expressed genes (DEGs) in plants elicited by the interaction with the two rhizobacteria. Additionally, droplet digital PCR was performed at 1, 48, 96 h, and also at 15 and 30 days to validate the expression patterns of selected DEGs. The banana cv. Williams transcriptome reported differential expression in a large number of genes of which 22 were experimentally validated. Genes validated experimentally correspond to growth promotion and regulation of specific functions (flowering, photosynthesis, glucose catabolism and root growth) as well as plant defense genes. This study focused on the analysis of 18 genes involved in growth promotion, defense and response to biotic or abiotic stress.

Conclusions

Differences in banana gene expression profiles in response to the rhizobacteria evaluated here (Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006) are influenced by separate bacterial colonization processes and levels that stimulate distinct groups of genes at various points in time.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5763-5) contains supplementary material, which is available to authorized users.

Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication

Background

Transcription factors (TFs) play a key role in regulating plant development and response to environmental stimuli. While most genes revert to single copy after whole genome duplication (WGD) event, transcription factors are retained at a significantly higher rate. Little is known about how TF duplicates have diverged in their expression and regulation, the answer to which may contribute to a better understanding of the elevated retention rate among TFs.

Results

Here we assessed what features may explain differences in the retention of TF duplicates and other genes using Arabidopsis thaliana as a model. We integrated 34 expression, sequence, and conservation features to build a linear model for predicting the extent of duplicate retention following WGD events among TFs and 19 groups of genes with other functions. We found that TFs was the least well predicted, demonstrating the features of TFs are substantially deviated from duplicate genes in other function groups. Consistent with this, the evolution of TF expression patterns and cis-regulatory cites favors the partitioning of ancestral states among the resulting duplicates: one “ancestral” TF duplicate retains most ancestral expression and cis-regulatory sites, while the “non-ancestral” duplicate is enriched for novel regulatory sites. By modeling the retention of ancestral expression and cis-regulatory states in duplicate pairs using a system of differential equations, we found that TF duplicate pairs in a partitioned state are preferentially maintained.

Conclusions

These TF duplicates with asymmetrically partitioned ancestral states are likely maintained because one copy retains ancestral functions while the other, at least in some cases, acquires novel cis-regulatory sites that may be important for novel, adaptive traits.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1398-z) contains supplementary material, which is available to authorized users.

Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination

BACKGROUND

Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene expression and the dynamic changes in the epigenome and small RNAs during germination is limited. The interactions between genome, transcriptome and epigenome must be revealed in order to identify the regulatory mechanisms that control seed germination.

RESULTS

We present an integrated analysis of high-resolution RNA sequencing, small RNA sequencing and MethylC sequencing over ten developmental time points in Arabidopsis thaliana seeds, finding extensive transcriptomic and epigenomic transformations associated with seed germination. We identify previously unannotated loci from which messenger RNAs are expressed transiently during germination and find widespread alternative splicing and divergent isoform abundance of genes involved in RNA processing and splicing. We generate the first dynamic transcription factor network model of germination, identifying known and novel regulatory factors. Expression of both microRNA and short interfering RNA loci changes significantly during germination, particularly between the seed and the post-germinative seedling. These are associated with changes in gene expression and large-scale demethylation observed towards the end of germination, as the epigenome transitions from an embryo-like to a vegetative seedling state.

CONCLUSIONS

This study reveals the complex dynamics and interactions of the transcriptome and epigenome during seed germination, including the extensive remodelling of the seed DNA methylome from an embryo-like to vegetative-like state during the seed-to-seedling transition. Data are available for exploration in a user-friendly browser at https://jbrowse.latrobe.edu.au/germination_epigenome .

The fruit-specific transcription factor FaDOF2 regulates the production of eugenol in ripe fruit receptacles

Only a few transcription factors have been described in the regulation of the strawberry (Fragaria x ananassa) fruit ripening process. Using a transcriptomic approach, we identified and functionally characterized FaDOF2, a DOF-type ripening-related transcription factor, which is hormonally regulated and specific to the receptacle, though high expression levels were also found in petals. The expression pattern of FaDOF2 correlated with eugenol content, a phenylpropanoid volatile, in both fruit receptacles and petals. When FaDOF2 expression was silenced in ripe strawberry receptacles, the expression of FaEOBII and FaEGS2, two key genes involved in eugenol production, were down-regulated. These fruits showed a concomitant decrease in eugenol content, which confirmed that FaDOF2 is a transcription factor that is involved in eugenol production in ripe fruit receptacles. By using the yeast two-hybrid system and bimolecular fluorescence complementation, we demonstrated that FaDOF2 interacts with FaEOBII, a previously reported regulator of eugenol production, which determines fine-tuning of the expression of key genes that are involved in eugenol production. These results provide evidence that FaDOF2 plays a subsidiary regulatory role with FaEOBII in the expression of genes encoding enzymes that control eugenol production. Taken together, our results provide new insights into the regulation of the volatile phenylpropanoid pathway in ripe strawberry receptacles.

ThDof1.4 and ThZFP1 constitute a transcriptional regulatory cascade involved in salt or osmotic stress in Tamarix hispida

Identification of the upstream regulators of a gene is important to characterize the transcriptional pathway and the function of the gene. Previously, we found that a zinc finger protein (ThZFP1) is involved in abiotic stress tolerance of Tamarix hispida. In the present study, we further investigated the transcriptional pathway of ThZFP1. Dof motifs are abundant in the ThZFP1 promoter; therefore, we used them to screen for transcriptional regulators of ThZFP1. A Dof protein, ThDof1.4, binds to the Dof motif specifically, and was hypothesized as the upstream regulator of ThZFP1. Further study showed that overexpression of ThDof1.4 in T. hispida activated the expression of GUS controlled by the ThZFP1 promoter. In T. hispida, transient overexpression of ThDof1.4 increased the transcripts of ThZFP1; conversely, transient RNAi-silencing of ThDof1.4 reduced the expression of ThZFP1. Chromatin immunoprecipitation indicated that ThDof1.4 binds to the ThZFP1 promoter. Additionally, ThDof1.4 and ThZFP1 share similar expression patterns in response to salt or drought stress. Furthermore, like ThZFP1, ThDof1.4 could increase the proline level and enhance ROS scavenging capability to improve salt and osmotic stress tolerance. Together, these results suggested that ThDof1.4 and ThZFP1 form a transcriptional regulatory cascade involved in abiotic stress resistance in T. hispida.

ZmDof30 Negatively Regulates the Promoter Activity of the Pollen-Specific Gene Zm908

The maize (Zea mays) pollen-predominant gene Zm908, a novel small-peptide gene, was reported to play critical roles in pollen germination and pollen tube growth in our previous work. In this study, we aimed to explore the regulatory mechanism of Zm908. The putative promoter of Zm908 was cloned and analyzed. The activity analysis of a series of promoter truncations in different tissues of transgenic tobacco plants indicated that the Zm908 promoter is pollen-specific and that the -126 to -68 region is crucial for pollen expression. The 5' deletion analysis of the -126 to -68 region revealed that the -126 to -102 region functions as a transcriptional suppression element. ZmDof30, which is predominantly expressed in pollen and whole anthers, was cloned and characterized. ZmDof30-GFP localized to the nuclei of maize protoplasts and possessed no transcriptional activation activity in a yeast system. ZmDof30 could bind to the AAAG elements in p184 sequence containing the -126 to +58 region of the Zm908 promoter in vitro and in vivo, and negatively regulated p184 activity in tobacco leaves. Collectively, ZmDof30 may function as a Zm908 transcriptional repressor in pollen, and these results may provide a better understanding of the regulation of the Zm908 gene. Additionally, the pollen-specific Zm908 promoter may be valuable for genetically engineering male sterility.

Genome-Wide Identification and Expression Profile of Dof Transcription Factor Gene Family in Pepper (Capsicum annuum L.)

Dof (DNA-binding One Zinc Finger) transcription factor family is unique to plants and has diverse roles associated with plant-specific phenomena, such as light, phytohormone and defense responses as well as seed development and germination. Although, genome-wide analysis of this family has been performed in many species, information regarding Dof genes in the pepper, Capsicum annuum L., is extremely limited. In this study, exhaustive searches of pepper genome revealed 33 potential CaDofs that were phylogenetically clustered into four subgroups. Twenty-nine of the 33 Dof genes could be mapped on 11 chromosomes, except for chromosome 7. The intron/exon organizations and conserved motif compositions of these genes were also analyzed. Additionally, phylogenetic analysis and classification of the Dof transcription factor family in eight plant species revealed that S. lycopersicum and C. annuum as well as O. sativa and S. bicolor Dof proteins may have evolved conservatively. Moreover, comprehensive expression analysis of CaDofs using a RNA-seq atlas and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that these genes exhibit a variety of expression patterns. Most of the CaDofs were expressed in at least one of the tissues tested, whereas several genes were identified as being highly responsive to heat and salt stresses. Overall, this study describes the first genome-wide analysis of the pepper Dof family, whose genes exhibited different expression patterns in all primary fruit developmental stages and tissue types, as in response to abiotic stress. In particular, some Dof genes might be used as biomarkers for heat and salt stress. The results could expand our understanding of the roles of Dof genes in pepper.

Transcriptome analyses of the Dof-like gene family in grapevine reveal its involvement in berry, flower and seed development

The Dof (DNA-binding with one finger) protein family spans a group of plant transcription factors involved in the regulation of several functions, such as plant responses to stress, hormones and light, phytochrome signaling and seed germination. Here we describe the Dof-like gene family in grapevine (Vitis vinifera L.), which consists of 25 genes coding for Dof. An extensive in silico characterization of the VviDofL gene family was performed. Additionally, the expression of the entire gene family was assessed in 54 grapevine tissues and organs using an integrated approach with microarray (cv Corvina) and real-time PCR (cv Pinot Noir) analyses. The phylogenetic analysis comparing grapevine sequences with those of Arabidopsis, tomato, poplar and already described Dof genes in other species allowed us to identify several duplicated genes. The diversification of grapevine DofL genes during evolution likely resulted in a broader range of biological roles. Furthermore, distinct expression patterns were identified between samples analyzed, corroborating such hypothesis. Our expression results indicate that several VviDofL genes perform their functional roles mainly during flower, berry and seed development, highlighting their importance for grapevine growth and production. The identification of similar expression profiles between both approaches strongly suggests that these genes have important regulatory roles that are evolutionally conserved between grapevine cvs Corvina and Pinot Noir.