Genetic and epigenetic signatures for improved breeding of cultivated blueberry.

Blueberry belongs to the Vaccinium genus and is a highly popular fruit crop with significant economic importance. It was not until the early twentieth century that they began to be domesticated through extensive interspecific hybridization. Here, we collected 220 Vaccinium accessions from various geographical locations, including 154 from the United States, 14 from China, eight from Australia, and 29 from Europe and other countries, comprising 164 Vaccinium corymbosum, 15 Vaccinium ashei, 10 lowbush blueberries, seven half-high blueberries, and others. We present the whole-genome variation map of 220 accessions and reconstructed the hundred-year molecular history of interspecific hybridization of blueberry. We focused on the two major blueberry subgroups, the northern highbush blueberry (NHB) and southern highbush blueberry (SHB) and identified candidate genes that contribute to their distinct traits in climate adaptability and fruit quality. Our analysis unveiled the role of gene introgression from Vaccinium darrowii and V. ashei into SHB in driving the differentiation between SHB and NHB, potentially facilitating SHB's adaptation to subtropical environments. Assisted by genome-wide association studies, our analysis suggested VcTBL44 as a pivotal gene regulator governing fruit firmness in SHB. Additionally, we conducted whole-genome bisulfite sequencing on nine NHB and 12 SHB cultivars, and characterized regions that are differentially methylated between the two subgroups. In particular, we discovered that the ß-alanine metabolic pathway genes were enriched for DNA methylation changes. Our study provides high-quality genetic and epigenetic variation maps for blueberry, which offer valuable insights and resources for future blueberry breeding.

The roles of epigenetic regulators in plant regeneration: Exploring patterns amidst complex conditions.

Plants possess remarkable capability to regenerate upon tissue damage or optimal environmental stimuli. This ability not only serves as a crucial strategy for immobile plants to survive through harsh environments, but also made numerous modern plant improvements techniques possible. At the cellular level, this biological process involves dynamic changes in gene expression that redirect cell fate transitions. It is increasingly recognized that chromatin epigenetic modifications, both activating and repressive, intricately interact to regulate this process. Moreover, the outcomes of epigenetic regulation on regeneration are influenced by factors such as the differences in regenerative plant species and donor tissue types, as well as the concentration and timing of hormone treatments. In this review, we focus on several well-characterized epigenetic modifications and their regulatory roles in the expression of widely studied morphogenic regulators, aiming to enhance our understanding of the mechanisms by which epigenetic modifications govern plant regeneration.

Prognostic value of initial routine laboratory blood tests in patients with aneurysmal subarachnoid hemorrhage requiring mechanical ventilation: a retrospective cohort study.

Background: Aneurysmal subarachnoid hemorrhage (aSAH) necessitating mechanical ventilation (MV) presents a serious challenge for intensivists. Laboratory blood tests reflect individual physiological and biochemical states, and provide a useful tool for identifying patients with critical condition and stratifying risk levels of death. This study aimed to determine the prognostic role of initial routine laboratory blood tests in these patients. Methods: This retrospective cohort study included 190 aSAH patients requiring MV in the neurosurgical intensive care unit from December 2019 to March 2022. Follow-up evaluation was performed in May 2022 via routine outpatient appointment or telephone interview. The primary outcomes were death occurring within 7 days after discharge (short-term mortality) or reported at time of follow-up (long-term mortality). Clinico-demographic and radiological characteristics, initial routine laboratory blood tests (e.g., metabolic panels and arterial blood gas analysis), and treatment were analyzed and compared in relation to mortality. Multivariable logistic and Cox regression analyses, with adjustment of other clinical predictors, were performed to determine independent laboratory test predictors for short- and long-term mortality, respectively. Results: The patients had a median age of 62 years, with a median World Federation of Neurosurgical Societies grade (WFNS) score of 5 and a median modified Fisher grade (mFisher) score of 4. The short- and long-term mortality of this cohort were 60.5% and 65.3%, respectively. Compared with survivors, non-survivors had more severe disease upon admission based on neurological status and imaging features and a shorter disease course, and were more likely to receive conservative treatment. Initial ionized calcium was found to be independently associate with both short-term [adjusted odds ratio (OR): 0.92; 95% confidence interval (CI): 0.86 to 0.99; P=0.020] and long-term mortality [adjusted hazard ratio (HR): 0.95; 95% CI: 0.92 to 0.99; P=0.010], after adjusting for potential confounders. Moreover, the admission glucose level was found to be associated only with short-term mortality (adjusted OR: 1.19; 95% CI: 1.06 to 1.34; P=0.004). Conclusions: Laboratory screening may provide a useful tool for the management of aSAH patients requiring MV in stratifying risk levels for mortality and for better clinical decision-making. Further study is needed to validate the effects of calcium supplementation and glucose-lowering therapy on the outcomes in this disease.

Transcriptomic and proteomic profiling of the anterior cingulate cortex in neuropathic pain model rats.

Background: Neuropathic pain (NP) takes a heavy toll on individual life quality, yet gaps in its molecular characterization persist and effective therapy is lacking. This study aimed to provide comprehensive knowledge by combining transcriptomic and proteomic data of molecular correlates of NP in the anterior cingulate cortex (ACC), a cortical hub responsible for affective pain processing. Methods: The NP model was established by spared nerve injury (SNI) in Sprague-Dawley rats. RNA sequencing and proteomic data from the ACC tissue isolated from sham and SNI rats 2 weeks after surgery were integrated to compare their gene and protein expression profiles. Bioinformatic analyses were performed to figure out the functions and signaling pathways of the differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) enriched in. Results: Transcriptomic analysis identified a total of 788 DEGs (with 49 genes upregulated) after SNI surgery, while proteomic analysis found 222 DEPs (with 89 proteins upregulated). While Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of the DEGs suggested that most of the altered genes were involved in synaptic transmission and plasticity, bioinformatics analysis of the DEPs revealed novel critical pathways associated with autophagy, mitophagy, and peroxisome. Notably, we noticed functionally important NP-related changes in the protein that occurred in the absence of corresponding changes at the level of transcription. Venn diagram analysis of the transcriptomic and proteomic data identified 10 overlapping targets, among which only three genes (XK-related protein 4, NIPA-like domain-containing 3, and homeodomain-interacting protein kinase 3) showed concordance in the directions of change and strong correlations between mRNA and protein levels. Conclusion: The present study identified novel pathways in the ACC in addition to confirming previously reported mechanisms for NP etiology, and provided novel mechanistic insights for future research on NP treatment. These findings also imply that mRNA profiling alone fails to provide a complete landscape of molecular pain in the ACC. Therefore, explorations of changes at the level of protein are necessary to understand NP processes that are not transcriptionally modulated.

Hybrid endoscopic-microscopic surgery for dumbbell-shaped trigeminal schwannoma: case report and literature review.

Background: The surgery of dumbbell-shaped trigeminal neurinomas (TN) remains one of the most formidable challenges for neurosurgeons because of its location at great depth in the cranium and proximity to vital neurovascular structures. Objective: To describe the feasibility of a novel technique, synchronous endoscopy and microsurgery via combined far-lateral supracerebellar-infratentorial and subtemporal approach, for resection of this rare entity. Methods: A 53-year-old women presented with progressive left facial numbness for 2 months. Imaging examinations revealed a left-sided dumbbell-shaped TN afflicting the middle and posterior cranial fossa, and a single-stage combined multiportal endoscopic microscopic approach was attempted for tumor resection. Initially, a purely endoscopic far-lateral supracerebellar-infratentorial approach was used to remove the posterior fossa component with the aid of tentorium incision. Subsequently, a microsurgical subtemporal interdural approach was performed for the exposure and separation of tumor within the Meckel cave. Finally, the tumor was pushed into the porus trigeminus under microscopy, thus enabling tumor extraction for the supracerebellar space under endoscopy without anterior petrosectomy. Results: The patient evolved favorably without additional neurological deficit after surgery, and postoperative imaging showed a complete resection of the tumor. Conclusion: We describe the first account of multi-corridor hybrid surgery for removal of TN in a dumbbell configuration, which enables one-stage total tumor removal with minimal added morbidity. This hybrid technique may be an effective piece of the surgeon's armamentarium to improve outcomes of patient with complex skull-base lesions. Further studies with larger case numbers are warranted to confirm the prognostic significance of this technique.

DDT-RELATED PROTEIN4-IMITATION SWITCH alters nucleosome distribution to relieve transcriptional silencing in Arabidopsis.

DNA methylation is a conserved epigenetic modification that is typically associated with silencing of transposable elements and promoter methylated genes. However, some DNA-methylated loci are protected from silencing, allowing transcriptional flexibility in response to environmental and developmental cues. Through a genetic screen in Arabidopsis (Arabidopsis thaliana), we uncovered an antagonistic relationship between the MICRORCHIDIA (MORC) protein and the IMITATION SWITCH (ISWI) complex in regulating the DNA-methylated SUPPRESSOR OF DRM1 DRM2 CMT3 (SDC) reporter. We demonstrate that components of the plant-specific ISWI complex, including CHROMATIN REMODELING PROTEIN11 (CHR11), CHR17, DDT-RELATED PROTEIN4 (DDR4), and DDR5, function to partially derepress silenced genes and transposable elements (TEs), through their function in regulating nucleosome distribution. This action also requires the known transcriptional activator DNAJ proteins, providing a mechanistic link between nucleosome remodeling and transcriptional activation. Genome-wide studies revealed that DDR4 causes changes in nucleosome distribution at numerous loci, a subset of which is associated with changes in DNA methylation and/or transcription. Our work reveals a mechanism for balancing transcriptional flexibility and faithful silencing of DNA-methylated loci. As both ISWI and MORC family genes are widely distributed across plant and animal species, our findings may represent a conserved eukaryotic mechanism for fine-tuning gene expression under epigenetic regulation.

Constructing a drug release model by central composite design to investigate the interaction between drugs and temperature-sensitive controlled release nanoparticles.

To study the release behavior of a thermosensitive controlled release drug delivery system and construct a predictable mathematical model of drug release, poly(N-isopropylacrylamide-co-Allylamine) (P(NIPA-AL17)) and ploy(styrene sulfonate) (PSS) were functionalized on the surface of hollow mesoporous carbon nanoparticles (HMCNs) through layer-by-layer (LBL) assembly to construct a photothermal responsive controlled release system. A five-level four-factorial central composite design (CCD) was performed to investigate the relationship between four independent variables including drug loading (A), number of polymer layers (B), temperature (C) and vibration rate of the shaker (D), and three dependent response variables, including cumulative release over 1 h (Y1), cumulative release over 24 h (Y2) and the release rate constant k (Y3). The CCD results indicate that A and C significantly affect Y1 (P < 0.05). C significantly affects Y2 (P < 0.05). A and B is found to affect Y3 (P < 0.05) significantly. When C is below 39 °C, Y1 and Y2 decrease with the increase of A and B, and when C is above 39 °C, they increase with the increase of A and B; Y3 decreases as A and B increase; and D shows the least or even no influence on Y1, Y2 and Y3. The constructed predictable mathematical model will provide a scientific reference for the further development and application of photothermal responsive controlled-release preparations.

Biosensor based on bimetallic/graphene composite for non-enzymatic detection of hydrogen peroxide in living tumor cells.

A highly sensitive electrochemical biosensor was manufactured with triple synergistic catalysis to detect hydrogen peroxide (H2 O2 ). In this study, a highly sensitive biosensor based on Prussian blue-chitosan/graphene-hemin nanomaterial/platinum and palladium nanoparticles (PB-CS/HGNs/Pt&Pd biosensor) was fabricated for the detection of H2 O2 . The materials described above were modified on the electrode surface and applied to catalyze the breakdown of hydrogen peroxide. The current response of the biosensor presented a linear relationship with H2 O2 concentration from 6 × 10-2 to 20 µM (R2 = 0.9766) and with the logarithm of H2 O2 concentration from 20 to 9×103  µM (R2 = 0.9782), the low detection limit of 25 nM was obtained at the signal/noise (S/N) ratio of 3. Besides, the biosensor showed an outstanding anti-interference ability and acceptable reproducibility. PB-CS/HGNs/Pt&Pd electrodes are effective in measuring H2 O2 from living tumor cells, which implies that the biosensor has the potential to assess reactive oxygen species in various living tumor cells.

D6 protein kinase in root xylem benefiting resistance to Fusarium reveals infection and defense mechanisms in tung trees.

Fusarium oxysporum, a global soil-borne pathogen, causes severe disease in various cultivated plants. The mechanism underlying infection and resistance remains largely elusive. Vernicia fordii, known as the tung tree, suffers from disease caused by F. oxysporum f. sp. fordiis (Fof-1), while its sister species V. montana displays high resistance to Fof-1. To investigate the process of infection and resistance ability, we demonstrated that Fof-1 can penetrate the epidermis of root hairs and then centripetally invade the cortex and phloem in both species. Furthermore, Fof-1 spread upwards through the root xylem in susceptible V. fordii trees, whereas it failed to infect the root xylem in resistant V. montana trees. We found that D6 PROTEIN KINASE LIKE 2 (VmD6PKL2) was specifically expressed in the lateral root xylem and was induced after Fof-1 infection in resistant trees. Transgenic analysis in Arabidopsis and tomato revealed that VmD6PKL2 significantly enhanced resistance in both species, whereas the d6pkl2 mutant displayed reduced resistance against Fof-1. Additionally, VmD6PKL2 was identified to interact directly with synaptotagmin (VmSYT3), which is specifically expressed in the root xylem and mediates the negative regulation responding to Fof-1. Our data suggested that VmD6PKL2 could act as a resistance gene against Fof-1 through suppression of VmSYT3-mediated negative regulation in the lateral root xylem of the resistant species. These findings provide novel insight into Fusarium wilt resistance in plants.

Research on PM2.5 Spatiotemporal Forecasting Model Based on LSTM Neural Network.

Accurate monitoring of air quality can no longer meet people's needs. People hope to predict air quality in advance and make timely warnings and defenses to minimize the threat to life. This paper proposed a new air quality spatiotemporal prediction model to predict future air quality and is based on a large number of environmental data and a long short-term memory (LSTM) neural network. In order to capture the spatial and temporal characteristics of the pollutant concentration data, the data of the five sites with the highest correlation of time-series concentration of PM2.5 (particles with aerodynamic diameter ≤2.5 mm) at the experimental site were first extracted, and the weather data and other pollutant data at the same time were merged in the next step, extracting advanced spatiotemporal features through long- and short-term memory neural networks. The model presented in this paper was compared with other baseline models on the hourly PM2.5 concentration data set collected at 35 air quality monitoring sites in Beijing from January 1, 2016, to December 31, 2017. The experimental results show that the performance of the proposed model is better than other baseline models.

The Litsea genome and the evolution of the laurel family.

The laurel family within the Magnoliids has attracted attentions owing to its scents, variable inflorescences, and controversial phylogenetic position. Here, we present a chromosome-level assembly of the Litsea cubeba genome, together with low-coverage genomic and transcriptomic data for many other Lauraceae. Phylogenomic analyses show phylogenetic discordance at the position of Magnoliids, suggesting incomplete lineage sorting during the divergence of monocots, eudicots, and Magnoliids. An ancient whole-genome duplication (WGD) event occurred just before the divergence of Laurales and Magnoliales; subsequently, independent WGDs occurred almost simultaneously in the three Lauralean lineages. The phylogenetic relationships within Lauraceae correspond to the divergence of inflorescences, as evidenced by the phylogeny of FUWA, a conserved gene involved in determining panicle architecture in Lauraceae. Monoterpene synthases responsible for production of specific volatile compounds in Lauraceae are functionally verified. Our work sheds light on the evolution of the Lauraceae, the genetic basis for floral evolution and specific scents.

Overexpression of the 3-hydroxy-3-methylglutaryl-CoA synthase gene LcHMGS effectively increases the yield of monoterpenes and sesquiterpenes.

Monoterpenes are important components of plant essential oils and have long been used as raw materials for spices and food flavorings. A number of studies have been performed to increase the content of monoterpenes in plants, but no obvious effect was observed. Exchange was observed between the methylerythritol phosphate (MEP) and mevalonic acid (MVA) metabolic pathways, which produce monoterpenes and sesquiterpenes, respectively. However, the specific details of the communication have not been elucidated. In the present study, we investigated the effects of overexpressing Litsea cubeba (Lour.) Persoon 3-hydroxy-3-methylglutaryl-coenzyme A synthase (LcHMGS) on the production of monoterpenes and sesquiterpenes. In addition, we also explored the flow of metabolic flux between the MEP and MVA pathways. We cloned LcHMGS and analyzed its expression pattern in various tissues. The overexpression of LcHMGS significantly increased the species and content of monoterpenes and sesquiterpenes. In addition, LcHMGS overexpression in plants induced such phenotypes as excessive growth, enlarged vegetative organs and early flowering by elevating the GA3 content. Our results demonstrate a metabolic engineering strategy to improve the yield of monoterpenes and sesquiterpenes and simultaneously increase the biomass of plants.

A highly scalable dielectric metamaterial with superior capacitor performance over a broad temperature.

Although many polymers exhibit excellent dielectric performance including high energy density with high efficiency at room temperature, their electric and dielectric performance deteriorates at high temperatures (~150°C). Here, we show that nanofillers at very low volume content in a high-temperature (high-glass transition temperature) semicrystalline dipolar polymer, poly(arylene ether urea), can generate local structural changes, leading to a marked increase in both dielectric constant and breakdown field, and substantially reduce conduction losses at high electric fields and over a broad temperature range. Consequently, the polymer with a low nanofiller loading (0.2 volume %) generates a high discharged energy density of ca. 5 J/cm3 with high efficiency at 150°C. The experimental data reveal microstructure changes in the nanocomposites, which, at 0.2 volume % nanofiller loading, reduce constraints on dipole motions locally in the glassy state of the polymer, reduce the mean free path for the mobile charges, and enhance the deep trap level.

Transcriptome Analysis of Litsea cubeba Floral Buds Reveals the Role of Hormones and Transcription Factors in the Differentiation Process.

BACKGROUND: Litsea cubeba (Lour.) Pers. is an important economic plant that is rich in valuable essential oil. The essential oil is often used as a raw material for perfumes, food additives, insecticides and bacteriostats. Most of the essential oil is contained in the fruit, and the quantity and quality of fruit are dependent on the flowers. To explore the molecular mechanism of floral bud differentiation, high-throughput RNA sequencing was used to detect differences in the gene expression of L. cubeba female and male floral buds at three differentiation stages. RESULTS: This study obtained 160.88 Gbp of clean data that were assembled into 100,072 unigenes, and a total of 38,658 unigenes were annotated. A total of 27,521 simple sequence repeats (SSRs) were identified after scanning the assembled transcriptome, and the mono-nucleotide repeats were predominant, followed by di-nucleotide and tri-nucleotide repeats. A total of 12,559 differentially expressed genes (DEGs) were detected from the female (F) and male (M) floral bud comparisons. The gene ontology (GO) databases revealed that these DEGs were primarily contained in "metabolic processes", "cellular processes", and "single-organism processes". The Kyoto Encyclopedia of Genes and Genomes (KEGG) databases suggested that the DEGs belonged to "plant hormone signal transduction" and accounted for a relatively large portion in all of these comparisons. We analyzed the expression level of plant hormone-related genes and detected the contents of several relevant plant hormones in different stages. The results revealed that the dynamic changes in each hormone content were almost consistent with the expression levels of relevant genes. The transcription factors selected from the DEGs were analyzed. Most DEGs of MADS-box were upregulated and most DEGs of bZIP were downregulated. The expression trends of the DEGs were nearly identical in female and male floral buds, and qRT-PCR analysis revealed consistency with the transcriptome data. CONCLUSIONS: We sequenced and assembled a high-quality L. cubeba floral bud transcriptome, and the data appeared to be well replicated (n = 3) over three developmental time points during flower development. Our study explored the changes in the contents of several plant hormones during floral bud differentiation using biochemical and molecular biology techniques, and the changes in expression levels of several flower development related transcription factors. These results revealed the role of these factors (i.e., hormones and transcription factors) and may advance our understanding of their functions in flower development in L. cubeba.

Design, synthesis and evaluation of 2,2-dimethyl-1,3-dioxolane derivatives as human rhinovirus 3C protease inhibitors.

The human rhinovirus (HRV) is the most significant cause of the common cold all over the world. The maturation and replication of this virus entirely depend on the activity of a virus-encoded 3C protease. Due to the high conservation among different serotypes and the minimal homology existing between 3C protease and known mammalian enzymes, 3C protease has been regarded as an attractive target for the treatment of HRV infections. In this study, we identified a novel (4R,5R)-N4-(2-((3-methoxyphenyl)amino)ethyl)-2,2-dimethyl-N5-(naphthalen-2-yl)-1,3-dioxolane-4,5-dicarboxamide (7a) to be a HRV 3C protease inhibitor via virtual screening. Further research has been focused on the design, synthesis and in vitro biological evaluation of 7a derivatives. The studies revealed that compound 7d has an IC50 value of 2.50±0.7µM against HRV 3C protease, and it thus could serve as a promising compound for the development of novel anti-rhinoviral medicines.

Improved electrical conductivity of TPU/carbon black composites by addition of COPA and selective localization of carbon black at the interface of sea-island structured polymer blends.

The electrical percolation threshold of carbon black (CB) in thermoplastic polyurethane (TPU) decreases by 46% with the incorporation of 20 wt% polyamide copolymer (COPA) through selective localization of CB particles at the interface of sea-island structured TPU/COPA blends. Composites with a composition of TPU/20 wt% COPA/9 wt% CB were prepared by four different mixing sequences and their morphologies were investigated by FESEM and TEM. The majority of CB particles were observed at the interface of sea-island structured blends irrespective of the compounding sequence used, although the percentage of CB particles at the interface is considerably less in the composite prepared by adding COPA to premixed TPU/CB. The driving force for the interfacial localization of most CB particles is the hydrogen bonding of CB with both TPU and COPA, which is confirmed by FTIR and DMA investigations. CB particles act like Janus particle-type compatibilizers with bonded TPU molecules toward the TPU phase and bonded COPA chains toward the COPA phase. Highly efficient conductive paths are formed through the CB-covered domains and a short inter-domain distance.

Tunable Electrical Conductivity of Carbon-Black-Filled Ternary Polymer Blends by Constructing a Hierarchical Structure.

A type of hierarchical structured composite composed of a minor thermoplastic polyurethane (TPU) phase spreading at the interface of two major phases polyoxymethylene/polyamide copolymer (POM/COPA) and carbon black (CB) particles selectively localized at the TPU/COPA interface of the tri-continuous blends was fabricated by melt compounding. The hierarchical structure was designed according to predictions and verified by a combination of electron microscopy and solvent extraction technique. The hierarchical structured composites show the dramatically decreased percolation threshold, a reduction of 60% compared to those without TPU where CB is selectively distributed in the COPA phase. The effects of CB contents and TPU on the phase morphology of POM/COPA were investigated, showing the occurrence of the POM/COPA phase inversion from a sea-island to a co-continuous structure beyond the percolation threshold of CB in the presence of TPU. The mechanism for the formation of conductive network is construction of CB network at the TPU/COPA interface of tri-continuous POM/COPA/TPU blends and double percolation effect.

Core Curriculum Comparisons in Master Degree Programs for Patient Safety.

A content analysis was performed to investigate core curriculum in master degree programs for patient safety. Twenty programs from six countries and 179 core curriculum/modules were extracted and reviewed. The curricula were compared to the topics recommended in WHO's Multi-professional Patient Safety Curriculum Guide and the core content relevant to patient safety issues in IMIA/AMIA recommendations for health informatics education. The differences between the identified curricula with those addressed in the aforementioned Guide/Recommendations were examined.

Divergent Expression Patterns in Two Vernicia Species Revealed the Potential Role of the Hub Gene VmAP2/ERF036 in Resistance to Fusarium oxysporum in Vernicia montana.

Tung oil tree (Vernicia fordii) is a promising industrial oil crop; however, this tree is highly susceptible to Fusarium wilt disease. Conversely, Vernicia montana is resistant to the pathogen. The APETALA2/ethylene-responsive element binding factor (AP2/ERF) transcription factor superfamily has been reported to play a significant role in resistance to Fusarium oxysporum. In this study, comprehensive analysis identified 75 and 81 putative Vf/VmAP2/ERF transcription factor-encoding genes in V. fordii and V. montana, respectively, which were divided into AP2, ERF, related to ABI3 and VP1 (RAV) and Soloist families. After F. oxysporum infection, a majority of AP2/ERF superfamily genes showed strong patterns of repression in both V. fordii and V. montana. We then identified 53 pairs of one-to-one orthologs in V. fordii and V. montana, with most pairs of orthologous genes exhibiting similar expression in response to the pathogen. Further investigation of Vf/VmAP2/ERF gene expression in plant tissues indicated that the pairs of genes with different expression patterns in response to F. oxysporum tended to exhibit different tissue profiles in the two species. In addition, VmAP2/ERF036, showing the strongest interactions with 666 genes, was identified as a core hub gene mediating resistance. Moreover, qRT-PCR results indicated VmAP2/ERF036 showed repressed expression while its orthologous gene VfAP2/ERF036 had the opposite expression pattern during pathogen infection. Overall, comparative analysis of the Vf/VmAP2/ERF superfamily and indication of a potential hub resistance gene in resistant and susceptible Vernicia species provides valuable information for understanding the molecular basis and selection of essential functional genes for V. fordii genetic engineering to control Fusarium wilt disease.

Comparative Transcriptomics Atlases Reveals Different Gene Expression Pattern Related to Fusarium Wilt Disease Resistance and Susceptibility in Two Vernicia Species.

Vernicia fordii (tung oil tree) is a promising industrial crop. Unfortunately, the devastating Fusarium wilt disease has caused its great losses, while its sister species (Vernicia montana) is remarkably resistant to this pathogen. However, the genetic mechanisms underlying this difference remain largely unknown. We here generated comparative transcriptomic atlases for different stages of Fusarium oxysporum infected Vernicia root. The transcriptomes of V. fordii and V. montana were assembled de novo and contained 258,430 and 245,240 non-redundant transcripts with N50 values of 1776 and 2452, respectively. A total of 44,310 pairs of putative one-to-one orthologous genes were identified in Vernicia species. Overall, the vast majority of orthologous genes shared a remarkably similar expression mode. The expression patterns of a small set of genes were further validated by quantitative real-time PCR. Moreover, 157 unigenes whose expression significantly correlated between the two species were defined, and gene set enrichment analysis indicated roles in increased defense response and in jasmonic and salicylic acid signaling responses during pathogen attack. Co-expression network analysis further identified the 17 hub unigenes, such as the serine/threonine protein kinase D6PK, leucine-rich repeat receptor-like kinase (LRR-RLK), and EREBP transcription factor, which play essential roles in plant pathogen resistance. Intriguingly, the expression of most hub genes differed significantly between V. montana and V. fordii. Based on our results, we propose a model to describe the major molecular reactions that underlie the defense responses of resistant V. montana to F. oxysporum. These data represent a crucial step toward breeding more pathogen-resistant V. fordii.