Reshaping epigenomic landscapes facilitated bread wheat speciation.

Polyploidization is a driving force of wheat (Triticum aestivum) evolution and speciation, yet its impact on epigenetic regulation and gene expression remains unclear. Here, we constructed a high-resolution epigenetic landscape across leaves, spikes, and roots of hexaploid wheat and its tetraploid and diploid relatives. Inter-species stably expressed genes exhibited conserved amino acid sequences under strong purifying selection, while dynamically expressed genes were linked to species-specific adaptation.

Dynamic regulation and embryo-endosperm crosstalk revealed by whole transcriptome profiling of wheat seed development.

Coordinated embryo and endosperm development determines wheat seed yield and grain quality. We present a strand-specific time-series transcriptome atlas of wheat seed, profiling embryo and endosperm from 2 to 38 days after pollination. The dataset captures 75,554 expressed genes and 24,079 long noncoding RNAs.

Intra-specific interactions disrupted the nutrient dynamics and multifactorial responses (drought and salinity) in Dalbergia odorifera in a pure planting system.

Woody species associated with coastal shelter forest ecosystems often face multiple types of stress including drought and salinity. The impact of these abiotic stresses when they occur individually, and in combination, can have substantial impacts on tree species distribution and survival. The effect of stressors can also be influenced by intra-specific biotic factors.

An elite allele TaDT1-A enhances drought tolerance via mediating autophagic pathways in wheat.

Drought stress constitutes a major threat to global wheat production. Identification of the genetic components underlying drought tolerance in wheat is highly important. Through a genome-wide association study, we identify a natural allele of the zinc finger-type transcription factor TaDT1-A on chromosome 2 A of the wheat genome that confers drought tolerance without imposing trade-offs between tolerance and yield.

Near-complete assembly and comprehensive annotation of the wheat Chinese Spring genome.

A complete reference genome assembly is crucial for biological research and genetic improvement. Owing to its large size and highly repetitive nature, there are numerous gaps in the globally used wheat Chinese Spring (CS) genome assembly. In this study, we generated a 14.

Natural variation in TaERF-A1 confers semi-dwarf and lodging-resistant plant architecture in wheat.

The introduction of Reduced height (Rht) genes into wheat varieties has been pivotal in developing semi-dwarf plant architectures, significantly improving lodging resistance and harvest indices. Therefore, identifying new Rht gene resources for breeding semi-dwarf wheat cultivars has been a key strategy for ensuring high and stable grain yields since the 1960s. In this study, we report the map-based cloning of TaERF-A1, which encodes an AP2/ERF (APETALA2/ethylene responsive factor) transcription factor that acts as a positive regulator of wheat stem elongation, as a novel gene that regulates plant height and spike length.

Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing.

Background: The massive structural variations and frequent introgression highly contribute to the genetic diversity of wheat, while the huge and complex genome of polyploid wheat hinders efficient genotyping of abundant varieties towards accurate identification, management, and exploitation of germplasm resources.

Results: We develop a novel workflow that identifies 1240 high-quality large copy number variation blocks (CNVb) in wheat at the pan-genome level, demonstrating that CNVb can serve as an ideal DNA fingerprinting marker for discriminating massive varieties, with the accuracy validated by PCR assay. We then construct a digitalized genotyping CNVb map across 1599 global wheat accessions.

Reshaped DNA methylation cooperating with homoeolog-divergent expression promotes improved root traits in synthesized tetraploid wheat.

Polyploidization is a major event driving plant evolution and domestication. However, how reshaped epigenetic modifications coordinate gene transcription to generate phenotypic variations during wheat polyploidization is currently elusive. Here, we profiled transcriptomes and DNA methylomes of two diploid wheat accessions (SS and AA) and their synthetic allotetraploid wheat line (SSAA), which displayed elongated root hair and improved root capability for nitrate uptake and assimilation after tetraploidization.

Physio-biochemical and metabolomic responses of the woody plant Dalbergia odorifera to salinity and waterlogging.

Background: Trees have developed a broad spectrum of molecular mechanisms to counteract oxidative stress. Secondary metabolites via phenolic compounds emblematized the hidden bridge among plant kingdom, human health, and oxidative stress. Although studies have demonstrated that abiotic stresses can increase the production of medicinal compounds in plants, research comparing the efficiency of these stresses still needs to be explored.

Dalbergia odorifera undergoes massive molecular shifts in response to waterlogging combined with salinity.

Field and greenhouse studies attempting to describe the molecular responses of plant species under waterlogging (WL) combined with salinity (ST) are almost nonexistent. We integrated transcriptional, metabolic, and physiological responses involving several crucial transcripts and common differentially expressed genes and metabolites in fragrant rosewood (Dalbergia odorifera) leaflets to dissect plant-specific molecular responses and patterns under WL combined with ST (SWL). We discovered that the synergistic pattern of the transcriptional response of fragrant rosewood under SWL was exclusively characterized by the number of regulated transcripts.

Intra- and interspecific ecophysiological responses to waterlogging stress in two contrasting waterlogging-tolerant arbor species.

At present, establishing planted forests, typically composed of not more than two tree species, to avoid forest losses has received increasing attention. In addition, investigating the impact of environmental stress such as waterlogging on different planting patterns is essential for improving wetland ecosystem resilience. Knowledge about the impact of waterlogging on planted forests is crucial for developing strategies to mitigate its adverse effects.

Deciphering the evolution and complexity of wheat germplasm from a genomic perspective.

Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research.

Pangenome-based trajectories of intracellular gene transfers in Poaceae unveil high cumulation in Triticeae.

Intracellular gene transfers (IGTs) between the nucleus and organelles, including plastids and mitochondria, constantly reshape the nuclear genome during evolution. Despite the substantial contribution of IGTs to genome variation, the dynamic trajectories of IGTs at the pangenomic level remain elusive. Here, we developed an approach, IGTminer, that maps the evolutionary trajectories of IGTs using collinearity and gene reannotation across multiple genome assemblies.

Exogenous ABA and IAA modulate physiological and hormonal adaptation strategies in Cleistocalyx operculatus and Syzygium jambos under long-term waterlogging conditions.

Background: The mechanisms of abscisic acid (ABA) and auxin (IAA) in inducing adventitious root (AR) formation, biomass accumulation, and plant development under long-term waterlogging (LT-WL) conditions are largely unexplored. This study aimed to determine the roles of exogenous application of ABA and IAA in two woody plants (Cleistocalyx operculatus and Syzygium jambos) under LT-WL conditions. A pot experiment was conducted using a complete randomized design with two factors: (i) LT-WL and (ii) application of exogenous phytohormones (ABA and IAA) for 120 d.

Dissecting the below- and aboveground specific responses of two waterlogging-tolerant arbor species to nutrient supply under waterlogging conditions.

Although environmental factors affecting adventitious root (AR) formation have been examined, how nutrient status affects ARs under waterlogging conditions remains unclear. In this study, plants' performance in responding to AR regulation based on nutrient supply was investigated in terms of plant morphology, physiology and AR traits. Results indicated that Cleistocalyx operculatus possesses higher waterlogging tolerance than Syzygium cumini according to the waterlogging tolerance coefficient, mainly because of the higher fresh weight, porosity and length of AR in C.

Competitive Relationship Between and Under Well-Watered Conditions Transforms Into a Mutualistic Relationship Under Waterlogging Stress.

Competition and abiotic stress such as waterlogging (WL) represent main factors limiting plant growth and determining plant resistance and distribution patterns in wetland ecosystems. One of the basic steps for wetland restoration is to plant trees to ensure a quicker recovery and prevent erosion. Plant survival and adaptation are considered criteria of principal priority for the screening of plant species for wetland ecosystem restoration.

Glucose Fluctuations Aggravate Myocardial Fibrosis the Nuclear Factor-κB-Mediated Nucleotide-Binding Oligomerization Domain-Like Receptor Protein 3 Inflammasome Activation.

Background: Glucose fluctuations may be associated with myocardial fibrosis. This study aimed to investigate the underlying mechanisms of glucose fluctuation-related myocardial fibrosis.

Methods: Streptozotocin (STZ)-injected type 1 diabetic rats were randomized to five groups: the controlled blood glucose (CBG) group, uncontrolled blood glucose (UBG) group, fluctuated blood glucose (FBG) group, FBG rats injected with 0.

Comparable and adaptable strategies to waterlogging stress regulated by adventitious roots between two contrasting species.

Cleistocalyx operculatus and Syzygium cumini possess a certain waterlogging tolerance. However, the comparable and adaptable strategies to waterlogging stress between these two species on the basis of waterlogging adventitious root (AR) regulation were still unclear. In this study, the plant performance in response to AR regulation based on AR removal (AR-R) and exogenous hormone application was investigated in terms of plant morphology, physiology, photosynthesis and AR traits.

Drought and Nitrogen Application Modulate the Morphological and Physiological Responses of to Different Niche Neighbors.

Mixed stands can be more productive if growth facilitation via niche segregation occurs. T. Chen, a tropical tree species endemic to Hainan Island with great economic values, belongs to the family Leguminosae.

Neighbors, Drought, and Nitrogen Application Affect the Root Morphological Plasticity of .

In forest systems, neighbor-induced root morphological plasticity (RMP) is species specific and environment dependent. However, related studies on leguminous woody trees remain sparse. The objectives of this study were to evaluate the root morphological response of the leguminous woody T.

Gly Betaine Surpasses Melatonin to Improve Salt Tolerance in .

Salinity is one of the most serious factors limiting plant growth which can provoke significant losses in agricultural crop production, particularly in arid and semi-arid areas. This study aimed to investigate whether melatonin (MT; 0.05 and 0.

Cardiovascular disease-specific mortality in 270,618 patients with non-small cell lung cancer.

Background: This study aimed to investigate the trend of cardiovascular disease (CVD)-specific mortality in patients with non-small cell lung cancer (NSCLC) and identify prognostic factors for CVD-specific death in stage NSCLC patients.

Methods: In this study, 270,618 NSCLC patients were collected from the Surveillance, Epidemiology, and End Results database. CVD- and NSCLC-specific cumulative mortality and proportion of death were calculated and graphically displayed to describe the probability of specific endpoints.

A method to screen left ventricular dysfunction through ECG based on convolutional neural network.

Objective: This study aims to develop an artificial intelligence-based method to screen patients with left ventricular ejection fraction (LVEF) of 50% or lesser using electrocardiogram (ECG) data alone.

Methods: Convolutional neural network (CNN) is a class of deep neural networks, which has been widely used in medical image recognition. We collected standard 12-lead ECG and transthoracic echocardiogram (TTE) data including the LVEF value.