Plant-LncPipe: a computational pipeline providing significant improvement in plant lncRNA identification.

Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited.

Moderate Salinity Stress Affects Rice Quality by Influencing Expression of Amylose- and Protein-Content-Associated Genes.

Salinity is an environmental stress that severely impacts rice grain yield and quality. However, limited information is available on the molecular mechanism by which salinity reduces grain quality. In this study, we investigated the milling, appearance, eating and cooking, and nutritional quality among three japonica rice cultivars grown either under moderate salinity with an electrical conductivity of 4 dS/m or under non-saline conditions in a paddy field in Dongying, Shandong, China.

Transcriptome profiling of aerial and subterranean peanut pod development.

Peanut (Arachis hypogaea) showcases geocarpic behavior, transitioning from aerial flowering to subterranean seed development. We recently obtained an atavistic variant of this species, capable of producing aerial and subterranean pods on a single plant. Notably, although these pod types share similar vigor levels, they exhibit distinct differences in their physical aspects, such as pod size, color, and shell thickness.

Comparative molecular dynamics simulations provided insights into the mechanisms of cold-adaption of alginate lyases from the PL7 family.

Alginate is an important polysaccharide that is abundant in the marine environments, including the Polar Regions, and bacterial alginate lyases play key roles in its degradation. Many reported alginate lyases show characteristics of cold-adapted enzymes, including relatively low temperature optimum of activities (T) and low thermal stabilities. However, the cold-adaption mechanisms of alginate lyases remain unclear.

Identification and Transcriptome Analysis of a Novel Allelic Mutant of in Rice.

Leaf morphology is a crucial aspect of plant architecture, yet the molecular mechanisms underlying leaf development remain incompletely understood. In this study, a narrow leaf mutant, was identified in rice ( L.), exhibiting pleiotropic developmental defects.

Physiological and biochemical mechanisms underlying the role of anthocyanin in acquired tolerance to salt stress in peanut ( L.).

Anthocyanin is an important pigment that prevents oxidative stress and mediates adaptation of plants to salt stress. Peanuts with dark red and black testa are rich in anthocyanin. However, correlation between salt tolerance and anthocyanin content in black and dark red testa peanuts is unknown.

High-density bin-based genetic map reveals a 530-kb chromosome segment derived from wild peanut contributing to late leaf spot resistance.

Twenty-eight QTLs for LLS disease resistance were identified using an amphidiploid constructed mapping population, a favorable 530-kb chromosome segment derived from wild species contributes to the LLS resistance. Late leaf spot (LLS) is one of the major foliar diseases of peanut, causing serious yield loss and affecting the quality of kernel and forage. Some wild Arachis species possess higher resistance to LLS as compared with cultivated peanut; however, ploidy level differences restrict utilization of wild species.

GTPase activity of porcine Mx1 plays a dominant role in inhibiting the N-Nsp9 interaction and thus inhibiting PRRSV replication.

Unlabelled: Porcine Mx1 is a type of interferon-induced GTPase that inhibits the replication of certain RNA viruses. However, the antiviral effects and the underlying mechanism of porcine Mx1 for porcine reproductive and respiratory syndrome virus (PRRSV) remain unknown. In this study, we demonstrated that porcine Mx1 could significantly inhibit PRRSV replication in MARC-145 cells.

Three novel species of (Distoseptisporales, Aquapteridosporaceae) from freshwater habitats in Tibetan Plateau, China.

During an investigation of lignicolous freshwater fungi in the Tibetan Plateau, three taxa were collected from freshwater habitats in Xizang, China. The new species possess polyblastic, sympodial, denticles conidiogenous cells and fusiform, septate, with or without sheath conidial, that fit within the generic concept of , and multi-gene phylogeny placed these species within . Detailed morphological observations clearly demarcate three of these from extant species and are hence described as new taxa.

Different roles of Ca and chitohexose in peanut () photosynthetic responses to PAMP-immunity.

Background: During active infections, plants prevent further spread of pathogenic microorganisms by inducing the rapid programmed death of cells around the infection point. This phenomenon is called the hypersensitive response and is a common feature of plant immune responses. Plants recognize conserved structures of pathogenic microorganisms, called pathogen-associated molecular patterns (PAMPs), .

Co-expression of metabolites and sensory attributes through weighted correlation network analysis to explore flavor-contributing factors in various spp. Cultivars.

Flavor profiles of various spp. cultivars exhibit significant variations, yet the underlying flavor-contributing factors remain elusive. In this investigation, a comprehensive approach encompassing metabolomics analysis, volatile fingerprint analysis, and descriptive sensory analysis was employed to elucidate the flavor disparities among Nanguoli, Korla fragrant pear, and Qiuyueli cultivars and uncover potential flavor contributor.

N-methyladenosine mRNA methylation positively regulated the response of poplar to salt stress.

As the most abundant form of methylation modification in messenger RNA (mRNA), the distribution of N-methyladenosine (mA) has been preliminarily revealed in herbaceous plants under salt stress, but its function and mechanism in woody plants were still unknown. Here, we showed that global mA levels increased during poplar response to salt stress. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) revealed that mA significantly enriched in the coding sequence region and 3'-untranslated regions in poplar, by recognising the conserved motifs, AGACU, GGACA and UGUAG.

Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn (), an oil-producing tree with significant deployment values.

(yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown.

Aging of polypropylene plastic and impacts on microbial community structure in constructed wetlands.

The COVID-19 pandemic has resulted in a substantial surge in the usage of disposable plastic masks, generating a significant volume of waste and contributing to environmental pollution. Wetland ecosystems function as crucial repositories for terrestrial pollutants and are highly effective in retaining disposable masks composed mainly of PP material. These masks can endure extended periods in wetlands, experiencing natural degradation that may have potential implications on wetland ecosystems.

Nitrogen application in pod zone improves yield and quality of two peanut cultivars by modulating nitrogen accumulation and metabolism.

Cultivated peanut (Arachis hypogaea L.) represents one of the most important oil and cash crops world-widely. Unlike many other legumes, peanuts absorb nitrogen through their underground pods.

Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations.

Accurate subgenome phasing is crucial for understanding the origin, evolution and adaptive potential of polyploid genomes. SubPhaser and WGDI software are two common methodologies for subgenome phasing in allopolyploids, particularly in scenarios lacking known diploid progenitors. Triggered by a recent debate over the subgenomic origins of the cultivated octoploid strawberry, we examined four well-documented complex allopolyploidy cases as benchmarks, to evaluate and compare the accuracy of the two software.

Source-sink coordinated peanut cultivar increases yield and kernel protein content through enhancing photosynthetic characteristics and regulating carbon and nitrogen metabolisms.

The grain yield of crops is determined by the synergistic interaction between source activity and sink capacity. However, source-sink interactions are far from being fully understood of peanut. Therefore, a 2-year field study (2018-2019) was conducted to compare differences in photosynthetic characteristics, carbon and nitrogen metabolism, and yield and quality of different source-sink peanut varieties.

Arbuscular mycorrhizal fungi increased peanut ( L.) yield by changing the rhizosphere microbial community structure in saline-alkali soil.

Arbuscular mycorrhizal fungi (AMF) have demonstrated the potential to enhance the saline-alkali tolerance in plants. Nevertheless, the extent to which AMF can ameliorate the tolerance of salt-sensitive plants to alkaline conditions necessitates further investigation. The current study is primarily centered on elucidating the impact of AMF on the growth of the Huayu22 (H22) when cultivated in saline-alkaline soil.

Fu Brick Tea as a Staple Food Supplement Attenuates High Fat Diet Induced Obesity in Mice.

Fu brick tea (FBT), a product of microbial fermentation from primary dark tea, also known as raw material tea (RMT), has been extensively studied for its functional properties. However, its potential as a staple food supplement for weight loss remains poorly understood. This study compared the weight loss effects of orlistat, traditional plain noodles (NN), and noodles supplemented with varying amounts of RMT (RMTN) and FBT (FBTN), with the aim to elucidate their lipid-reducing effects and underlying mechanisms.

The response of LncRNAs associated with photosynthesis-and pigment synthesis-related genes to green light in Chlamydomonas reinhardtii.

The quality of light is an important abiotic factor that affects the growth and development of green plants. Ultraviolet, red, blue, and far-red light all have demonstrated roles in regulating green plant growth and development, as well as light morphogenesis. However, the mechanism underlying photosynthetic organism responses to green light throughout the life of them are not clear.

The Na /Ca antiporter slr0681 affects carotenoid production in Synechocystis sp. PCC 6803 under high-light stress.

Background: Carotenoids play key roles in photosynthesis and are widely used in foods as natural pigments, antioxidants, and health-promoting compounds. Enhancing carotenoid production in microalgae via biotechnology has become an important area of research.

Results: We knocked out the Na /Ca antiporter gene slr0681 in Synechocystis sp.