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BACKGROUND AND AIMS: Intestinal farnesoid X receptor (FXR) plays a critical role in alcohol-associated liver disease (ALD). We aimed to investigate whether alcohol-induced dysbiosis increased intestinal microRNA194 (miR194) that suppressed Fxr transcription and whether Lactobacillus rhamnosus GG-derived exosome-like nanoparticles (LDNPs) protected against ALD through regulation of intestinal miR194-FXR signaling in mice. APPROACH AND RESULTS: Binge-on-chronic alcohol exposure mouse model was utilized. In addition to the decreased ligand-mediated FXR activation, alcohol feeding repressed intestinal Fxr transcription and increased miR194 expression. This transcriptional suppression of Fxr by miR194 was confirmed in intestinal epithelial Caco-2 cells and mouse enteriods. The alcohol feeding-reduced intestinal FXR activation was further demonstrated by the reduced FXR reporter activity in fecal samples and by the decreased fibroblast growth factor 15 (Fgf15) messenger RNA (mRNA) in intestine and protein levels in the serum, which caused an increased hepatic bile acid synthesis and lipogeneses. We further demonstrated that alcohol feeding increased-miR194 expression was mediated by taurine-upregulated gene 1 (Tug1) through gut microbiota regulation of taurine metabolism. Importantly, 3-day oral administration of LDNPs increased bile salt hydrolase (BSH)-harboring bacteria that decreased conjugated bile acids and increased gut taurine concentration, which upregulated Tug1, leading to a suppression of intestinal miR194 expression and recovery of FXR activation. Activated FXR upregulated FGF15 signaling and subsequently reduced hepatic bile acid synthesis and lipogenesis and attenuated ALD. These protective effects of LDNPs were eliminated in intestinal FxrΔIEC and Fgf15-/- mice. We further showed that miR194 was upregulated, whereas BSH activity and taurine levels were decreased in fecal samples of patients with ALD. CONCLUSIONS: Our results demonstrated that gut microbiota-mediated miR194 regulation contributes to ALD pathogenesis and to the protective effects of LDNPs through modulating intestinal FXR signaling.
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Hepatopatias Alcoólicas , MicroRNAs , Animais , Humanos , Camundongos , Ácidos e Sais Biliares/metabolismo , Células CACO-2 , Etanol/farmacologia , Fígado/patologia , Hepatopatias Alcoólicas/metabolismo , Camundongos Endogâmicos C57BL , MicroRNAs/metabolismo , Receptores Citoplasmáticos e Nucleares/metabolismo , Taurina/farmacologia , NanopartículasRESUMO
Desilication in alkaline medium has been widely used in construction of hierarchical zeolites for industrially relevant catalytic processes. The built of hierarchy in zeolites, especially with low aluminum stability or high Si/Al ratio, often suffers from uncontrolled destruction of zeolitic framework, accompanied by a significant loss of microporous domains and intrinsic acidity after desilication. Here, we report a novel and simple methodology for preparation of hierarchical zeolites with highly complete framework and minimum sacrifice of microporosity and acidity. The pre-impregnated amines in zeolite micropores act as inner pore-directing agents (iPDAs), largely protecting the zeolitic framework and moderating the silicon extraction during the alkaline treatment. The resulting hierarchical zeolites exhibit high crystallinity, tunable hierarchy, stable framework, and well-preserved acidity, endowing them with significantly improved mass transport properties and enhanced activities in catalytic conversion of methanol or furfural.
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Jasminum sambac is a well-known plant for its attractive and exceptional fragrance, the flowers of which are used to produce scented tea. Jasmonate (JA), an important plant hormone was first identified in Jasminum species. Jasmine plants contain abundant JA naturally, of which the molecular mechanisms of synthesis and accumulation are not clearly understood. Here, we report a telomere-to-telomere consensus assembly of a double-petal J. sambac genome along with two haplotype-resolved genomes. We found that gain-and-loss, positive selection, and allelic specific expression of aromatic volatile-related genes contributed to the stronger flower fragrance in double-petal J. sambac compared with single- and multi-petal jasmines. Through comprehensive comparative genomic, transcriptomic, and metabolomic analyses of double-petal J. sambac, we revealed the genetic basis of the production of aromatic volatiles and salicylic acid (SA), and the accumulation of JA under non-stress conditions. We identified several key genes associated with JA biosynthesis, and their non-stress related activities lead to extraordinarily high concentrations of JA in tissues. High JA synthesis coupled with low degradation in J. sambac results in accumulation of high JA under typical environmental conditions, similar to the accumulation mechanism of SA. This study offers important insights into the biology of J. sambac, and provides valuable genomic resources for further utilization of natural products.
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Jasminum , Jasminum/genética , Perfilação da Expressão Gênica , Transcriptoma , OdorantesRESUMO
African swine fever (ASF) is a highly contagious viral disease of domestic pigs and wild boars. For disease surveillance and control, we developed a rapid and easy luciferase immunoprecipitation assay (MB-LIPS) to detect ASF virus (ASFV) antibody. The MB-LIPS is based on magnetic beads modified with protein A/G and the recombinant fusion protein of ASFV p30 and luciferase, where p30 functioned as the recognition element and luciferase as the signal component. Incubation and washing could be finished automatically on a machine with magnetic rods. Under optimal conditions, the MB-LIPS showed 96.3% agreement to a commercial enzyme-linked immunosorbent assay (ELISA) kit for detecting ASFV antibody in swine sera. Analyzing serial dilutions of a swine serum sample showed that the MP-LIPS assay was 4 times more sensitive than the ELISA kit. The whole run of the MB-LIPS could be completed within 30 min. With its high sensitivity and simple operation, the MB-LIPS platform has great potential to be used for the detection of ASFV antibody and ASF control in small labs and farms.
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Vírus da Febre Suína Africana , Febre Suína Africana , Febre Suína Africana/diagnóstico , Vírus da Febre Suína Africana/genética , Animais , Imunoprecipitação , Luciferases/genética , Sus scrofa , SuínosRESUMO
BACKGROUND AND AIMS: Cholestatic liver disease is characterized by gut dysbiosis and excessive toxic hepatic bile acids (BAs). Modification of gut microbiota and repression of BA synthesis are potential strategies for the treatment of cholestatic liver disease. The purpose of this study was to examine the effects and to understand the mechanisms of the probiotic Lactobacillus rhamnosus GG (LGG) on hepatic BA synthesis, liver injury, and fibrosis in bile duct ligation (BDL) and multidrug resistance protein 2 knockout (Mdr2-/- ) mice. APPROACH AND RESULTS: Global and intestine-specific farnesoid X receptor (FXR) inhibitors were used to dissect the role of FXR. LGG treatment significantly attenuated liver inflammation, injury, and fibrosis with a significant reduction of hepatic BAs in BDL mice. Hepatic concentration of taurine-ß-muricholic acid (T-ßMCA), an FXR antagonist, was markedly increased in BDL mice and reduced in LGG-treated mice, while chenodeoxycholic acid, an FXR agonist, was decreased in BDL mice and normalized in LGG-treated mice. LGG treatment significantly increased the expression of serum and ileum fibroblast growth factor 15 (FGF-15) and subsequently reduced hepatic cholesterol 7α-hydroxylase and BA synthesis in BDL and Mdr2-/- mice. At the molecular level, these changes were reversed by global and intestine-specific FXR inhibitors in BDL mice. In addition, LGG treatment altered gut microbiota, which was associated with increased BA deconjugation and increased fecal and urine BA excretion in both BDL and Mdr2-/- mice. In vitro studies showed that LGG suppressed the inhibitory effect of T-ßMCA on FXR and FGF-19 expression in Caco-2 cells. CONCLUSION: LGG supplementation decreases hepatic BA by increasing intestinal FXR-FGF-15 signaling pathway-mediated suppression of BA de novo synthesis and enhances BA excretion, which prevents excessive BA-induced liver injury and fibrosis in mice.
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Ácidos e Sais Biliares , Colestase , Fatores de Crescimento de Fibroblastos/metabolismo , Lacticaseibacillus rhamnosus/metabolismo , Cirrose Hepática , Receptores Citoplasmáticos e Nucleares , Subfamília B de Transportador de Cassetes de Ligação de ATP/genética , Animais , Ácidos e Sais Biliares/biossíntese , Ácidos e Sais Biliares/metabolismo , Ácido Quenodesoxicólico/farmacologia , Colestase/complicações , Colestase/metabolismo , Colestase/terapia , Ácidos Cólicos/farmacologia , Microbioma Gastrointestinal/efeitos dos fármacos , Humanos , Intestinos/microbiologia , Cirrose Hepática/etiologia , Cirrose Hepática/prevenção & controle , Camundongos , Camundongos Knockout , Probióticos/farmacologia , Receptores Citoplasmáticos e Nucleares/agonistas , Receptores Citoplasmáticos e Nucleares/antagonistas & inibidores , Receptores Citoplasmáticos e Nucleares/metabolismo , Transdução de Sinais/efeitos dos fármacos , Membro 4 da Subfamília B de Transportadores de Cassetes de Ligação de ATPRESUMO
Alcoholic liver disease (ALD) is associated with gut dysbiosis and hepatic inflammasome activation. While it is known that antimicrobial peptides (AMPs) play a critical role in the regulation of bacterial homeostasis in ALD, the functional role of AMPs in the alcohol-induced inflammasome activation is unclear. The aim of this study was to determine the effects of cathelicidin-related antimicrobial peptide (CRAMP) on inflammasome activation in ALD. CRAMP knockout (Camp-/-) and wild-type (WT) mice were subjected to binge-on-chronic alcohol feeding and synthetic CRAMP peptide was administered. Serum/plasma and hepatic tissue samples from human subjects with alcohol use disorder and/or alcoholic hepatitis were analyzed. CRAMP deficiency exacerbated ALD with enhanced inflammasome activation as shown by elevated serum interleukin (IL)-1ß levels. Although Camp-/- mice had comparable serum endotoxin levels compared to WT mice after alcohol feeding, hepatic lipopolysaccharide (LPS) binding protein (LBP) and cluster of differentiation (CD) 14 were increased. Serum levels of uric acid (UA), a Signal 2 molecule in inflammasome activation, were positively correlated with serum levels of IL-1ß in alcohol use disorder patients with ALD and were increased in Camp-/- mice fed alcohol. In vitro studies showed that CRAMP peptide inhibited LPS binding to macrophages and inflammasome activation stimulated by a combination of LPS and UA. Synthetic CRAMP peptide administration decreased serum UA and IL-1ß concentrations and rescued the liver from alcohol-induced damage in both WT and Camp-/- mice. In summary, CRAMP exhibited a protective role against binge-on-chronic alcohol-induced liver damage via regulation of inflammasome activation by decreasing LPS binding and UA production. CRAMP administration may represent a novel strategy for treating ALD. © 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Peptídeos Catiônicos Antimicrobianos/metabolismo , Inflamassomos/metabolismo , Hepatopatias Alcoólicas/metabolismo , Fígado/metabolismo , Animais , Peptídeos Catiônicos Antimicrobianos/genética , Biomarcadores/sangue , Disbiose/genética , Disbiose/metabolismo , Disbiose/patologia , Humanos , Inflamassomos/genética , Interleucina-1beta/sangue , Fígado/patologia , Hepatopatias Alcoólicas/genética , Hepatopatias Alcoólicas/patologia , Masculino , Camundongos , Camundongos Knockout , Estresse Oxidativo/genética , Ácido Úrico/sangue , CatelicidinasRESUMO
Wastewater-based epidemiology (WBE) is a valuable complement to clinical monitoring, allowing for effective surveillance of viral infections in populations, and tracking the presence and the epidemiological dynamics of various infectious pathogens in communities. However, virus loads are usually low-abundant in wastewater, and current virus concentration methods for WBE are laborious and time-consuming with low recovery efficiency. To address these challenges, we have developed a magnetic bead-based semi-automated method involving extraction and purification to directly concentrate viral nucleic acids from sewage within 55 min. Prior to concentration, 0.5 % LDS was introduced to pretreat wastewater to inactivate viruses and release viral nucleic acids from both liquid and solid fractions to improve recovery. Under optimal conditions, the concentration method combined with reverse transcription-quantitative polymerase chain reaction (RT-qPCR) can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA added exogenously in wastewater as low as 4.9 copies/mL within 2.5 h, with an average recovery rate exceeding 80 %. Testing real sewages proved the applicability of the method to detect multiple viruses in different sewages. Additionally, variants of SARS-CoV-2 were successfully identified by multiplex amplicon sequencing in two samples. In conclusion, the new method could provide a much more efficient way for WBE of pathogenic viruses in various sewages.
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Most fresh bananas belong to the Cavendish and Gros Michel subgroups. Here, we report chromosome-scale genome assemblies of Cavendish (1.48 Gb) and Gros Michel (1.33 Gb), defining three subgenomes, Ban, Dh and Ze, with Musa acuminata ssp. banksii, malaccensis and zebrina as their major ancestral contributors, respectively. The insertion of repeat sequences in the Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 RGA2 (resistance gene analog 2) promoter was identified in most diploid and triploid bananas. We found that the receptor-like protein (RLP) locus, including Foc race 1-resistant genes, is absent in the Gros Michel Ze subgenome. We identified two NAP (NAC-like, activated by apetala3/pistillata) transcription factor homologs specifically and highly expressed in fruit that directly bind to the promoters of many fruit ripening genes and may be key regulators of fruit ripening. Our genome data should facilitate the breeding and super-domestication of bananas.
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Fusarium , Musa , Musa/genética , Fusarium/genética , Triploidia , Melhoramento Vegetal , Fatores de Transcrição/genética , Doenças das Plantas/genéticaRESUMO
Polyploidy has been observed throughout major eukaryotic clades and has played a vital role in the evolution of angiosperms. Recent polyploidizations often result in highly complex genome structures, posing challenges to genome assembly and phasing. Recent advances in sequencing technologies and genome assembly algorithms have enabled high-quality, near-complete chromosome-level assemblies of polyploid genomes. Advances in novel sequencing technologies include highly accurate single-molecule sequencing with HiFi reads, chromosome conformation capture with Hi-C technique, and linked reads sequencing. Additionally, new computational approaches have also significantly improved the precision and reliability of polyploid genome assembly and phasing, such as HiCanu, hifiasm, ALLHiC, and PolyGembler. Herein, we review recently published polyploid genomes and compare the various sequencing, assembly, and phasing approaches that are utilized in these genome studies. Finally, we anticipate that accurate and telomere-to-telomere chromosome-level assembly of polyploid genomes could ultimately become a routine procedure in the near future.
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Algoritmos , Eucariotos , Humanos , Reprodutibilidade dos Testes , Células Eucarióticas , PoliploidiaRESUMO
Cell wall polysaccharides and physicochemical properties are the major quality characteristics of fruit, but they are significantly affected by the postharvest disease. In this study, the influence of Alternaria alternata-induced disease on the contents of cell wall polysaccharides and physicochemical properties in 'Korla' pear flesh during storage, as well as their relationships of the optical absorption (µa) and reduced scattering (µs') were explored. The infected pear had lower individual sugars, covalent-soluble pectin, cellulose and hemicellulose contents than the healthy ones. The successive decreases of µa and increases of µs' in pears were observed while the process of pathogen infection. Path-coefficient analysis indicated the ionic-soluble pectin was the main reason responsible for the change of µs' in infected pear at 675 nm and 980 nm. This study indicated the optical properties have the possibility to present the physicochemical characteristics and cell wall polysaccharides of pears during postharvest pathogen infection.
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Pyrus , Pyrus/química , Polissacarídeos/química , Parede Celular/química , Pectinas/análise , Alternaria , Frutas/químicaRESUMO
In this work, a single integrating sphere system was applied to characterize the optical absorption (µa) and reduced scattering (µs') properties (550 - 1050 nm) in winter jujube flesh infected by Alternaria alternata during storage at 4 and 20 °C, respectively. Meanwhile, physical (L*, a*, weight loss) and biochemical characteristics (soluble solids content, titratable acids, chlorophyll, total phenolic, and ascorbic acid) of winter jujubes were measured. Among them, chlorophyll, weight loss and ascorbic acid were highly correlated with µa at 680 nm, 690 nm, while chlorophyll and a* had the best correlations with µs' at 700 - 920 nm. These optimal optical properties were proved efficiently contributed to the disease detection of winter jujubes after 12 days at 4 °C and 3 days at 20 °C during storage, with satisfactory discrimination accuracies (acc > 93.75 %). Consequently, optical properties in Vis-NIR region were available to detect the postharvest disease in winter jujubes.
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Ziziphus , Ziziphus/química , Alternaria , Ácido Ascórbico , ClorofilaRESUMO
In this work, the potential of a hyperspectral imaging (HSI) system for the detection of black spot disease on winter jujubes infected by Alternaria alternata during postharvest storage was investigated. The HSI images were acquired using two systems in the visible and near-infrared (Vis-NIR, 400-1000 nm) and short-wave infrared (SWIR, 1000-2000 nm) spectral regions. Meanwhile, the change of physical (peel color, weight loss) and chemical parameters (soluble solids content, chlorophyll) and the microstructure of winter jujubes during the pathogenic process were measured. The results showed the spectral reflectance of jujubes in both the Vis-NIR and SWIR wavelength ranges presented an overall downtrend during the infection. Partial least squares discriminant models (PLS-DA) based on the HSI spectra in Vis-NIR and SWIR regions of jujubes both gave satisfactory discrimination accuracy for the disease detection, with classification rates of over 92.31% and 91.03%, respectively. Principal component analysis (PCA) was carried out on the HSI images of jujubes to visualize their infected areas during the pathogenic process. The first principal component of the HSI spectra in the Vis-NIR region could highlight the diseased areas of the infected jujubes. Consequently, Vis-NIR HSI and NIR HSI techniques had the potential to detect the black spot disease on winter jujubes during the postharvest storage, and the Vis-NIR HSI spectral information could visualize the diseased areas of jujubes during the pathogenic process.
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Wax apple (Syzygium samarangense) is an economically important fruit crop with great potential value to human health because of its richness in antioxidant substances. Here, we present a haplotype-resolved autotetraploid genome assembly of the wax apple with a size of 1.59 Gb. Comparative genomic analysis revealed three rounds of whole-genome duplication (WGD) events, including two independent WGDs after WGT-γ. Resequencing analysis of 35 accessions partitioned these individuals into two distinct groups, including 28 landraces and seven cultivated species, and several genes subject to selective sweeps possibly contributed to fruit growth, including the KRP1-like, IAA17-like, GME-like, and FLACCA-like genes. Transcriptome analysis of three different varieties during flower and fruit development identified key genes related to fruit size, sugar content, and male sterility. We found that AP2 also affected fruit size by regulating sepal development in wax apples. The expression of sugar transport-related genes (SWEETs and SUTs) was high in 'ZY', likely contributing to its high sugar content. Male sterility in 'Tub' was associated with tapetal abnormalities due to the decreased expression of DYT1, TDF1, and AMS, which affected early tapetum development. The chromosome-scale genome and large-scale transcriptome data presented in this study offer new valuable resources for biological research on S. samarangense and shed new light on fruit size control, sugar metabolism, and male sterility regulatory metabolism in wax apple.
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In plants, 5mC DNA methylation is an important and conserved epistatic mark involving genomic stability, gene transcriptional regulation, developmental regulation, abiotic stress response, metabolite synthesis, etc. However, the roles of 5mC DNA methylation modification (5mC methylation) in tea plant growth and development (in pre-harvest processing) and flavor substance synthesis in pre- and post-harvest processing are unknown. We therefore conducted a comprehensive methylation analysis of four key pre-harvest tissues (root, leaf, flower, and fruit) and two processed leaves during oolong tea post-harvest processing. We found that differential 5mC methylation among four key tissues is closely related to tissue functional differentiation and that genes expressed tissue-specifically, responsible for tissue-specific functions, maintain relatively low 5mC methylation levels relative to non-tissue-specifically expressed genes. Importantly, hypomethylation modifications of CsAlaDC and TS/GS genes in roots provided the molecular basis for the dominant synthesis of theanine in roots. In addition, integration of 5mC DNA methylationomics, metabolomics, and transcriptomics of post-harvest leaves revealed that content changes in flavor metabolites during oolong tea processing were closely associated with transcription level changes in corresponding metabolite synthesis genes, and changes in transcript levels of these important synthesis genes were strictly regulated by 5mC methylation. We further report that some key genes during processing are regulated by 5mC methylation, which can effectively explain the content changes of important aroma metabolites, including α-farnesene, nerolidol, lipids, and taste substances such as catechins. Our results not only highlight the key roles of 5mC methylation in important flavor substance synthesis in pre- and post-harvest processing, but also provide epimutation-related gene targets for future improvement of tea quality or breeding of whole-tissue high-theanine varieties.
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The study aimed to investigate the effect of isoliquiritigenin (ISL) on model of alcoholic liver fibrosis (ALF). C57BL/6 mice were used to establish animal model of ALF, HSC-T6 cells were used to establish alcohol-activated cell model, and tandem mass tag (TMT) assays were used to analyze the proteome. The results showed that ISL obviously alleviated hepatic fibrosis in model mice. ISL visually improved the area of liver pathological stasis and deposition of fibrillar collagen (Sirius Red staining, Masson staining), inhibited the mRNA expression levels of interleukin 6 (IL-6), tumor necrosis factor α (TNF-α) and interleukin 1ß (IL-1ß) in liver tissues. ISL down-regulated the mRNA expression levels of IL-6 and transforming growth factor-ß1(TGF-ß1) in activated hepatic stellate cells (HSCs). And ISL significantly reduced annexin A2 (ANXA2) in vitro detected by TMT proteomics technology. Interestingly, it was found for the first time that ISL could inhibit ANXA2 expression both in vivo and in vitro, block the sphingosine kinases (SPHKs)/sphingosine-1-phosphate (S1P)/interleukin 17 (IL-17) signaling pathway and regulate the expression of α-smooth muscle actin (α-SMA) by inhibiting the phosphorylation of signal transducer and activator of transcription 3 (STAT3) at the downstream signal to finally reverse HSCs activation and hepatic fibrosis. Thus, we demonstrated that ISL is a drug monomer with notable anti-hepatic fibrosis activity.
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Anexina A2 , Interleucina-6 , Camundongos , Animais , Interleucina-6/metabolismo , Anexina A2/metabolismo , Camundongos Endogâmicos C57BL , Cirrose Hepática/induzido quimicamente , Cirrose Hepática/tratamento farmacológico , Cirrose Hepática/metabolismo , Fígado , Fator de Crescimento Transformador beta1/metabolismo , Células Estreladas do Fígado/metabolismo , RNA Mensageiro/metabolismoRESUMO
The lemon (Citrus limon; family Rutaceae) is one of the most important and popular fruits worldwide. Lemon also tolerates huanglongbing (HLB) disease, which is a devastating citrus disease. Here we produced a gap-free and haplotype-resolved chromosome-scale genome assembly of the lemon by combining Pacific Biosciences circular consensus sequencing, Oxford Nanopore 50-kb ultra-long, and high-throughput chromatin conformation capture technologies. The assembly contained nine-pair chromosomes with a contig N50 of 35.6 Mb and zero gaps, while a total of 633.0 Mb genomic sequences were generated. The origination analysis identified 338.5 Mb genomic sequences originating from citron (53.5%), 147.4 Mb from mandarin (23.3%), and 147.1 Mb from pummelo (23.2%). The genome included 30 528 protein-coding genes, and most of the assembled sequences were found to be repetitive sequences. Several significantly expanded gene families were associated with plant-pathogen interactions, plant hormone signal transduction, and the biosynthesis of major active components, such as terpenoids and flavor compounds. Most HLB-tolerant genes were expanded in the lemon genome, such as 2-oxoglutarate (2OG)/Fe(II)-dependent oxygenase and constitutive disease resistance 1, cell wall-related genes, and lignin synthesis genes. Comparative transcriptomic analysis showed that phloem regeneration and lower levels of phloem plugging are the elements that contribute to HLB tolerance in lemon. Our results provide insight into lemon genome evolution, active component biosynthesis, and genes associated with HLB tolerance.
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Soil salinity is a growing concern for global crop production and the sustainable development of humanity. Therefore, it is crucial to comprehend salt tolerance mechanisms and identify salt-tolerance genes to enhance crop tolerance to salt stress. Suaeda glauca, a halophyte species well adapted to the seawater environment, possesses a unique ability to absorb and retain high salt concentrations within its cells, particularly in its leaves, suggesting the presence of a distinct mechanism for salt tolerance. In this study, we performed de novo sequencing of the S. glauca genome. The genome has a size of 1.02 Gb (consisting of two sets of haplotypes) and contains 54 761 annotated genes, including alleles and repeats. Comparative genomic analysis revealed a strong synteny between the genomes of S. glauca and Beta vulgaris. Of the S. glauca genome, 70.56% comprises repeat sequences, with retroelements being the most abundant. Leveraging the allele-aware assembly of the S. glauca genome, we investigated genome-wide allele-specific expression in the analyzed samples. The results indicated that the diversity in promoter sequences might contribute to consistent allele-specific expression. Moreover, a systematic analysis of the ABCE gene families shed light on the formation of S. glauca's flower morphology, suggesting that dysfunction of A-class genes is responsible for the absence of petals in S. glauca. Gene family expansion analysis demonstrated significant enrichment of Gene Ontology (GO) terms associated with DNA repair, chromosome stability, DNA demethylation, cation binding, and red/far-red light signaling pathways in the co-expanded gene families of S. glauca and S. aralocaspica, in comparison with glycophytic species within the chenopodium family. Time-course transcriptome analysis under salt treatments revealed detailed responses of S. glauca to salt tolerance, and the enrichment of the transition-upregulated genes in the leaves associated with DNA repair and chromosome stability, lipid biosynthetic process, and isoprenoid metabolic process. Additionally, genome-wide analysis of transcription factors indicated a significant expansion of FAR1 gene family. However, further investigation is needed to determine the exact role of the FAR1 gene family in salt tolerance in S. glauca.
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Tea is one of the world's oldest crops and is cultivated to produce beverages with various flavours. Despite advances in sequencing technologies, the genetic mechanisms underlying key agronomic traits of tea remain unclear. In this study, we present a high-quality pangenome of 22 elite cultivars, representing broad genetic diversity in the species. Our analysis reveals that a recent long terminal repeat burst contributed nearly 20% of gene copies, introducing functional genetic variants that affect phenotypes such as leaf colour. Our graphical pangenome improves the efficiency of genome-wide association studies and allows the identification of key genes controlling bud flush timing. We also identified strong correlations between allelic variants and flavour-related chemistries. These findings deepen our understanding of the genetic basis of tea quality and provide valuable genomic resources to facilitate its genomics-assisted breeding.
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Camellia sinensis , Camellia sinensis/genética , Estudo de Associação Genômica Ampla , Melhoramento Vegetal , Genômica , CháRESUMO
Introduction: African Swine Fever (ASF) is a highly infectious disease of pigs, caused by African swine fever virus (ASFV). The lack of vaccines and drugs makes strict disinfection practices to be one of the main measurements to curb the transmission of ASF. Therefore, it is important to assess if all viruses are inactivated after disinfection or after long time exposure in their natural conditions. Currently, the infectivity of ASFV is determined by virus isolation and culture in a biosafety level 3 (BSL-3) laboratory. However, BSL-3 laboratories are not readily available, need skilled expertise and may be time consuming. Methods: In this study, a Triton X-100 assisted PMAxx-qPCR method was developed for rapid assessment of infectious ASFV in samples. PMAxx, an improved version of propidium monoazide (PMA), can covalently cross-link with naked ASFV-DNA or DNA inside inactivated ASFV virions under assistance of 0.1% (v/v) TritonX-100, but not with ASFV-DNA inside live virions. Formation of PMAxx-DNA conjugates prevents PCR amplification, leaving only infectious virions to be detected. Under optimum conditions, the limit of detection of the PMAxx-qPCR assay was 2.32log10HAD50/mL of infectious ASFV. Testing different samples showed that the PMAxx-qPCR assay was effective to evaluate intact ASFV virions after treatment by heat or chemical disinfectants and in simulated samples such as swine tissue homogenate, swine saliva swabs, and environmental swabs. However, whole-blood and saliva need to be diluted before testing because they may inhibit the PCR reaction or the cross-linking of PMAxx with DNA. Conclusion: The Triton X-100 assisted PMAxx-qPCR assay took less than 3 h from sample to result, offering an easier and faster way for assessing infectious ASFV in samples from places like pig farms and pork markets.