Echinococcus granulosus ubiquitin-conjugating enzymes (E2D2 and E2N) promote the formation of liver fibrosis in TGFβ1-induced LX-2 cells

BACKGROUND

Cystic echinococcosis (CE) is a widespread zoonosis caused by the infection with Echinococcus granulosus sensu lato (E. granulosus s.l.). CE cysts mainly develop in the liver of intermediate hosts, characterized by the fibrotic tissue that separates host organ from parasite. However, precise mechanism underlying the formation of fibrotic tissue in CE remains unclear.

METHODS

To investigate the potential impact of ubiquitin-conjugating enzymes on liver fibrosis formation in CE, two members of ubiquitin-conjugating (UBC) enzyme of Echinococcus granulosus (EgE2D2 and EgE2N) were recombinantly expressed in Escherichia coli and analyzed for bioinformatics, immunogenicity, localization, and enzyme activity. In addition, the secretory pathway and their effects on the formation of liver fibrosis were also explored.

RESULTS

Both rEgE2D2 and rEgE2N possess intact UBC domains and active sites, exhibiting classical ubiquitin binding activity and strong immunoreactivity. Additionally, EgE2D2 and EgE2N were widely distributed in protoscoleces and germinal layer, with differences observed in their distribution in 25-day strobilated worms. Further, these two enzymes were secreted to the hydatid fluid and CE-infected sheep liver tissues via a non-classical secretory pathway. Notably, TGFβ1-induced LX-2 cells exposed to rEgE2D2 and rEgE2N resulted in increasing expression of fibrosis-related genes, enhancing cell proliferation, and facilitating cell migration.

CONCLUSIONS

Our findings suggest that EgE2D2 and EgE2N could secrete into the liver and may interact with hepatic stellate cells, thereby promoting the formation of liver fibrosis.

Resequencing Analyses Revealed Genetic Diversity and Selection Signatures during Rabbit Breeding and Improvement

Domestication has shaped the diverse characteristics of rabbits, including coat color, fur structure, body size, and various physiological traits. Utilizing whole-genome resequencing (DNBSEQ-T7), we analyzed the genetic diversity, population structure, and genomic selection across 180 rabbits from 17 distinct breeds to uncover the genetic basis of these traits. We conducted whole-genome sequencing on 17 rabbit breeds, identifying 17,430,184 high-quality SNPs and analyzing genomic diversity, patterns of genomic variation, population structure, and selection signatures related to coat color, coat structure, long hair, body size, reproductive capacity, and disease resistance. Through PCA and NJ tree analyses, distinct clusters emerged among Chinese indigenous rabbits, suggesting varied origins and domestication histories. Selective sweep testing pinpointed regions and genes linked to domestication and key morphological and economic traits, including those affecting coat color (TYR, ASIP), structure (LIPH), body size (INSIG2, GLI3), fertility (EDNRA, SRD5A2), heat stress adaptation (PLCB1), and immune response (SEC31A, CD86, LAP3). Our study identified key genomic signatures of selection related to traits such as coat color, fur structure, body size, and fertility; these findings highlight the genetic basis underlying phenotypic diversification in rabbits and have implications for breeding programs aiming to improve productive, reproductive, and adaptive traits. The detected genomic signatures of selection also provide insights into rabbit domestication and can aid conservation efforts for indigenous breeds.

Genome-wide identification of the TIFY gene family in tobacco and expression analysis in response to Ralstonia solanacearum infection

The TIFY gene family plays an essential role in plant development and abiotic and biotic stress responses. In this study, genome-wide identification of TIFY members in tobacco and their expression pattern analysis in response to Ralstonia solanacearum infection were performed. A total of 33 TIFY genes were identified, including the TIFY, PPD, ZIM&ZML and JAZ subfamilies. Promoter analysis results indicated that a quantity of light-response, drought-response, SA-response and JA-response cis-elements exist in promoter regions. The TIFY gene family exhibited expansion and possessed gene redundancy resulting from tobacco ploidy change. In addition, most NtTIFYs equivalently expressed in roots, stems and leaves, while NtTIFY1, NtTIFY4, NtTIFY18 and NtTIFY30 preferentially expressed in roots. The JAZ III clade showed significant expression changes after inoculation with R. solanacearum, and the expression of NtTIFY7 in resistant varieties, compared with susceptible varieties, was more stably induced. Furthermore, NtTIFY7-silenced plants, compared with the control plants, were more susceptible to bacterial wilt. These results lay a foundation for exploring the evolutionary history of TIFY gene family and revealing gene function of NtTIFYs in tobacco bacterial wilt resistance.

Integrated transmission electron microscopy and proteomic analyses reveal the cytoarchitectural response to cucumber mosaic virus infection in tobacco

Cucumber mosaic virus (CMV) causes huge economic losses to agriculture every year; thus, understanding the mechanism of plant resistance to CMV is imperative. In this study, an integrated analysis of transmission electron microscopy (TEM) observations and proteomic results was used to identify cytoarchitectural differences in Nicotiana tabacum cv. NC82 (susceptible) and cv. Taiyan 8 (T.T.8; resistant) following infection with CMV. The TEM observations showed that the structure of the chloroplasts and mitochondria was severely damaged at the late stage of infection in NC82. Moreover, the chloroplast stroma and mitochondrial cristae were reduced and disaggregated. However, in T.T.8, organelle structure remained largely intact Selective autophagy predominated in T.T.8, whereas non-selective autophagy dominated in NC82, resembling cellular disorder. Proteomic analysis of T.T.8 revealed differentially expressed proteins (DEPs) mostly associated with photosynthesis, respiration, reactive oxygen species (ROS) scavenging, and cellular autophagy. Biochemical analyses revealed that ROS-related catalase, autophagy-related disulfide isomerase, and jasmonic acid and antioxidant secondary metabolite synthesis-related 4-coumarate:CoA ligase (Nt4CL) exhibited different trends and significant differences in expression in the two cultivars after CMV inoculation. Furthermore, mutant phenotyping verified that reduced Nt4CL expression impaired resistance in T.T.8. The identified DEPs are crucial for maintaining intracellular homeostatic balance and likely contribute to the mechanism of CMV resistance in tobacco. These findings increase our understanding of plant cytological mechanisms conferring resistance to CMV infection.

Transcriptomics and virus-induced gene silencing identify defence-related genes during Ralstonia solanacearum infection in resistant and susceptible tobacco

Bacterial wilt (BW) caused by Ralstonia solanacearum is a globally prevalent bacterial soil-borne disease. In this study, transcriptome sequencing were subjected to roots after infection with the R. solanacearum in the resistant and susceptible tobacco variety. DEGs that responded to R. solanacearum infection in both resistant and susceptible tobacco contributed to pectinase and peroxidase development and were enriched in plant hormone signal transduction, signal transduction and MAPK signalling pathway KEGG terms. Core DEGs in the resistant tobacco response to R. solanacearum infection were enriched in cell wall, membrane, abscisic acid and ethylene terms. qRT-PCR indicated that Nitab4.5_0004899g0110, Nitab4.5_0004234g0080 and Nitab4.5_0001439g0050 contributed to the response to R. solanacearum infection in different resistant and susceptible tobacco. Silencing the p450 gene Nitab4.5_0001439g0050 reduced tobacco resistance to bacterial wilt. These results improve our understanding of the molecular mechanism of BW resistance in tobacco and solanaceous plants.

Effects of annexin B18 from Echinococcus granulosus sensu lato on mouse macrophages

Cystic echinococcosis (CE) is a zoonotic disease, caused by Echinococcus granulosus sensu lato (E. granulosus s. l.), which posed significant public health concern globally. E. granulosus s. l. annexin B18 (EgANXB18) acts as a secretory protein, exerting a crucial influence in mediating host-parasite interactions. Recombinant annexin B18 (rEgANXB18) was expressed by Escherichia coli and the immunoreactivity was assessed by western blotting. The binding affinity between rEgANXB18 and total protein of RAW264.7 cells was assessed by ELISA. The impact of rEgANXB18 on the metabolic activity of RAW264.7 cells was assayed by Cell Counting Kit-8 assay. The mRNA levels of polarization markers (inducible nitrous oxide synthase (iNOS) and arginase 1 (Arg1)) and key cellular factors (IL-1β，IL-6，IL-10 and TNFα) were evaluated by qRT-PCR. rEgANXB18 was successfully expressed and recognized by E. granulosus s.l. infected canine sera, as well as could bind to the total protein of RAW264.7 cells. Additionally, rEgANXB18 could promote metabolic activity at 5, 10, 20, and 40 μg/mL while no significant impact on metabolic activity was observed at 80 μg/mL. Co-culture RAW264.7 cells with rEgANXB18 resulted in significantly upregulation of the transcript levels of polarization markers iNOS and Arg1. Moreover, rEgANXB18 significantly upregulated the transcript levels of IL-1β, IL-6, TNFα, and IL-10, while dose-effect relationship was observed in IL-1β, IL-6, and IL-10. Our results indicated that EgANXB18 showed the potential to regulate immune response of macrophages by shifting the cell polarization and cytokine profile, thereby promoting the parasitism of CE.

Fine mapping and identification of two NtTOM2A homeologs responsible for tobacco mosaic virus replication in tobacco (Nicotiana tabacum L.)

BACKGROUND

Tobacco mosaic virus (TMV) is a widely distributed viral disease that threatens many vegetables and horticultural species. Using the resistance gene N which induces a hypersensitivity reaction, is a common strategy for controlling this disease in tobacco (Nicotiana tabacum L.). However, N gene-mediated resistance has its limitations, consequently, identifying resistance genes from resistant germplasms and developing resistant cultivars is an ideal strategy for controlling the damage caused by TMV.

RESULTS

Here, we identified highly TMV-resistant tobacco germplasm, JT88, with markedly reduced viral accumulation following TMV infection. We mapped and cloned two tobamovirus multiplication protein 2A (TOM2A) homeologs responsible for TMV replication using an F2 population derived from a cross between the TMV-susceptible cultivar K326 and the TMV-resistant cultivar JT88. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated loss-of-function mutations of two NtTOM2A homeologs almost completely suppressed TMV replication; however, the single gene mutants showed symptoms similar to those of the wild type. Moreover, NtTOM2A natural mutations were rarely detected in 577 tobacco germplasms, and CRISPR/Cas9-mediated variation of NtTOM2A led to shortened plant height, these results indicating that the natural variations in NtTOM2A were rarely applied in tobacco breeding and the NtTOM2A maybe has an impact on growth and development.

CONCLUSIONS

The two NtTOM2A homeologs are functionally redundant and negatively regulate TMV resistance. These results deepen our understanding of the molecular mechanisms underlying TMV resistance in tobacco and provide important information for the potential application of NtTOM2A in TMV resistance breeding.

Rastonia solanacearum type Ⅲ effectors target host 14-3-3 proteins to suppress plant immunity

14-3-3 proteins play important roles in plant metabolism and stress response. Tomato 14-3-3 proteins, SlTFT4 and SlTFT7, serve as hubs of plant immunity and are targeted by some pathogen effectors. Ralstonia solanacearum with more than 70 type Ⅲ effectors (T3Es) is one of the most destructive plant pathogens. However, little is known on whether R. solanacearum T3Es target SlTFT4 and SlTFT7 and hence interfere with plant immunity. We first detected the associations of SlTFT4/SlTFT7 with R. solanacearum T3Es by luciferase complementation assay, and then confirmed the interactions by yeast two-hybrid approach. We demonstrated that 22 Ralstonia T3Es were associated with both SlTFT4 and SlTFT7, and five among them suppressed the hypersensitive response induced by MAPKKKα, a protein kinase which associated with SlTFT4/SlTFT7. We further demonstrated that suppression of MAPKKKα-induced HR and plant basal defense by the T3E RipAC depend on its association with 14-3-3 proteins. Our findings firstly demonstrate that R. solanacearum T3Es can manipulate plant immunity by targeting 14-3-3 proteins, SlTFT4 and SlTFT7, providing new insights into plant-R. solanacearum interactions.

Low H3K27me3 deposition at CYP82E4 determines the nicotinic conversion rate in Nicotiana tabacum

Nicotine conversion is the process by which nornicotine is synthesized from nicotine. The capacity of a plant to carry out this process is represented by the nicotine conversion rate (NCR), which is defined as the percentage of nornicotine content out of the total nicotine + nornicotine content. Nicotine conversion in tobacco is mediated by CYP82E4. Although there are cultivar-specific differences in NCR, these do not correspond to differences in the CYP82E4 promoter or gene body sequences, and little is known about the underlying regulatory mechanism. Here, we found that histone H3 Lysine 27 trimethylation (H3K27me3) was involved in CYP82E4 expression, functioning as a transcriptional repressor. Compared to a high-NCR near-isogenic line, a low-NCR cultivar showed increased levels of the repressive histone modification markers H3K27me3 and H3K9me3 at CYP82E4. Comparison of histone markers between several cultivars with varying NCRs showed that H3K27me3 and H3K9me3 levels were significantly associated with cultivar-specific differences in NCR. Treatment with the H3K27me3 demethylase inhibitor GSK-J4 increased total H3K27me3 levels and enriched H3K27me3 at the CYP82E4 locus; the increased levels of H3K27me3 further inhibited CYP82E4 expression. Knocking out E(z), an indispensable gene for H3K27me3 formation, decreased H3K27me3 levels at CYP82E4, leading to a more than three-fold increase in CYP82E4 expression. Changes in CYP82E4 expression during leaf senescence and chilling stress were also strongly correlated with H3K27me3 levels. These findings reveal a strong correlation between CYP82E4 expression and histone modifications, and demonstrate an instance of histone-mediated alkaloid regulation for the first time.

Subcellular compartmentalization in the biosynthesis and engineering of plant natural products

Plant natural products (PNPs) are specialized metabolites with diverse bioactivities. They are extensively used in the pharmaceutical, cosmeceutical and food industries. PNPs are synthesized in plant cells by enzymes that are distributed in different subcellular compartments with unique microenvironments, such as ions, co-factors and substrates. Plant metabolic engineering is an emerging and promising approach for the sustainable production of PNPs, for which the knowledge of the subcellular compartmentalization of their biosynthesis is instrumental. In this review we describe the state of the art on the role of subcellular compartments in the biosynthesis of major types of PNPs, including terpenoids, phenylpropanoids, alkaloids and glucosinolates, and highlight the efforts to target biosynthetic pathways to subcellular compartments in plants. In addition, we will discuss the challenges and strategies in the field of plant synthetic biology and subcellular engineering. We expect that newly developed methods and tools, together with the knowledge gained from the microbial chassis, will greatly advance plant metabolic engineering.

Comprehensive transcriptome and WGCNA analysis reveals the potential function of anthocyanins in low-temperature resistance of a red flower mutant tobacco

The anthocyanin is a protective substance in various plants, and plays important roles in resisting to low-temperature. Here, we explored transcriptome analysis of pink flower (as CK) and the natural mutant red flower (as research objects) under low-temperature conditions, and aimed to reveal the potential functions of anthocyanins and anthocyanin-related regulatory factors in resistance to low-temperature. Our results showed that most of the differentially expressed genes (DEGs) encoding key enzymes in the late stage of anthocyanin metabolism in the mutant were significantly up-regulated. Meanwhile, several genes significantly differentially expressed in CK or mutant were obtained by classification and analysis of transcription factors (TFs), phytohormones and osmoregulators. Additionally, WGCNA was carried out to mine hub genes resistanted to low-temperature stress in flavonoid pathway. Finally, one UFGT family gene, three MYB and one bHLH were obtained as the future hub genes of this study. Combined with the above information, we concluded that the ability of the red flower mutant to grow and develop normally at low-temperatures was the result of a combination of flavonoids and cold resistance genes.

Protective efficacy of six recombinant proteins as vaccine candidates against Echinococcus granulosus in dogs

BACKGROUND

Cystic echinococcosis (CE) is caused by the infection of Echinococcus granulosus sensu lato (E. granulosus s.l.), one of the most harmful zoonotic helminths worldwide. Infected dogs are the major source of CE transmission. While praziquantel-based deworming is a main measure employed to control dog infections, its efficacy is at times compromised by the persistent high rate of dog re-infection and the copious discharge of E. granulosus eggs into the environment. Therefore, the dog vaccine is a welcome development, as it offers a substantial reduction in the biomass of E. granulosus. This study aimed to use previous insights into E. granulosus functional genes to further assess the protective efficacy of six recombinant proteins in dogs using a two-time injection vaccination strategy.

METHODS

We expressed and combined recombinant E. granulosus triosephosphate isomerase (rEgTIM) with annexin B3 (rEgANXB3), adenylate kinase 1 (rEgADK1) with Echinococcus protoscolex calcium binding protein 1 (rEgEPC1), and fatty acid-binding protein (rEgFABP) with paramyosin (rEgA31). Beagle dogs received two subcutaneous vaccinations mixed with Quil-A adjuvant, and subsequently orally challenged with protoscoleces two weeks after booster vaccination. All dogs were sacrificed for counting and measuring E. granulosus tapeworms at 28 days post-infection, and the level of serum IgG was detected by ELISA.

RESULTS

Dogs vaccinated with rEgTIM&rEgANXB3, rEgADK1&rEgEPC1, and rEgFABP-EgA31 protein groups exhibited significant protectiveness, with a worm reduction rate of 71%, 57%, and 67%, respectively, compared to the control group (P < 0.05). Additionally, the vaccinated groups exhibited an inhibition of worm growth, as evidenced by a reduction in body length and width (P < 0.05). Furthermore, the level of IgG in the vaccinated dogs was significantly higher than that of the control dogs (P < 0.05).

CONCLUSION

These verified candidates may be promising vaccines for the prevention of E. granulosus infection in dogs following two injections. The rEgTIM&rEgANXB3 co-administrated vaccine underscored the potential for the highest protective efficacy and superior protection stability for controlling E. granulosus infections in dogs.

PIF1, a phytochrome-interacting factor negatively regulates drought tolerance and carotenoids biosynthesis in tobacco

The phytochrome-interacting factors (PIFs) function crucially in multiple physiological processes, but the biological functions of some PIFs remain elusive in some species. Here, a PIF transcription factor NtPIF1 was cloned and characterized in tobacco (Nicotiana tabacum L.). The transcript of NtPIF1 was significantly induced by drought stress treatments, and it localized in the nuclear. Knockout of NtPIF1 by CRISPR/Cas9 system led to the improved drought tolerance of tobacco with increased osmotic adjustment, antioxidant activity, photosynthetic efficiency and decreased water loss rate. On the contrary, NtPIF1-overexpression plants displays drought-sensitive phenotypes. In addition, NtPIF1 reduced the biosynthesis of abscisic acid (ABA) and its upstream carotenoids by regulating the expression of genes involved in ABA and carotenoids biosynthetic pathway upon drought stress. Electrophoretic mobility shift and dual-luciferase assays illustrated that, NtPIF1 directly bind to the E-box elements within the promoters of NtNCED3, NtABI5, NtZDS and Ntβ-LCY to repress their transcription. Overall, these data suggested that NtPIF1 negatively regulate tobacco adaptive response to drought stress and carotenoids biosynthesis; moreover, NtPIF1 has the potential to develop drought-tolerant tobacco plants using CRISPR/Cas9 system.

Genome-wide analysis of UDP-glycosyltransferases family and identification of UGT genes involved in abiotic stress and flavonol biosynthesis in Nicotiana tabacum

BACKGROUND

Uridine disphosphate (UDP) glycosyltransferases (UGTs) act upon a huge variety of highly diverse and complex substrates, such as phytohormones and specialized metabolites, to regulate plant growth, development, disease resistance, and environmental interactions. However, a comprehensive investigation of UGT genes in tobacco has not been conducted.

RESULTS

In this study, we carried out a genome-wide analysis of family-1 UDP glycosyltransferases in Nicotiana tabacum. We predicted 276 NtUGT genes, which were classified into 18 major phylogenetic subgroups. The NtUGT genes were invariably distributed among all the 24 chromosomes with structural diversity in exon/intron structure, conserved motifs, and cis-acting elements of promoters. Three groups of proteins which involved in flavonoid biosynthesis, plant growth and development, transportation and modification were identified that interact with NtUGT proteins using the PPI analysis. Expression analysis of NtUGT genes in cold stress, drought stress and different flower color using both online RNA-Seq data and the realtime PCR analysis, suggested the distinct role of NtUGT genes in resistance of cold, drought and in flavonoid biosynthesis. The enzymatic activities of seven NtUGT proteins that potentially involved in flavonoid glycosylation were analyzed, and found that all seven exhibited activity on myricetin; six (NtUGT108, NtUGT123, NtUGT141, NtUGT155, NtUGT179, and NtUGT195) showed activity on cyanidin; and three (NtUGT108, NtUGT195, and NtUGT217) were active on the flavonol aglycones kaempferol and quercetin, which catalyzing the substrates (myricetin, cyanidin or flavonol) to form new products. We further investigated the enzymatic products and enzymatic properties of NtUGT108, NtUGT195, and NtUGT217, suggested their diverse enzymatic activity toward flavonol, and NtUGT217 showed the highest catalyzed efficient toward quercetin. Overexpression of NtUGT217 significantly increase the content levels of the quercetin-3-O-glucoside, quercetin-3-O-rutinoside and kaempferol-3-O-rutinoside in transgenic tobacco leaves.

CONCLUSION

We identified 276 UGT genes in Nicotiana tabacum. Our study uncovered valuable information about the phylogenetic structure, distribution, genomic characters, expression patterns and enzymatic activity of NtUGT genes in tobacco. We further identified three NtUGT genes involved in flavonoid biosynthesis, and overexpressed NtUGT217 to validate its function in catalyze quercetin. The results provide key candidate NtUGT genes for future breeding of cold and drought resistance and for potential metabolic engineering of flavonoid compounds.

Development of a MAGIC population and high-resolution quantitative trait mapping for nicotine content in tobacco

Multiparent Advanced Generation Inter-Cross (MAGIC) population is an ideal genetic and breeding material for quantitative trait locus (QTL) mapping and molecular breeding. In this study, a MAGIC population derived from eight tobacco parents was developed. Eight parents and 560 homozygous lines were genotyped by a 430K single-nucleotide polymorphism (SNP) chip assay and phenotyped for nicotine content under different conditions. Four QTLs associated with nicotine content were detected by genome-wide association mapping (GWAS), and one major QTL, named qNIC7-1, was mapped repeatedly under different conditions. Furthermore, by combining forward mapping, bioinformatics analysis and gene editing, we identified an ethylene response factor (ERF) transcription factor as a candidate gene underlying the major QTL qNIC7-1 for nicotine content in tobacco. A presence/absence variation (PAV) at qNIC7-1 confers changes in nicotine content. Overall, the large size of this MAGIC population, diverse genetic composition, balanced parental contributions and high levels of recombination all contribute to its value as a genetic and breeding resource. The application of the tobacco MAGIC population for QTL mapping and detecting rare allelic variation was demonstrated using nicotine content as a proof of principle.

A screening of inhibitors targeting the receptor kinase FERONIA reveals small molecules that enhance plant root immunity

Receptor-like kinases (RLKs) constitute the largest receptor family involved in the regulation of plant immunity and growth, but small-molecule inhibitors that target RLKs to improve agronomic traits remain unexplored. The RLK member FERONIA (FER) negatively regulates plant resistance to certain soil-borne diseases that are difficult to control and cause huge losses in crop yields and economy. Here, we identified 33 highly effective FER kinase inhibitors from 1494 small molecules by monitoring FER autophosphorylation in vitro. Four representative inhibitors (reversine, cenisertib, staurosporine and lavendustin A) inhibited the kinase activity of FER and its homologues in several crops by targeting the conserved ATP pocket in the kinase structure. FER contributes to the physiological impact of representative inhibitors in plants. The treatment of roots with reversine, staurosporine and lavendustin A enhanced innate immunity in plant roots and thus alleviated soil-borne diseases in tobacco, tomato and rice without growth penalties. Consistently, RNA sequencing assays showed that lavendustin A and reversine exert profound impacts on immunity-related gene expression. Our results will set a new milestone in the development of the plant RLK kinase regulation theory and provide a novel strategy for the prevention and control of plant soil-borne diseases without growth penalties.

Naringenin confers defence against Phytophthora nicotianae through antimicrobial activity and induction of pathogen resistance in tobacco

Tobacco black shank caused by Phytophthora nicotianae is a serious disease in tobacco cultivation. We found that naringenin is a key factor that causes different sensitivity to P. nicotianae between resistant and susceptible tobacco. The level of basal flavonoids in resistant tobacco was distinct from that in susceptible tobacco. Of all flavonoids with different content, naringenin showed the best antimicrobial activity against mycelial growth and sporangia production of P. nicotianae in vitro. However, naringenin showed very low or no antimicrobial activity to other plant pathogens. We found that naringenin induced not only the accumulation of reactive oxygen species, but also the expression of salicylic acid biosynthesis-related genes. Naringenin induced the expression of the basal pathogen resistance gene PR1 and the SAR8.2 gene that contributes to plant resistance to P. nicotianae. We then interfered with the expression of the chalcone synthase (NtCHS) gene, the key gene of the naringenin synthesis pathway, to inhibit naringenin biosynthesis. NtCHS-RNAi rendered tobacco highly sensitive to P. nicotianae, but there was no change in susceptibility to another plant pathogen, Ralstonia solanacearum. Finally, exogenous application of naringenin on susceptible tobacco enhanced resistance to P. nicotianae and naringenin was very stable in this environment. Our findings revealed that naringenin plays a core role in the defence against P. nicotianae and expanded the possibilities for the application of plant secondary metabolites in the control of P. nicotianae.

Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing

Background

Rabbit wool traits are important in fiber production and for model organism research on hair growth, but their genetic architecture remains obscure. In this study, we focused on wool characteristics in Angora rabbits, a breed well-known for the quality of its wool. Considering the cost to generate population-scale sequence data and the biased detection of variants using chip data, developing an effective genotyping strategy using low-coverage whole-genome sequencing (LCS) data is necessary to conduct genetic analyses.

Results

Different genotype imputation strategies (BaseVar + STITCH, Bcftools + Beagle4, and GATK + Beagle5), sequencing coverages (0.1X, 0.5X, 1.0X, 1.5X, and 2.0X), and sample sizes (100, 200, 300, 400, 500, and 600) were compared. Our results showed that using BaseVar + STITCH at a sequencing depth of 1.0X with a sample size larger than 300 resulted in the highest genotyping accuracy, with a genotype concordance higher than 98.8% and genotype accuracy higher than 0.97. We performed multivariate genome-wide association studies (GWAS), followed by conditional GWAS and estimation of the confidence intervals of quantitative trait loci (QTL) to investigate the genetic architecture of wool traits. Six QTL were detected, which explained 0.4 to 7.5% of the phenotypic variation. Gene-level mapping identified the fibroblast growth factor 10 (FGF10) gene as associated with fiber growth and diameter, which agrees with previous results from functional data analyses on the FGF gene family in other species, and is relevant for wool rabbit breeding.

Conclusions

We suggest that LCS followed by imputation can be a cost-effective alternative to array and high-depth sequencing for assessing common variants. GWAS combined with LCS can identify new QTL and candidate genes that are associated with quantitative traits. This study provides a cost-effective and powerful method for investigating the genetic architecture of complex traits, which will be useful for genomic breeding applications.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-022-00766-y.

Patients not taking a previously prescribed bone active medication now prescribed medication through Ontario FLS

In an Ontario fracture liaison service (FLS), we compared medication prescription rates among patients not taking a previously prescribed bone active medication to those with no previous prescription. Prescription rates were similar between these two groups of patients. The FLS provided a secondary opportunity for patients to initiate bone active medication.

PURPOSE

We compared bone active medication prescription rates among patients presenting to an Ontario fracture liaison service (FLS) who reported not taking a previously prescribed bone active medication to those with no history of prescription.

METHODS

Eligible patients were those screened in 39 fracture clinics between July 1, 2017, and September 15, 2019, who were not taking bone active medication at the time of screening and classified as high risk for future fracture based on CAROC or FRAX. Sociodemographic and clinical risk factor variables were assessed at screening. Bone active medication prescription rate was assessed within 6 months of screening and defined as having received a prescription for the medication from either a specialist or primary care provider. In cases where a specialist report was not available, patient self-reported data were collected. The chi-square test of independence was used to assess differences in prescription rates.

RESULTS

Of 17,575 patients screened, eligible patients were 350 with a previous prescription and 2644 without a previous prescription. Compared with patients who reported no previous prescription, those who had a previous prescription were older, more likely to be female and to report a previous fracture, and less likely to smoke. There was no statistically significant difference between the medication prescription rate of patients with a previous prescription (73.7%) compared to patients with no previous prescription (70.7%) (p = 0.157).

CONCLUSION

A large jurisdiction-wide FLS approach provided a secondary opportunity to patients who were not taking a previously prescribed bone active medication to initiate that medication.

Phosphorylation-mediated inactivation of C3H14 by MPK4 enhances bacterial-triggered immunity in Arabidopsis

Perception of pathogen-associated molecular patterns (PAMPs) triggers mitogen-activated protein (MAP) kinase 4 (MPK4)-mediated phosphorylation and induces downstream transcriptional reprogramming, but the mechanisms of the MPK4 defense pathway are poorly understood. Here, we showed that phosphorylation-mediated inactivation of the CCCH protein C3H14 by MPK4 positively regulates the immune response in Arabidopsis (Arabidopsis thaliana). Compared with wild-type plants, loss-of-function mutations in C3H14 and its paralog C3H15 resulted in enhanced defense against Pst DC3000 in infected leaves and the development of systemic acquired resistance (SAR), whereas C3H14 or C3H15 overexpression enhanced susceptibility to this pathogen and failed to induce SAR. The functions of C3H14 in PAMP-triggered immunity (PTI) and SAR were dependent on MPK4-mediated phosphorylation. Challenge with Pst DC3000 or the flagellin peptide flg22 enhanced the phosphorylation of C3H14 by MPK4 in the cytoplasm, relieving C3H14-inhibited expression of PTI-related genes and attenuating C3H14-activated expression of its targets NIM1-INTERACTING1 (NIMIN1) and NIMIN2, two negative regulators of SAR. Salicylic acid (SA) affected the MPK4-C3H14-NIMIN1/2 cascades in immunity, but SA signaling mediated by the C3H14-NIMIN1/2 cascades was independent of MPK4 phosphorylation. Our study suggests that C3H14 might be a negative component of the MPK4 defense signaling pathway.

Deciphering the roles of tobacco MYB transcription factors in environmental stress tolerance

The MYB members play important roles in development, metabolism, and stress tolerance in plants. In the current study, a total of 246 tobacco R2R3-MYB transcription factors were identified and systemically analyzed from the latest genome annotation. The newly identified tobacco members were divided into 33 subgroups together with the Arabidopsis members. Furthermore, 44 NtMYB gene pairs were identified to arise from duplication events, which might lead to the expansion of tobacco MYB genes. The expression patterns were revealed by transcriptomic analysis. Notably, the results from phylogenetic analysis, synthetic analysis, and expression analysis were integrated to predict the potential functions of these members. Particularly, NtMYB102 was found to act as the homolog of AtMYB70 and significantly induced by drought and salt treatments. The further assays revealed that NtMYB102 had transcriptional activities, and the overexpression of the encoding gene enhanced the drought and salt stress tolerance in transgenic tobacco. The results of this study may be relevant for future functional analyses of the MYB genes in tobacco.

Marker density and statistical model designs to increase accuracy of genomic selection for wool traits in Angora rabbits

The Angora rabbit, a well-known breed for fiber production, has been undergoing traditional breeding programs relying mainly on phenotypes. Genomic selection (GS) uses genomic information and promises to accelerate genetic gain. Practically, to implement GS in Angora rabbit breeding, it is necessary to evaluate different marker densities and GS models to develop suitable strategies for an optimized breeding pipeline. Considering a lack in microarray, low-coverage sequencing combined with genotype imputation was used to boost the number of SNPs across the rabbit genome. Here, in a population of 629 Angora rabbits, a total of 18,577,154 high-quality SNPs were imputed (imputation accuracy above 98%) based on low-coverage sequencing of 3.84X genomic coverage, and wool traits and body weight were measured at 70, 140 and 210 days of age. From the original markers, 0.5K, 1K, 3K, 5K, 10K, 50K, 100K, 500K, 1M and 2M were randomly selected and evaluated, resulting in 50K markers as the baseline for the heritability estimation and genomic prediction. Comparing to the GS performance of single-trait models, the prediction accuracy of nearly all traits could be improved by multi-trait models, which might because multiple-trait models used information from genetically correlated traits. Furthermore, we observed high significant negative correlation between the increased prediction accuracy from single-trait to multiple-trait models and estimated heritability. The results indicated that low-heritability traits could borrow more information from correlated traits and hence achieve higher prediction accuracy. The research first reported heritability estimation in rabbits by using genome-wide markers, and provided 50K as an optimal marker density for further microarray design, genetic evaluation and genomic selection in Angora rabbits. We expect that the work could provide strategies for GS in early selection, and optimize breeding programs in rabbits.

Fragility fracture patients with a history of prior fractures more likely to present with multiple risk factors: findings from a province-wide fracture liaison service

We examined the demographic characteristics and risk factors of FLS fragility fracture patients who had sustained prior fragility fracture(s) and found that this is an important high-risk subgroup that warrants further attention within FLS priority pathways in order to disrupt their fragility fracture cycle.

PURPOSE

Our primary objective was to examine whether fragility fracture patients presenting to a provincial fracture liaison service (FLS) having a history of prior fractures, versus those without, differ in demographic characteristics and risk factors for future fracture. A secondary objective was to understand if those who report two or more prior fractures differ from those reporting one prior fracture.

METHODS

This cohort study included fragility fracture patients aged 50 + enrolled in the Ontario FLS between July 2017 and September 2019. Patients with versus those without prior fractures were compared on age, sex, index fracture site, biological parents' history of hip fracture, current fracture due to a fall, history of feeling unsteady when walking, history of falls in the past year, smoking, oral steroid use, and comorbid chronic conditions. Pearson's chi-square, Fischer's exact, and analysis of variance tests were used to assess differences.

RESULTS

Among 14,454 patients, 16.8% (n = 2428) reported a history of one or more prior fractures after the age of 40. They were significantly more likely to be older, female, with a higher number of comorbidities, with greater incidence of falls, and feel unsteady when walking. Compared to those with one prior fracture, patients with greater than one prior fracture were more likely to report falls in the past year and feel unsteady when walking.

CONCLUSION

Findings suggest that FLS fragility fracture patients who had sustained prior fragility fracture are an important high-risk subgroup that warrants further attention within FLS priority pathways in order to disrupt their fragility fracture cycle.

Characterization of trichome-specific BAHD acyltransferases involved in acylsugar biosynthesis in Nicotiana tabacum

Glandular trichomes of tobacco (Nicotiana tabacum) produce blends of acylsucroses that contribute to defence against pathogens and herbivorous insects, but the mechanism of assembly of these acylsugars has not yet been determined. In this study, we isolated and characterized two trichome-specific acylsugar acyltransferases that are localized in the endoplasmic reticulum, NtASAT1 and NtASAT2. They sequentially catalyse two additive steps of acyl donors to sucrose to produce di-acylsucrose. Knocking out of NtASAT1 or NtASAT2 resulted in deficiency of acylsucrose; however, there was no effect on acylsugar accumulation in plants overexpressing NtASAT1 or NtASAT2. Genomic analysis and profiling revealed that NtASATs originated from the T subgenome, which is derived from the acylsugar-producing diploid ancestor N. tomentosiformis. Our identification of NtASAT1 and NtASAT2 as enzymes involved in acylsugar assembly in tobacco potentially provides a new approach and target genes for improving crop resistance against pathogens and insects.

Systematic Analysis of Tobacco CrRLK1L Family Genes and Functional Identification of NtCrRLK1L47 in Environmental Stresses

The Catharanthus roseus RLK1-like (CrRLK1L) family is involved in the regulation of plant reproduction, growth and development, cell wall integrity sensing, as well as responses to both biotic and abiotic stress conditions. Extraordinary progress has been made in elucidating the CrRLK1L family receptor kinases-mediated signaling pathway, while limited research addressed the functions of CrRLK1L proteins in tobacco. In this study, we identified and analyzed 48 NtCrRLK1L members from the tobacco genome. The newly identified NtCrRLK1L members were divided into seven groups together with the Arabidopsis CrRLK1L members. The syntenic analysis revealed that four pairs of NtCrRLK1L genes were predicted to have arisen from segmental duplication events. Expression profiling showed that the NtCrRLK1L genes were expressed in various tissues, and most NtCrRLK1L genes were induced by salt and drought stress conditions. Notably, NtCrRLK1L47 was upregulated under drought and salinity stresses, and the NtCrRLK1L47-GFP fusion protein was located in the cell membrane. Furthermore, overexpression of the NtCrRLK1L47 gene enhanced the salt tolerance in tobacco seedlings.

Identification of QTLs Associated With Agronomic Traits in Tobacco via a Biparental Population and an Eight-Way MAGIC Population

Agronomic traits such as plant height (PH), leaf number (LN), leaf length (LL), and leaf width (LW), which are closely related to yield and quality, are important in tobacco (Nicotiana tabacum L.). To identify quantitative trait loci (QTLs) associated with agronomic traits in tobacco, 209 recombinant inbred lines (RILs) and 537 multiparent advanced generation intercross (MAGIC) lines were developed. The biparental RIL and MAGIC lines were genotyped using a 430 K single-nucleotide polymorphism (SNP) chip assay, and their agronomic traits were repeatedly evaluated under different conditions. A total of 43 QTLs associated with agronomic traits were identified through a combination of linkage mapping (LM) and association mapping (AM) methods. Among these 43 QTLs, three major QTLs, namely qPH13-3, qPH17-1, and qLW20-1, were repeatedly identified by the use of various genetically diverse populations across different environments. The candidate genes for these major QTLs were subsequently predicted. Validation and utilization of the major QTL qLW20-1 for the improvement of LW in tobacco were investigated. These results could be applied to molecular marker-assisted selection (MAS) for breeding important agronomic traits in tobacco.

Comprehensive Analysis Reveals the Genetic and Pathogenic Diversity of Ralstonia solanacearum Species Complex and Benefits Its Taxonomic Classification

Ralstonia solanacearum species complex (RSSC) is a diverse group of plant pathogens that attack a wide range of hosts and cause devastating losses worldwide. In this study, we conducted a comprehensive analysis of 131 RSSC strains to detect their genetic diversity, pathogenicity, and evolution dynamics. Average nucleotide identity analysis was performed to explore the genomic relatedness among these strains, and finally obtained an open pangenome with 32,961 gene families. To better understand the diverse evolution and pathogenicity, we also conducted a series of analyses of virulence factors (VFs) and horizontal gene transfer (HGT) in the pangenome and at the single genome level. The distribution of VFs and mobile genetic elements (MGEs) showed significant differences among different groups and strains, which were consistent with the new nomenclatures of the RSSC with three distinct species. Further functional analysis showed that most HGT events conferred from Burkholderiales and played a great role in shaping the genomic plasticity and genetic diversity of RSSC genomes. Our work provides insights into the genetic polymorphism, evolution dynamics, and pathogenetic variety of RSSC and provides strong supports for the new taxonomic classification, as well as abundant resources for studying host specificity and pathogen emergence.

NtNAC053, A Novel NAC Transcription Factor, Confers Drought and Salt Tolerances in Tobacco

The NAC (NAM, ATAF1/2, and CUC2) family acts as one of the largest families of the transcription factor in the plant kingdom and was revealed to function as the important regulators in various environmental stresses. However, a few studies were reported about the biofunctions of the NAC transcription factor in tobacco. In the current study, we characterized a novel NAC transcription factor encoding the gene NtNAC053 in tobacco, which was significantly up-regulated when exposed to salt and drought treatments. The results of cis-acting elements analysis suggested that the promoter region of NtNAC053 gene possesses a number of stress-responsive elements, and this gene could be induced by exogenous abscisic acid (ABA) treatment. Moreover, the NtNAC053-GFP fusion protein was localized in the cell nucleus and possessed a transactivation domain in its C-terminal, implying that NtNAC053 may undertake as a transcriptional activator in tobacco. Notably, the overexpression of NtNAC053 in tobacco resulted in hypersensitivity to ABA treatment. Furthermore, these overexpression lines showed significantly enhanced tolerances to drought and salt stresses. Under salt and drought stresses, these overexpression lines possessed higher superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) activities. Interestingly, the expressions of putative stress-related genes, including NtCOR15A, NtRAB18, NtDREB1A, NtERF5, NtKAT2, and NtERD11, were up-regulated in these overexpression lines when subjected to salt and drought stresses. The clues provided in our study suggested that the NtNAC053 gene encodes a novel NAC transcription factor and could confer the drought and salt stress tolerances by inspiring the downstream stress-responsive genes and antioxidant system in tobacco.

Screening of Tobacco Genotypes for Phytophthora nicotianae Resistance

Black shank, caused by the oomycetes Phytophthora nicotianae, is destructive to tobacco, and this pathogen is highly pathogenic to many solanaceous crops. P. nicotianae is well adapted to high temperatures; therefore, research on this pathogen is gaining importance in agriculture worldwide because of global warming. P. nicotianae-resistant varieties of tobacco plants are commonly screened by inoculation with oat grains colonized by P. nicotianae and monitoring for the disease symptoms. However, it is difficult to quantify the inoculation intensity since accurate inoculation is crucial in this case. This study aimed to develop an efficient and reliable method for evaluating the resistance of tobacco to infection with P. nicotianae. This method has been successfully used to identify resistant varieties, and the inoculation efficiency was confirmed by real-time PCR. The resistance evaluation method presented in this study is efficient and practical for precision breeding, as well as molecular mechanism research.

Epidemiological analysis of cystic echinococcosis and alveolar echinococcosis in an extremely high prevalence region: Population-based survey and host animal monitoring in Shiqu County, China

Echinococcosis is the most common parasitic disease in the Tibetan Plateau, placing a large disease burden on the local population. Shiqu County, located in western Sichuan Tibetan region, had a particularly high prevalence rate of cystic echinococcosis (CE) and alveolar echinococcosis (AE) in previous surveys. From 2015 to 2018, a population-based field survey was conducted to explore the epidemic situation. Epidemiological features were examined through demographic analysis and mapping. In addition, the infection prevalence of Echinococcus in dogs was also investigated and mapped by spatial autoregression. A total of 84,768 people were screened by abdominal ultrasound inspection, and 2,341 CE and 3,930 AE cases were detected, with a corresponding prevalence of 2.76% and 4.64%, respectively. This made Shiqu County one of the most severe echinococcosis endemic regions in the world, especially with regard to AE. The cases were not evenly distributed among towns: particularly, the AE rates in the northwest towns were very high and closely related to the infection rate of neighboring host animals. Simultaneously, a comprehensive prevention project including patient treatment and host management was conducted and achieved preliminary success in source control. According to feces monitoring findings, the infection rate of dogs declined from 26.38% in early 2016 to 3.71% in 2018. Combined with host animal distribution data at the town level, the predicted risk ranks were categorized by risk index and mapped to guide further control operations.

Cell type diversity in scallop adductor muscles revealed by single-cell RNA-Seq

Studies on cell atlas in marine invertebrates provide a better understanding of cell types, stem cell maintenance, and lineages of cell differentiation. To investigate the molecular features of various cell types in molluscan muscles, we performed single-cell RNA sequencing (scRNA-seq) to map cell types in scallop adductor muscles. We uncovered the cell type-specific features of 20 cell clusters defined by the expression of multiple specific molecular markers. These cell clusters are mainly classified into four broad classes, including mesenchymal stem cells, muscle cells, neurons, and haemolymph cells. In particular, we identified a diverse repertoire of neurons in the striated adductor muscle, but not in the smooth muscle. We further reconstructed the cell differentiation events using all the cell clusters by single-cell pseudotemporal trajectories. By integrating dual BrdU-PCNA immunodetection, neuron-specific staining and electron microscopy observation, we showed the spatial distribution of mesenchymal stem cells and neurons in striated adductor muscle of scallops. The present findings will not only be useful to address the cell type-specific gene expression profiles in scallop muscles, but also provide valuable resources for cross-species comparison of marine organisms.

Patients 80 + have similar medication initiation rates to those aged 50-79 in Ontario FLS

Among individuals presenting to an Ontario FLS, we compared bone active medication initiation rates of patients 80 years and older with those 50-79 years old. After accounting for fracture risk status, there was no statistically significant difference in medication initiation rates between the two age groups INTRODUCTION: A Fracture Liaison Service (FLS) offers post-fracture services to individuals over the age of 50 years and could potentially address age inequities in pharmacotherapy often observed for older adults. Among individuals presenting to an Ontario FLS and classified as being at high risk for future fracture, our objective was to compare bone active medication initiation rates of patients 80 years and older with those 50-79 years old.

METHODS

In 39 FLS fracture clinics across Ontario, Canada, fracture prevention coordinators identified, assessed, and facilitated the referral of eligible patients for bone densitometry, fracture risk assessment, and implementation of pharmacotherapy in patients classified as high risk for future fracture. Variables assessed at baseline included age, sex, marital status, living location, fracture location, history of previous fracture, parent's history of hip fracture, history of falls, and fracture risk status. At 6 months, bone active medication initiation was assessed in patients classified as high risk for future fracture. The Chi-square test of independence was used to compare medication initiation rates between patients 80 + and those 50-79 years old.

RESULTS

Our sample size consisted of 808 patients aged 50-79 years and 346 aged 80 + years. After accounting for fracture risk status, there was no statistically significant difference in medication initiation rates of patients 50-79 and 80 + years old (76.9% versus 73.7%, p = 0.251).

CONCLUSION

A systematic approach to identifying patients at high risk for future fracture and tailoring treatment recommendations to these patients appeared to eliminate differences in treatment initiation rates based on older age.

Integrated transcriptome and metabolome analysis reveals molecular responses of the clams to acute hypoxia

Mudflat shellfish have evolved well-adapted strategies for coping with dynamic environmental fluxes and stressful conditions, including oxygen availability. The Manila clams Ruditapes philippinarum are worldwide cultured shellfish in marine intertidal zone, which usually encounter great risk of acute hypoxia exposure in coastal habitats. To reveal the effects of acute hypoxia on metabolic changes of the clams, we performed the integrated analysis of transcriptomics and metabolomics to investigate the global changes of genes and metabolites during acute hypoxia stress at the whole-organism level. The comparative transcriptome analysis reveals that the clams show the remarkable depression in a variety of biological performance, such as metabolic rates, neuronal activity, biomineralization activity, and cell proliferation and differentiation at the hypoxic condition. The metabolomic analysis reveals that amino acid metabolism plays a critical role in the metabolic changes of the clams in response to acute hypoxia. A variety of free amino acids may not only be served as the potential osmolytes for osmotic regulation, but also may contribute to energy production during the acute hypoxia exposure. The metabolite analysis also reveals several important biomarkers for metabolic changes, and provides new insights into how clams deal with acute hypoxia. These findings suggest that clams may get through acute hypoxia stress by the adaptive metabolic strategy to survive short-period of acute hypoxia which is likely to occur in their typical habitat. The present findings will not only shed lights on the molecular and metabolic mechanisms of adaptive strategies under stressful conditions, but also provide the signaling metabolites to assess the physiological states of clams in aquaculture.

Development of EST-SSRs from the ark shell (Scapharca broughtonii) transcriptome and their application in genetic analysis of four populations

BACKGROUND

The ark shell (Scapharca broughtonii) is one of the most economically important mollusks in the Bohai Sea and Yellow Sea of China. In recent years, ark shells from the Korean population were introduced to China for seed propagation and culture.

OBJECTIVE

To explore the impact of the introduction of Korean ark shell on the genetic diversity of native population in China.

METHODS

Simple sequence repeat (SSR) is effective and widely used tool for genetic analysis. In this study, 180 EST-SSRs were selected and verified by polymerase chain reaction and polyacrylamide gel electrophoresis. Subsequently, five polymorphic EST-SSRs were screened and their primers were modified by fluorescein for use in the genetic analysis of four populations.

RESULTS

Genetic analysis showed that 361 alleles amplified by five SSR loci were detected in the four populations. The number of alleles for the five SSRs ranged from 8 to 30, with a mean of 18.05 (standard deviation, SD = 6.492). The effective number of alleles varied from 2.253 to 22.222, with a mean of 10.596 (SD = 4.713). Observed heterozygosity and expected heterozygosity were 0.167-0.833 and 0.566-0.971, with average values of 0.520 (SD = 0.177) and 0.891 (SD = 0.062), respectively. Polymorphic information content ranged from 0.521 to 0.953, with a mean of 0.865 (SD = 0.070). The pairwise genetic differentiation coefficient (F_ST) of the four populations ranged from 0.0267 to 0.0477, showing low genetic differentiation. The phylogenetic tree constructed by neighbor-joining method showed that the genetic distance between the Chinese Dalian native population and three Korean populations was relatively more far than that among those Korean populations.

CONCLUSION

The results indicated that the genetic structure of the Dalian wild population was less affected by the introduced Korean wild populations.

Vibrio harveyi isolated from marine aquaculture species in eastern China and virulence to the large yellow croaker (Larimichthys crocea)

AIMS

Diseases of maricultured species caused by Vibrio harveyi are increasing in China and other regions. This study examined the genetic diversity, antimicrobial susceptibility, plasmid profiles and virulence potential of the V. harveyi isolated from marine organisms farmed in two provinces in eastern China between 2014 and 2019.

METHODS AND RESULTS

A total of 54 V. harveyi were obtained from seven marine species. Enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting revealed substantial genetic heterogeneity among the V. harveyi isolates. There was no significant correlation between ERIC-PCR genotypes and host origins or fish farms. All the isolates were resistant to amoxicillin and ampicillin, and 79·6% to kanamycin. We found that 61·1% of the V. harveyi isolates had plasmid(s) and there were 14 different plasmid profiles. Most isolates from fish hosts (76·5%) contained plasmids; however, 75% of isolates from nonfish hosts lacked plasmids. Experimental infection results showed that isolates with plasmid(s) were more virulent to large yellow croaker than isolates lacking plasmids (P < 0·05).

CONCLUSIONS

This study confirmed that V. harveyi isolates obtained from animals farmed in the coastal region of east China were genetically diverse. Our results suggest that the virulence of various V. harveyi strains to fish is associated with the plasmids they carry.

SIGNIFICANCE AND IMPACT OF THE STUDY

More than 50% of the V. harveyi isolates carried one to 11 plasmids. The plasmid-borne traits of V. harveyi strains might be important for host adaptation and virulence, but they were not associated with susceptibility to the tested antibiotics.

A graphical method for breaking logical loops based on multi-tree structure

Logical loops or circular logics, interpreted as circular supporting relations among systems, remain a longstanding challenge in the probabilistic safety assessment (PSA). Logical loops are commonly found in complex industrial systems. Due to the existence of the logical loops, the minimal cut sets cannot be directly obtained. In order to solve this problem, the logical loops should be broken properly. This paper proposes a graphical method based on multi-tree structure. By constructing the simplified multi-tree, logical loops both in linearly and non-linearly interrelated systems are solved. To illustrate this method, examples of linearly interrelated systems and non-linearly interrelated systems are given in this paper. As a supplement, this method is applied to the well-known complex logical loops in the nuclear power plant. It shows that this method is highly intuitive and efficient by means of graphs.

A graphical method for breaking logical loops based on multi-tree structure

Logical loops or circular logics, interpreted as circular supporting relations among systems, remain a longstanding challenge in the probabilistic safety assessment (PSA). Logical loops are commonly found in complex industrial systems. Due to the existence of the logical loops, the minimal cut sets cannot be directly obtained. In order to solve this problem, the logical loops should be broken properly. This paper proposes a graphical method based on multi-tree structure. By constructing the simplified multi-tree, logical loops both in linearly and non-linearly interrelated systems are solved. To illustrate this method, examples of linearly interrelated systems and non-linearly interrelated systems are given in this paper. As a supplement, this method is applied to the well-known complex logical loops in the nuclear power plant. It shows that this method is highly intuitive and efficient by means of graphs.

Pilot validation of blood-based biomarkers during pregnancy and postpartum in women with prior or current depression

Major depressive disorder (MDD) is more common in women than in men, and evidence of gender-related subtypes of depression is emerging. Previously identified blood-based transcriptomic biomarkers distinguished male and female subjects with MDD from those without the disorder. In the present pilot study, we investigated the performance of these biomarkers in pregnant and postpartum women with prior major depressive episodes, some of whom had current symptomatology. The symptom scores of 13 pregnant and 15 postpartum women were identified by the Inventory of Depressive Symptoms (IDS-SR-30) at the time of blood sampling. Blood levels of the 20 transcriptomic biomarkers and that of estrogen receptor 2 (ESR2), membrane progesterone receptor alpha and beta (mPRα, mPRβ) were measured. In pregnant women, transcript levels of ADCY3, ASAH1, ATP11C, CDR2, ESR2, FAM46A, mPRβ, NAGA, RAPH1, TLR7, and ZNF291/SCAPER showed significant association with IDS-SR-30 scores, of which ADCY3, FAM46A, RAPH1, and TLR7 were identified in previous studies for their diagnostic potential for major depression. ASAH1 and ATP11C were previously also identified as potential markers of treatment efficacy. In postpartum women, transcript levels of CAT, CD59, and RAPH1 demonstrated a trend of association with IDS-SR-30 scores. Transcript levels of ADCY3, ATP11C, FAM46A, RAPH1, and ZNF291/SCAPER correlated with ESR2 and mPRβ expressions in pregnant women, whereas these associations only existed for mPRβ in postpartum women. These results suggest that a blood biomarker panel can identify depression symptomatology in pregnant women and that expression of these biomarker genes are affected by estrogen and/or progesterone binding differently during pregnancy and postpartum.

Comparative transcriptome analysis reveals resistant and susceptible genes in tobacco cultivars in response to infection by Phytophthora nicotianae

Phytophthora nicotianae is highly pathogenic to Solanaceous crops and is a major problem in tobacco production. The tobacco cultivar Beihart1000-1 (BH) is resistant, whereas the Xiaohuangjin 1025 (XHJ) cultivar is susceptible to infection. Here, BH and XHJ were used as models to identify resistant and susceptible genes using RNA sequencing (RNA-seq). Roots were sampled at 0, 6, 12, 24, and 60 h post infection. In total, 23,753 and 25,187 differentially expressed genes (DEGs) were identified in BH and XHJ, respectively. By mapping upregulated DEGs to the KEGG database, changes of the rich factor of "plant pathogen interaction pathway" were corresponded to the infection process. Of all the DEGs in this pathway, 38 were specifically regulated in BH. These genes included 11 disease-resistance proteins, 3 pathogenesis-related proteins, 4 RLP/RLKs, 2 CNGCs, 7 calcium-dependent protein kinases, 4 calcium-binding proteins, 1 mitogen-activated protein kinase kinase, 1 protein EDS1L, 2 WRKY transcription factors, 1 mannosyltransferase, and 1 calmodulin-like protein. By combining the analysis of reported susceptible (S) gene homologs and DEGs in XHJ, 9 S gene homologs were identified, which included 1 calmodulin-binding transcription activator, 1 cyclic nucleotide-gated ion channel, 1 protein trichome birefringence-like protein, 1 plant UBX domain-containing protein, 1 ADP-ribosylation factor GTPase-activating protein, 2 callose synthases, and 2 cellulose synthase A catalytic subunits. qRT-PCR was used to validate the RNA-seq data. The comprehensive transcriptome dataset described here, including candidate resistant and susceptible genes, will provide a valuable resource for breeding tobacco plants resistant to P. nicotianae infections.

Construction of a SNP Fingerprinting Database and Population Genetic Analysis of Cigar Tobacco Germplasm Resources in China

Cigar tobacco is an important economic crop that is widely grown around the world. In recent years, varietal identification has become a frequent problem in germplasm preservation collections, which causes considerable inconvenience and uncertainty in the cataloging and preservation of cigar germplasm resources, in the selection of parental lines for breeding, and in the promotion and use of high quality varieties. Therefore, the use of DNA fingerprints to achieve rapid and accurate identification of varieties can play an important role in germplasm identification and property rights disputes. In this study, we used genotyping-by-sequencing (GBS) on 113 cigar tobacco accessions to develop SNP markers. After filtering, 580,942 high-quality SNPs were obtained. We used the 580,942 SNPs to perform principal component analysis (PCA), population structure analysis, and neighbor joining (NJ) cluster analysis on the 113 cigar tobacco accessions. The results showed that the accessions were not completely classified based on their geographical origins, and the genetic backgrounds of these cigar resources are complex and diverse. We further selected from these high-quality SNPs to obtained 163 SNP sites, 133 of which were successfully converted into KASP markers. Finally, 47 core KASP markers and 24 candidate core markers were developed. Using the core markers, we performed variety identification and fingerprinting in 216 cigar germplasm accessions. The results of SNP fingerprinting, 2D barcoding, and genetic analysis of cigar tobacco germplasm in this study provide a scientific basis for screening and identifying high-quality cigar tobacco germplasm, mining important genes, and broadening the basis of cigar tobacco genetics and subsequent breeding work at the molecular level.

Comparative Transcriptome Profiling Reveals Defense-Related Genes Against Ralstonia solanacearum Infection in Tobacco

Bacterial wilt (BW) caused by Ralstonia solanacearum (R. solanacearum), is a vascular disease affecting diverse solanaceous crops and causing tremendous damage to crop production. However, our knowledge of the mechanism underlying its resistance or susceptibility is very limited. In this study, we characterized the physiological differences and compared the defense-related transcriptomes of two tobacco varieties, 4411-3 (highly resistant, HR) and K326 (moderately resistant, MR), after R. solanacearum infection at 0, 10, and 17 days after inoculation (dpi). A total of 3967 differentially expressed genes (DEGs) were identified between the HR and MR genotypes under mock condition at three time points, including1395 up-regulated genes in the HR genotype and 2640 up-regulated genes in the MR genotype. Also, 6,233 and 21,541 DEGs were induced in the HR and MR genotypes after R. solanacearum infection, respectively. Furthermore, GO and KEGG analyses revealed that DEGs in the HR genotype were related to the cell wall, starch and sucrose metabolism, glutathione metabolism, ABC transporters, endocytosis, glycerolipid metabolism, and glycerophospholipid metabolism. The defense-related genes generally showed genotype-specific regulation and expression differences after R. solanacearum infection. In addition, genes related to auxin and ABA were dramatically up-regulated in the HR genotype. The contents of auxin and ABA in the MR genotype were significantly higher than those in the HR genotype after R. solanacearum infection, providing insight into the defense mechanisms of tobacco. Altogether, these results clarify the physiological and transcriptional regulation of R. solanacearum resistance infection in tobacco, and improve our understanding of the molecular mechanism underlying the plant-pathogen interaction.