The plant trans-Golgi network component ECHIDNA regulates defense, cell death, and endoplasmic reticulum stress.

The trans-Golgi network (TGN) acts as a central platform for sorting and secreting various cargoes to the cell surface, thus being essential for the full execution of plant immunity. However, the fine-tuned regulation of TGN components in plant defense and stress response has been not fully elucidated. Our study revealed that despite largely compromising penetration resistance, the loss-of-function mutation of the TGN component protein ECHIDNA (ECH) induced enhanced postinvasion resistance to powdery mildew in Arabidopsis thaliana. Genetic and transcriptome analyses and hormone profiling demonstrated that ECH loss resulted in salicylic acid (SA) hyperaccumulation via the ISOCHORISMATE SYNTHASE 1 biosynthesis pathway, thereby constitutively activating SA-dependent innate immunity that was largely responsible for the enhanced postinvasion resistance. Furthermore, the ech mutant displayed accelerated SA-independent spontaneous cell death and constitutive POWDERY MILDEW RESISTANCE 4-mediated callose depositions. In addition, ECH loss led to a chronically prolonged endoplasmic reticulum stress in the ech mutant. These results provide insights into understanding the role of TGN components in the regulation of plant immunity and stress responses.

Lead remediation by geological fluorapatite combined with Penicillium Oxalicum and Red yeast.

Phosphate solubilizing fungi Penicillium oxalicum (POX) and Red yeast Rhodotorula mucilaginosa (Rho) have been applied in Pb remediation with the combination of fluorapatite (FAp), respectively. The secretion of oxalic acid by POX and the production of extracellular polymers (EPS) by Rho dominate the Pb remediation. In this study, the potential of Pb remediation by the fungal combined system (POX and Rho) with FAp was investigated. After six days of incubation, the combination of POX and Rho showed the highest Pb remove ratio (99.7%) and the lowest TCLP-Pb concentration (2.9 mg/L). The EPS combined with POX also enhanced Pb remediation, which has a 99.3% Pb removal ratio and 5.5 mg/L TCLP-Pb concentration. Meanwhile, Rho and EPS can also stimulate POX to secrete more oxalic acid, which reached 1510.1 and 1450.6 mg/L in six days, respectively. The secreted oxalic acid can promote FAp dissolution and the formation of lead oxalate and pyromorphite. Meanwhile, the EPS produced by Rho can combine with Pb to form EPS-Pb. In the combined system of POX + Rho and POX + EPS, all of the lead oxalate, pyromorphite, and EPS-Pb were observed. Our findings suggest that the combined application of POX and Rho with FAp is an effective approach for enhancing Pb remediation.

Pathotype Characterization of Plasmodiophora brassicae by European Clubroot Differential and Williams Sets in China.

Clubroot disease caused by the soil-borne Plasmodiophora brassicae is devastating to Brassicaceae crops and spreading rapidly in China in recent years, resulting in great yield losses annually. Virulence of P. brassicae populations specializes and is in dynamic change in the fields. Information on the pathotypes and their distributions is crucial to control the clubroot disease. Presently, the pathotypes of P. brassicae prevalent in China, however, are not well determined. In this study, we used 16 Brassica hosts, including the European Clubroot Differential (ECD) and Williams sets, to designate the pathotypes of 33 P. brassicae populations from 13 provinces. The 33 P. brassicae populations could be divided into 26 pathotypes by the ECD set or seven pathotypes by the Williams set, revealing ECD16/15/31 and ECD16/31/31 or P4 and P2 as the predominant pathotypes. We found that the Brassica rapa differentials ECD01 to ECD04 showed stable and high levels of resistance to most pathotypes of P. brassicae in China, thereby providing valuable resources for clubroot-resistance breeding of Brassicaceae crops. The ECD set exhibited much higher discernibility and further divided the isolates that belonged to the P4 pathotype into 10 ECD pathotypes. Isolates of ECD16/23/31 and ECD16/15/31 were strongly virulent on Huashuang 5R, the first and widely used clubroot-resistant cultivar of oilseed rape in China. As we learn, 26 pathotypes are the most diverse populations of P. brassicae characterized until now in China. Our study provides new insights into virulence specialization of P. brassicae and their geographical distributions, contributing to exploitation of clubroot-resistant resources and the field layout of the present resistant Brassica crops in China.

Kimura's disease successively affecting multiple body parts: a case-based literature review.

BACKGROUND: Kimura's disease is a rare, benign, chronic inflammatory disease that presents as painless, solid masses mainly affecting the deep subcutaneous areas of the head and neck, especially the salivary glands, parotid glands and nearby lymph nodes. It is characterized by elevated peripheral blood eosinophil and Immunoglobulin E (IgE) levels. CASE PRESENTATION: A 31-year-old Asian male presented with an orbital space-occupying lesion lasting for 1.5 years. Ten years prior, surgical excision of bilateral fossa cubitalis and groin masses was performed, and the pathological examination showed "lymphoproliferative disease". One year later, masses reappeared near the surgical sites; they grew slowly and shrank after glucocorticoid treatment. At this point, admission examinations showed in the peripheral blood an eosinophil proportion of 13.4%, a total IgE level of 26,900.00 IU/mL, prurigo present on the whole body, and multiple palpable masses near the bilateral fossa cubitalis and groin. The left eyeball was exophthalmic. The left elbow mass was excised, and the pathological examination confirmed Kimura's disease. Oral glucocorticoid therapy is taken and tapering regularly. The eosinophil count returned to normal, the IgE level gradually decreased, the orbital space-occupying lesion and elbow and groin masses shrank significantly, and the whole-body skin prurigo disappeared. Currently, the patient has been in a stable condition for eighteen months. CONCLUSION: Our case provides a novel insight that Kimura's disease should be involved in the differential diagnosis of inflammatory lesion mass of orbit and also supports systemic regular glucocorticoid as a valuable therapy of such condition, but close follow-up and long-term observation are crucial.

The Characterization of the Phloem Protein 2 Gene Family Associated with Resistance to Sclerotinia sclerotiorum in Brassica napus.

In plants, phloem is not only a vital structure that is used for nutrient transportation, but it is also the location of a response that defends against various stresses, named phloem-based defense (PBD). Phloem proteins (PP2s) are among the predominant proteins in phloem, indicating their potential functional role in PBD. Sclerotinia disease (SD), which is caused by the necrotrophic fungal pathogen S. sclerotiorum (Sclerotinia sclerotiorum), is a devastating disease that affects oil crops, especially Brassica napus (B. napus), mainly by blocking nutrition and water transportation through xylem and phloem. Presently, the role of PP2s in SD resistance is still largely estimated. Therefore, in this study, we identified 62 members of the PP2 gene family in the B. napus genome with an uneven distribution across the 19 chromosomes. A phylogenetic analysis classified the BnPP2s into four clusters (I-IV), with cluster I containing the most members (28 genes) as a consequence of its frequent genome segmental duplication. A comparison of the gene structures and conserved motifs suggested that BnPP2 genes were well conserved in clusters II to IV, but were variable in cluster I. Interestingly, the motifs in different clusters displayed unique features, such as motif 6 specifically existing in cluster III and motif 1 being excluded from cluster IV. These results indicated the possible functional specification of BnPP2s. A transcriptome data analysis showed that the genes in clusters II to IV exhibited dynamic expression alternation in tissues and the stimulation of S. sclerotiorum, suggesting that they could participate in SD resistance. A GWAS analysis of a rapeseed population comprising 324 accessions identified four BnPP2 genes that were potentially responsible for SD resistance and a transgenic study that was conducted by transiently expressing BnPP2-6 in tobacco (Nicotiana tabacum) leaves validated their positive role in regulating SD resistance in terms of reduced lesion size after inoculation with S. sclerotiorum hyphal plugs. This study provides useful information on PP2 gene functions in B. napus and could aid elaborated functional studies on the PP2 gene family.

Genome-Wide Characterization of Trehalose-6-Phosphate Synthase Gene Family of Brassica napus and Potential Links with Agronomic Traits.

Trehalose and trehalose-6 phosphate played important roles in floral organ development, embryonic development, cell morphogenesis, and signal transduction under abiotic stress. However, little is known about the trehalose-6-phosphate synthase (TPS) gene family in Brassica napus. In this study, in total, 26 TPS genes in B. napus (BnTPS genes) were identified and classified into two groups. In each group, the BnTPS genes showed relatively conserved gene structures. The protein-protein interaction (PPI) network and enrichment analysis indicated that BnTPS genes were involved in the glycolysis/gluconeogenesis, fructose and mannose metabolism, galactose metabolism, pentose phosphate pathway, carbohydrate transmembrane transport, trehalose-phosphatase activity, etc. The expression of BnTPS genes varied greatly across different tissues, while most of the BnTPS genes showed a considerable improvement in expression under different abiotic stresses, indicating that BnTPS genes were significantly responsive to the abiotic treatments. In addition, the association mapping analysis revealed that eight BnTPS genes were potential regulators of particular agronomic traits. Among them, the gene BnTPS23 was significantly associated with the primary flowering time (PFT), full flowering time (FFT1), and final flowering time (FFT2), suggesting that BnTPS genes may play an important role in regulating key agronomic traits in B. napus. In summary, our research provides a better understanding of BnTPS genes, facilitates the breeding of superior B. napus varieties, and paves the way for future functional studies.

Genome-Wide Identification and Analysis of Ariadne Gene Family Reveal Its Genetic Effects on Agronomic Traits of Brassica napus.

E3 ligases promote protein ubiquitination and degradation, which regulate every aspect of eukaryotic life. The Ariadne (ARI) proteins of RBR (ring between ring fingers) protein subfamily has been discovered as a group of potential E3 ubiquitin ligases. Only a few available research studies show their role in plant adaptations processes against the external environment. Presently, the functions of ARI proteins are largely unknown in plants. Therefore, in this study, we performed genome-wide analysis to identify the ARI gene family and explore their potential importance in B. napus. A total of 39 ARI genes were identified in the B. napus genome and were classified into three subfamilies (A, B and C) based on phylogenetic analysis. The protein-protein interaction networks and enrichment analysis indicated that BnARI genes could be involved in endoreduplication, DNA repair, proteasome assembly, ubiquitination, protein kinase activity and stress adaptation. The transcriptome data analysis in various tissues provided us an indication of some BnARI genes' functional importance in tissue development. We also identified potential BnARI genes that were significantly responsive towards the abiotic stresses. Furthermore, eight BnARI genes were identified as candidate genes for multiple agronomic traits through association mapping analysis in B. napus; among them, BnaA02g12100D, which is the ortholog of AtARI8, was significantly associated with ten agronomic traits. This study provided useful information on BnARI genes, which could aid targeted functional research and genetic improvement for breeding in B. napus.

A global survey of the transcriptome of allopolyploid Brassica napus based on single-molecule long-read isoform sequencing and Illumina-based RNA sequencing data.

Brassica napus is a recent allopolyploid derived from the hybridization of Brassica rapa (Ar Ar ) and Brassica oleracea (Co Co ). Because of the high sequence similarity between the An and Cn subgenomes, it is difficult to provide an accurate landscape of the whole transcriptome of B. napus. To overcome this problem, we applied a single-molecule long-read isoform sequencing (Iso-Seq) technique that can produce long reads to explore the complex transcriptome of B. napus at the isoform level. From the Iso-Seq data, we obtained 147 698 non-redundant isoforms, capturing 37 403 annotated genes. A total of 18.1% (14 934/82 367) of the multi-exonic genes showed alternative splicing (AS). In addition, we identified 549 long non-coding RNAs, the majority of which displayed tissue-specific expression profiles, and detected 7742 annotated genes that possessed isoforms containing alternative polyadenylation sites. Moreover, 31 591 AS events located in open reading frames (ORFs) lead to potential protein isoforms by in-frame or frameshift changes in the ORF. Illumina RNA sequencing of five tissues that were pooled for Iso-Seq was also performed and showed that 69% of the AS events were tissue-specific. Our data provide abundant transcriptome resources for a transcript isoform catalog of B. napus, which will facilitate genome reannotation, strengthen our understanding of the B. napus transcriptome and be applied for further functional genomic research.

Inhibition of hsa_circ_0003489 shifts balance from autophagy to apoptosis and sensitizes multiple myeloma cells to bortezomib via miR-874-3p/HDAC1 axis.

BACKGROUND: Circular RNAs (circRNAs) crucially regulate tumor progression. In this study, we examined the functional roles and mechanisms of hsa_circ_0003489 in multiple myeloma (MM). METHODS: Upon altering the expressions of hsa_circ_0003489, miR-874-3p, and/or histone deacetylase 1 (HDAC1) in MM1.R cells and treating them with bortezomib (BTZ), cell viability was examined by CCK-8 assay; cell proliferation by Ki-67 immunofluorescence; apoptosis by TUNEL staining, flow cytometry, and western blot; and autophagy by electron microscopy and western blot. The interaction between hsa_circ_0003489 and miR-874-3p as well as that between miR-874-3p and HDAC1 was examined by expressional analysis, dual luciferase reporter assay, and RNA immunoprecipitation. The in vivo impacts of hsa_circ_0003489 on MM growth and sensitivity to BTZ were examined using an MM xenograft mouse model. RESULTS: Knocking down hsa_circ_0003489 significantly inhibited the viability, cell proliferation, and autophagy, while promoting the apoptosis of MM cells in vitro and MM xenograft in vivo. Suppressing hsa_circ_0003489 also further boosted the cytotoxic effects of BTZ in MM cells and reversed its promoting effect on autophagy. Mechanically, hsa_circ_0003489 acted as a sponge of miR-874-3p and positively regulated the expression of miR-874-3p target, HDAC1. MiR-874-3p and HDAC1 essentially mediated the effects of hsa_circ_0003489 on cell viability, proliferation, apoptosis, and autophagy. CONCLUSION: The hsa_circ_0003489/miR-874-3p/HDAC1 axis critically regulates the balance between apoptosis and autophagy. Silencing hsa_circ_0003489 sensitizes MM cells to BTZ by inhibiting autophagy and thus may boost the therapeutic effects of BTZ.

Genome Sequence Resource for the Plant Pathogen Sclerotinia sclerotiorum WH6 Isolated in China.

Sclerotinia sclerotiorum is a notorious fungal pathogen that causes sclerotinia stem rot (SSR) on many important crops in China and worldwide. Here, we present a high-quality genome assembly of S. sclerotiorum strain WH6 using the PacBio SMRT cell platform. The assembled genome has a total size of 38.96 Mbp, with a contig N50 length of 1.90 Mbp, and encodes 10,512 predicted coding genes, including 685 secreted proteins and 65 effector candidates. This is the first report of a S. sclerotiorum genome sequence from China. The WH6 genome sequence provides a valuable resource for facilitating our understanding of S. sclerotiorum-host interactions and SSR control in China and the world.

LDAI-ISPS: LncRNA-Disease Associations Inference Based on Integrated Space Projection Scores.

Long non-coding RNAs (long ncRNAs, lncRNAs) of all kinds have been implicated in a range of cell developmental processes and diseases, while they are not translated into proteins. Inferring diseases associated lncRNAs by computational methods can be helpful to understand the pathogenesis of diseases, but those current computational methods still have not achieved remarkable predictive performance: such as the inaccurate construction of similarity networks and inadequate numbers of known lncRNA-disease associations. In this research, we proposed a lncRNA-disease associations inference based on integrated space projection scores (LDAI-ISPS) composed of the following key steps: changing the Boolean network of known lncRNA-disease associations into the weighted networks via combining all the global information (e.g., disease semantic similarities, lncRNA functional similarities, and known lncRNA-disease associations); obtaining the space projection scores via vector projections of the weighted networks to form the final prediction scores without biases. The leave-one-out cross validation (LOOCV) results showed that, compared with other methods, LDAI-ISPS had a higher accuracy with area-under-the-curve (AUC) value of 0.9154 for inferring diseases, with AUC value of 0.8865 for inferring new lncRNAs (whose associations related to diseases are unknown), with AUC value of 0.7518 for inferring isolated diseases (whose associations related to lncRNAs are unknown). A case study also confirmed the predictive performance of LDAI-ISPS as a helper for traditional biological experiments in inferring the potential LncRNA-disease associations and isolated diseases.

Identification of Flower-Specific Promoters through Comparative Transcriptome Analysis in Brassica napus.

Brassica napus (oilseed rape) is an economically important oil crop worldwide. Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum is a threat to oilseed rape production. Because the flower petals play pivotal roles in the SSR disease cycle, it is useful to express the resistance-related genes specifically in flowers to hinder further infection with S. sclerotiorum. To screen flower-specific promoters, we first analyzed the transcriptome data from 12 different tissues of the B. napus line ZS11. In total, 249 flower-specific candidate genes with high expression in petals were identified, and the expression patterns of 30 candidate genes were verified by quantitative real-time transcription-PCR (qRT-PCR) analysis. Furthermore, two novel flower-specific promoters (FSP046 and FSP061 promoter) were identified, and the tissue specificity and continuous expression in petals were determined in transgenic Arabidopsis thaliana with fusing the promoters to ß-glucuronidase (GUS)-reporter gene. GUS staining, transcript expression pattern, and GUS activity analysis indicated that FSP046 and FSP061 promoter were strictly flower-specific promoters, and FSP046 promoter had a stronger activity. The two promoters were further confirmed to be able to direct GUS expression in B. napus flowers using transient expression system. The transcriptome data and the flower-specific promoters screened in the present study will benefit fundamental research for improving the agronomic traits as well as disease and pest control in a tissue-specific manner.

Syntenic quantitative trait loci and genomic divergence for Sclerotinia resistance and flowering time in Brassica napus.

Oilseed rape (Brassica napus) is an allotetraploid with two subgenomes descended from a common ancestor. Accordingly, its genome contains syntenic regions with many duplicate genes, some of which may have retained their original functions, whereas others may have diverged. Here, we mapped quantitative trait loci (QTL) for stem rot resistance (SRR), a disease caused by the fungus Sclerotinia sclerotiorum, and flowering time (FT) in a recombinant inbred line population. The population was genotyped using B. napus 60K single nucleotide polymorphism arrays and phenotyped in six (FT) and nine (SSR) experimental conditions or environments. In total, we detected 30 SRR QTL and 22 FT QTL and show that some of the major QTL associated with these two traits were co-localized, suggesting a genetic linkage between them. Two SRR QTL on chromosome A2 and two on chromosome C2 were shown to be syntenic, suggesting the functional conservation of these regions. We used the syntenic properties of the genomic regions to exclude genes for selection candidates responsible for QTL-associated traits. For example, 152 of the 185 genes could be excluded from a syntenic A2-C2 region. These findings will help to elucidate polyploid genomics in future studies, in addition to providing useful information for B. napus breeding programs.

Esthetic Evaluation of Implant-Supported Single Crowns: The Implant Restoration Esthetic Index and Patient Perception.

PURPOSE: To test the validity and reliability of a newly developed Implant Restoration Esthetic Index (IREI) and to compare esthetic outcomes reported by patients and professionals. MATERIALS AND METHODS: Ten graduate students and 10 prosthodontists assessed esthetic outcomes of 27 single-tooth implants with the IREI. Six peri-implant soft tissue parameters were measured using visual analog scales: mesial papilla presence, distal papilla presence, gingival trigone, soft tissue curvature, alveolar process deficiency, and soft tissue color and texture, as well as the six crown parameters: crown contour, crown position, crown labial convexity, crown characterization, crown color and translucency, and abutment visibility. The validity was tested based on Pearson's correlation. The internal consistency reliability was analyzed by Cronbach's alpha. Interclass correlation coefficients (ICC) were calculated to express the test-retest reliability and the inter-rater reliability. The correlations between patient and professional evaluations were analyzed by Pearson's correlation. RESULTS: The IREI demonstrated significant correlation (p < 0.05) to the pink esthetic score and white esthetic score (PES/WES). The internal consistency reliability showed a Cronbach's Alpha of 0.830. The test-retest reliability was excellent in both the graduate student group and the prosthodontist group, with ICCs of 0.961 and 0.952, respectively (p < 0.05). The inter-rater reliability was acceptable, with ICCs of 0.649 and 0.667, respectively (p < 0.05). Low correlation coefficients were found between patient and professional evaluations. CONCLUSIONS: The results of this study indicated that the IREI was considered a valid and reliable index involving sufficient parameters for professional esthetic evaluation of single-tooth implant restorations. The patient-reported esthetic outcomes had poor or no significant correlation to professional-reported outcomes.

A Thermodynamic Constitutive Model for Saturated Sand.

This paper establishes a non-equilibrium thermodynamic constitutive model that can predict the undrained shear behavior of saturated sand. Starting from the basic laws of thermodynamics, the model does not require the classical concepts in elasto-plastic models, such as the yield function, the flow rule, and the hardening rule. It is also different from the existing thermodynamic constitutive models in soil mechanics literatures. The model does not use a complex nonlinear elastic potential as usually and introduces a coupling energy dissipative mechanism between the viscosity and elasticity relaxation, which is essential in granular materials. Then this model was used to simulate the undrained shear test of Toyoura sand. The model can predict the critical state, dilatancy-contraction and hardening-softening characteristics of sand during undrained triaxial shearing.

Simultaneous determination of metolazone and valsartan in plasma by on-line SPE coupled with liquid chromatography/tandem mass spectrometry.

Combination of metolazone (0.5 mg) and valsartan (80 mg) has been verified as a promising therapy treatment for hypertension. In order to facilitate to pharmacokinetic research, it needs a method for the simultaneously determination of metolazone and valsartan in biological samples. However, there are no relative reports so far. In order to facilitate to pharmacokinetic research, an on-line solid phase extraction coupled with liquid chromatography-tandem mass spectrometry method for the simultaneous determination of metolazone and valsartan in beagle dog plasma was developed and validated in this study. An on-line solid phase extraction column Retain PEP Javelin (10 mm × 2.1 mm) was used to remove impurities in plasma samples. The metolazone, valsartan and internal standard (losartan) were separated on a Poroshell 120 SB-C18 column (4.6 mm × 50 mm × 2.7 µm) with a gradient elution procedure. Acidified acetonitrile/water mixture was used as a mobile phase. The selected multiple-reaction monitoring mode in positive ion was performed and the parent to the product transitions m/z 366/259, m/z 436.2/291 and m/z 423.4/207 were used to measure the metolazone, valsartan and losartan. The method was linear over the range of 0.1-100 ng/mL and 1-1000 ng/mL for metolazone and valsartan, respectively. This method was validated in terms of specificity, linearity, sensitivity, precision, accuracy, matrix effect, and stability and then successfully applied to pharmacokinetic studies of the metolazone and valsartan combination tablets in beagle dogs.

Influence of Lateral-Medial Sinus Width on No-Grafting Inlay Osteotome Sinus Augmentation Outcomes.

PURPOSE: Intrasinus new bone formation (BF) has been observed after no-grafting osteotome sinus augmentation, and it is hypothesized to be influenced by the dimensions of the maxillary sinus. The aim of this clinical trial is to evaluate the influence of lateral-medial sinus width (SW) on no-grafting osteotome sinus augmentation outcomes using cone-beam computed tomography. PATIENTS AND METHODS: All patients recruited for this prospective study were treated with no-grafting osteotome sinus augmentation with simultaneous implant placement. Cone-beam computed tomography was obtained before, immediately after, and 6 months after the surgical procedure to use for measurements. Descriptive statistics were calculated and univariate, bivariate, and multivariate analysis were conducted to evaluate the influence of average SW and other relevant factors on procedure outcomes, including new BF, residual bone resorption (BR), and change of peri-implant bone height (CPBH). RESULTS: A total of 48 implants placed in 32 elevated sinuses of 29 patients were included. The average SW was 11.3 ± 1.8 mm. Intrasinus BF measured 1.7 ± 0.9 mm at 6 months after surgery. The amount of BR was 0.3 ± 0.9 mm, and CPBH was calculated as 1.3 ± 1.3 mm. Multivariate analysis showed a negative correlation between SW and BF (r = -0.469, P = .001), as well as between SW and CPBH (r = -0.562, P = .001). A positive correlation was discovered between SW and BR (r = 0.311, P = .027) in general. CONCLUSIONS: The lateral-medial SW was observed to have a negative correlation with new BF and CPBH after no-grafting osteotome sinus augmentation.

Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana.

BACKGROUND: Plant disease resistance (R) genes with the nucleotide binding site (NBS) play an important role in offering resistance to pathogens. The availability of complete genome sequences of Brassica oleracea and Brassica rapa provides an important opportunity for researchers to identify and characterize NBS-encoding R genes in Brassica species and to compare with analogues in Arabidopsis thaliana based on a comparative genomics approach. However, little is known about the evolutionary fate of NBS-encoding genes in the Brassica lineage after split from A. thaliana. RESULTS: Here we present genome-wide analysis of NBS-encoding genes in B. oleracea, B. rapa and A. thaliana. Through the employment of HMM search and manual curation, we identified 157, 206 and 167 NBS-encoding genes in B. oleracea, B. rapa and A. thaliana genomes, respectively. Phylogenetic analysis among 3 species classified NBS-encoding genes into 6 subgroups. Tandem duplication and whole genome triplication (WGT) analyses revealed that after WGT of the Brassica ancestor, NBS-encoding homologous gene pairs on triplicated regions in Brassica ancestor were deleted or lost quickly, but NBS-encoding genes in Brassica species experienced species-specific gene amplification by tandem duplication after divergence of B. rapa and B. oleracea. Expression profiling of NBS-encoding orthologous gene pairs indicated the differential expression pattern of retained orthologous gene copies in B. oleracea and B. rapa. Furthermore, evolutionary analysis of CNL type NBS-encoding orthologous gene pairs among 3 species suggested that orthologous genes in B. rapa species have undergone stronger negative selection than those in B .oleracea species. But for TNL type, there are no significant differences in the orthologous gene pairs between the two species. CONCLUSION: This study is first identification and characterization of NBS-encoding genes in B. rapa and B. oleracea based on whole genome sequences. Through tandem duplication and whole genome triplication analysis in B. oleracea, B. rapa and A. thaliana genomes, our study provides insight into the evolutionary history of NBS-encoding genes after divergence of A. thaliana and the Brassica lineage. These results together with expression pattern analysis of NBS-encoding orthologous genes provide useful resource for functional characterization of these genes and genetic improvement of relevant crops.

GIS-based non-grain cultivated land susceptibility prediction using data mining methods.

The purpose of the present study is to predict and draw up non-grain cultivated land (NCL) susceptibility map based on optimized Extreme Gradient Boosting (XGBoost) model using the Particle Swarm Optimization (PSO) metaheuristic algorithm. In order to, a total of 184 NCL areas were identified based on historical records, and a total of 16 NCL susceptibility conditioning factors (NCLSCFs) were considered, based on both a systematic literature survey and local environmental conditions. The results showed that the XGBoost model optimized by PSO performed well in comparison to other machine learning algorithms; the values of sensitivity, specificity, PPV, NPV, and AUC are 0.93, 0.89, 0.88, 0.93, and 0.96, respectively. Slope, rainfall, fault density, distance from fault and drainage density are most important variables. According to the results of this study, the use of meta-innovative algorithms such as PSO can greatly enhance the ability of machine learning models.