Data from: Genetic divergence, range expansion and possible homoploid hybrid speciation among pine species in northeast China

Although homoploid hybrid speciation in plants is probably more common than previously realized, there are few well-documented cases of homoploid hybrid origin in conifers. We examined genetic divergence between two currently widespread pines in northeast China, Pinus sylvestris var. mongolica and P. densiflora, and also whether two narrowly distributed pines in the same region, P. funebris and P. takahasii, might have originated from the two widespread species by homoploid hybrid speciation. Our results, based on population genetic analysis of chloroplast (cp), mitochondrial (mt) DNA, and nuclear gene sequence variation, showed that the two widespread species were divergent for both cp- and mtDNA variation, and also for haplotype variation at two of eight nuclear gene loci surveyed. Our analysis further indicated that P. sylvestris var. mongolica and P. densiflora remained allopatric during the most severe Quaternary glacial period that occurred in northeast China, but subsequently exhibited rapid range expansions. Pinus funebris and P. takahasii, were found to contain a mixture of chlorotypes and nuclear haplotypes that distinguish P. sylvestris var. mongolica and P. densiflora, in support of the hypothesis that they possibly originated via homoploid hybrid speciation following secondary contact and hybridization between P. sylvestris var. mongolica and P. densiflora

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The characteristics and clinical relevance of tumor fusion burden in head and neck squamous cell carcinoma

Abstract Background Recent studies suggest that tumor fusion burden (TFB) is a hallmark of immune infiltration in prostate cancer, the correlation of TFB with immune microenvironment, and genomic patterns in head and neck squamous cell carcinomas (HNSC) remain largely unclear. Methods Gene fusion, genomic, transcriptomic, and clinical data of HNSC patients from the cancer genome atlas (TCGA) database were collected to analyze the correlation of TFB with mutation patterns, tumor immune microenvironment, and survival time in HNSC patients. Results Human papillomavirus (HPV) (−) patients with low TFB exhibited significantly enhanced CD8+ T cells infiltration and cytolysis activity and increased level of interferon‐gamma (IL‐γ), human leukocyte antigen (HLA) class I, and chemokines. Moreover, TFB was positively correlated with TP53 mutation, score of gene copy number, and loss of heterozygosity (LOH), as well as the biological progress of epithelial‐mesenchymal transition (EMT), metastasis, and stem cell characteristics. Further analysis revealed that HPV (−) HNSC patients with low TFB have a better prognosis. Conclusions Our data revealed the correlation of TFB with tumor immune microenvironment and predictive features for immunotherapy, implying tumors with low TFB may be potential candidates for immunotherapeutic agents. Moreover, the TFB low group had prolonged overall survival (OS) in the HPV (−) HNSC cohort

Synergistic Activity of Dimethyl Disulfide Mixtures with Two Chemical Compounds against <i>Meloidogyne incognita</i>

The prevention and control of root-knot nematode disease is a worldwide challenge and there are not many varieties of pesticides for nematode control. To meet the huge market demand, the development of new nematicides is urgently needed. The lethal effects of soil fumigant dimethyl disulfide (DMDS) mixed with the chemical compounds copper sulfate (CuSO4) and ammonium bicarbonate (NH4HCO3) on Meloidogyne incognita were tested using the immersion method. The results showed that the LC50 of DMDS, CuSO4, and NH4HCO3 on the second stage juveniles (J2) of M. incognita were 19.28, 187.42, and 213.49 mg/L, respectively. The lethal effect on J2 were enhanced with the combination of DMDS and CuSO4 or NH4HCO3. The compound uses of DMDS (2.5 mg/L) and CuSO4 (46.58 mg/L) or NH4HCO3 (80.25 mg/L) have obvious synergistic effects on the control of M. incognita, with corrected mortalities of 97.09% and 94.00%, respectively. The synergistic effect of fumigant and chemical compounds on M. incognita was investigated to provide a new concept for the control of root-knot nematode disease

Effects of Granule Size Ranges on Dazomet Degradation and Its Persistence with Different Environmental Factors

Pesticides are considered the most effective way to protect crops. However, irrational use has caused resources waste and environmental pollution. Dazomet (DZ) is a soil fumigant that has been used in many countries for decades, although it has caused occasional crop damage or insufficient control efficacy in some circumstances. In this study, the effects of DZ&rsquo;s granule size and exposure to various environmental conditions on DZ degradation when used as a fumigant were demonstrated. The degradation rate of DZ was closely related to granule size. The half-life of larger DZ granules was longer than smaller granules with all studied environmental factors. The degradation rate decreased as the DZ usage (90&ndash;360 mg/kg) increased and different granule sizes showed the same variation trend. The half-life in each of the five granule size ranges tested decreased significantly as the temperature increased. DZ half-life decreased by 4.67&ndash;6.59 times as the temperature increased from 4 to 35 &deg;C. Moreover, DZ usage and temperature affected the half-life of granules &gt;400 and 300&ndash;400 &mu;m in diameter significantly more than &lt;100 &mu;m granules. The half-life of all DZ granule sizes was reduced by 13.9&ndash;47.4% in alkaline compared to acidic conditions (pH from 9 to 5). Moreover, elevated temperatures could not only promote the production of methyl isothiocyanate (MITC) but accelerate its dissipation. The interactions between DZ granule size, dosage, temperature, and pH provide practical guidance on methods to improve DZ&rsquo;s efficacy against pests and reduce the risk of phytotoxicity

Effects of Granule Size Ranges on Dazomet Degradation and Its Persistence with Different Environmental Factors

Pesticides are considered the most effective way to protect crops. However, irrational use has caused resources waste and environmental pollution. Dazomet (DZ) is a soil fumigant that has been used in many countries for decades, although it has caused occasional crop damage or insufficient control efficacy in some circumstances. In this study, the effects of DZ’s granule size and exposure to various environmental conditions on DZ degradation when used as a fumigant were demonstrated. The degradation rate of DZ was closely related to granule size. The half-life of larger DZ granules was longer than smaller granules with all studied environmental factors. The degradation rate decreased as the DZ usage (90–360 mg/kg) increased and different granule sizes showed the same variation trend. The half-life in each of the five granule size ranges tested decreased significantly as the temperature increased. DZ half-life decreased by 4.67–6.59 times as the temperature increased from 4 to 35 °C. Moreover, DZ usage and temperature affected the half-life of granules >400 and 300–400 μm in diameter significantly more than <100 μm granules. The half-life of all DZ granule sizes was reduced by 13.9–47.4% in alkaline compared to acidic conditions (pH from 9 to 5). Moreover, elevated temperatures could not only promote the production of methyl isothiocyanate (MITC) but accelerate its dissipation. The interactions between DZ granule size, dosage, temperature, and pH provide practical guidance on methods to improve DZ’s efficacy against pests and reduce the risk of phytotoxicity

Bio-activation of soil with beneficial microbes after soil fumigation reduces soil-borne pathogens and increases tomato yield.

peer reviewedSoil-borne diseases have become increasingly problematic for farmers producing crops intensively under protected agriculture. Although soil fumigants are convenient and effective for minimizing the impact of soil-borne disease, they are most often detrimental to beneficial soil microorganisms. Previous research showed that bio-activation of soil using biological control agents present in biofertilizers or organic fertilizers offered promise as a strategy for controlling soil-borne pathogens when the soil was bio-activated after fumigation. Our research sought to determine how bio-activation can selectively inhibit pathogens while promoting the recovery of beneficial microbes. We monitored changes in the soil's physicochemical properties, its microbial community and reductions in soil-borne pathogens. We found that the population density of Fusarium and Phytophthora were significantly reduced and tomato yield was significantly increased when the soil was bio-activated. Soil pH and soil catalase activity were significantly increased, and the soil's microbial community structure was changed, which may have enhanced the soil's ability to reduce Fusarium and Phytophthora. Our results showed that soil microbial diversity and relative abundance of beneficial microorganisms (such as Sphingomonas, Bacillus, Mortierella and Trichoderma) increased shortly after bio-activation of the soil, and were significantly and positively correlated with pathogen suppression. The reduction in pathogens may have been due to a combination of fumigation-fertilizer that reduced pathogens directly, or the indirect effect of an optimized soil microbiome that improved the soil's non-biological factors (such as soil pH, fertility structure), enhanced the soil's functional properties and increased tomato yield

Transcriptome Analysis and Genome-Wide Gene Family Identification Enhance Insights into Bacterial Wilt Resistance in Tobacco

Bacterial wilt, caused by the Ralstonia solanacearum species complex, is one of the most damaging bacterial diseases in tobacco and other Solanaceae crops. In this study, we conducted an analysis and comparison of transcriptome landscape changes in seedling roots of three tobacco BC4F5 lines, C244, C010, and C035, with different resistance to bacterial wilt at 3, 9, 24, and 48 h after R. solanacearum infection. A number of biological processes were highlighted for their differential enrichment between C244, C010, and C035, especially those associated with cell wall development, protein quality control, and stress response. Hence, we performed a genome-wide identification of seven cell wall development-related gene families and six heat shock protein (Hsp) families and proposed that genes induced by R. solanacearum and showing distinct expression patterns in C244, C010, and C035 could serve as a potential gene resource for enhancing bacterial wilt resistance. Additionally, a comparative transcriptome analysis of R. solanacearum-inoculated root samples from C244 and C035, as well as C010 and C035, resulted in the identification of a further 33 candidate genes, of which Nitab4.5_0007488g0040, a member of the pathogenesis-related protein 1 (PR-1) family, was found to positively regulate bacterial wilt resistance, supported by real-time quantitative PCR (qRT-PCR) and virus-induced gene silencing (VIGS) assays. Our results contribute to a better understanding of molecular mechanisms underlying bacterial wilt resistance and provide novel alternative genes for resistance improvement

The Appropriate Particle Size of Dazomet Can Ensure the Soil Fumigation Effect from the Source

Dazomet (DZ) is a soil fumigant that has been used for decades at many countries, however it was reported to have caused phytotoxicity and reduced crop yield in many countries. In this experiment, in order to clarify whether the diameter of DZ is related to phytotoxicity, this research investigated the degradation rate of DZ with different diameter ranges under three soil types held at 15, 20 or 30% soil water content at 4, 15, 25 or 37 &deg;C, and monitored concentrations of methyl isothiocyanate (MITC) produced when Shunyi soil was fumigated with DZ using the different particle sizes ranges. When the soil water content and temperature increased, the degradation rate of DZ with different particle sizes accelerated. However, the degradation rate of DZ with large particle sizes was still lower than small particle sizes. NO3&minus;-N, available phosphorus (AP), available potassium (AK), pH and silt content in the soil were all significantly positively correlated with &lt;100 &mu;m DZ, and significantly negatively correlated with 300&ndash;400 &mu;m and &gt;400 &mu;m DZ. However, organic matter (OM) and sand content produced the opposite result. The maximum concentration of MITC produced by 100&ndash;300 &mu;m of DZ in 25 &deg;C Shunyi soil at 30% water content were 102.2 mg/kg at 24 h. DZ produced peaks significantly higher and earlier at 30% than at 20% soil water content. We recommend selecting DZ manufactured with particle in the range of 100 to 300 &mu;m, fumigating at about 25 &deg;C and ensuring that about 30% soil water content is present in the soil immediately after fumigation

Identification of stably expressed QTL for resistance to black shank disease in tobacco (Nicotiana tabacum L.) line Beinhart 1000-1

Cigar line Beinhart 1000-1 has effective durable resistance to black shank (BS) and is considered one of the most resistant sources in tobacco (Nicotiana tabacum L.). To investigate the inheritance and identification of stable quantitative trait loci (QTL) for BS response, F2, BC1F2 individuals and BC1F2:3 lines were produced from a cross between Beinhart 1000-1 and Xiaohuangjin 1025. Two major quantitative trait loci (M-QTL) named qBS7 and qBS17 were repeatedly detected under different conditions. QTL qBS7 was mapped to the region between PT30174 and PT60621 and explained 17.40%–25.60% of the phenotypic variance under different conditions. The other QTL qBS17 in interval PT61564–PT61538 of linkage group 17 was detected in a BC1F2 population in the field and in BC1F2:3 in both the field and at the seedling stage, explaining 6.90% to 11.60% of the phenotypic variance. The results improve our understanding of the inheritance of resistance to BS and provide information that can be used in marker-assisted breeding. Keywords: Phytophthora nicotianae, Quantitative trait locus, Plant disease resistance, Simple sequence repeat