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The Oomycete plant pathogen,Phytophthora capsici, causes root, crown, and fruit rot of winter squash (Cucurbita moschata) and limits production. SomeC. moschatacultivars develop age-related resistance (ARR), whereby fruit develop resistance toP. capsici14 to 21 days postpollination (DPP) because of thickened exocarp; however, wounding negates ARR. We uncovered the genetic mechanisms of ARR of twoC. moschatacultivars, Chieftain and Dickenson Field, that exhibit ARR at 14 and 21 DPP, respectively, using RNA sequencing. The sequencing was conducted using RNA samples from ‘Chieftain’ and ‘Dickenson Field’ fruit at 7, 10, 14, and 21 DPP. A differential expression and subsequent gene set enrichment analysis revealed an overrepresentation of upregulated genes in functional categories relevant to cell wall structure biosynthesis, cell wall modification/organization, transcription regulation, and metabolic processes. A pathway enrichment analysis detected upregulated genes in cutin, suberin monomer, and phenylpropanoid biosynthetic pathways. A further analysis of the expression profile of genes in those pathways revealed upregulation of genes in monolignol biosynthesis and lignin polymerization in the resistant fruit peel. Our findings suggest a shift in gene expression toward the physical strengthening of the cell wall associated with ARR toP. capsici. These findings provide candidate genes for developingCucurbitacultivars with resistance toP. capsiciand improve fruit rot management inCucurbitaspecies. 

Reaction of aldehydes with pivaloyl chloride and then zinc offers versatile and comparatively safe access to carbenes. 

Abstract Background Availability of plant genome sequences has led to significant advances. However, with few exceptions, the great majority of existing genome assemblies are derived from short read sequencing technologies with highly uneven read coverages indicative of sequencing and assembly issues that could significantly impact any downstream analysis of plant genomes. In tomato for example, 0.6% (5.1 Mb) and 9.7% (79.6 Mb) of short-read based assembly had significantly higher and lower coverage compared to background, respectively. Results To understand what the causes may be for such uneven coverage, we first established machine learning models capable of predicting genomic regions with variable coverages and found that high coverage regions tend to have higher simple sequence repeat and tandem gene densities compared to background regions. To determine if the high coverage regions were misassembled, we examined a recently available tomato long-read based assembly and found that 27.8% (1.41 Mb) of high coverage regions were potentially misassembled of duplicate sequences, compared to 1.4% in background regions. In addition, using a predictive model that can distinguish correctly and incorrectly assembled high coverage regions, we found that misassembled, high coverage regions tend to be flanked by simple sequence repeats, pseudogenes, and transposon elements. Conclusions Our study provides insights on the causes of variable coverage regions and a quantitative assessment of factors contributing to plant genome misassembly when using short reads and the generality of these causes and factors should be tested further in other species.