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Variant linkage analysis using de novo transcriptome sequencing identifies a conserved phosphine resistance gene in insects

ABSTRACT: Variant linkage analysis using de novo transcriptome sequencing identifies the conserved phosphine resistance locus rph1 in insects

PROVIDER: PRJEB24430 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2253745_1.fastq.gz	Fastqsanger.gz
	ERR2253745_2.fastq.gz	Fastqsanger.gz
	ERR2255746_1.fastq.gz	Fastqsanger.gz
	ERR2255746_2.fastq.gz	Fastqsanger.gz
	ERR2260791_1.fastq.gz	Fastqsanger.gz

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Variant Linkage Analysis Using de Novo Transcriptome Sequencing Identifies a Conserved Phosphine Resistance Gene in Insects.

Project description:Next-generation sequencing methods enable identification of the genetic basis of traits in species that have no prior genomic information available. The combination of next-generation sequencing, variant analysis, and linkage is a powerful way of identifying candidate genes for a trait of interest. Here, we used a comparative transcriptomics [RNA sequencing (RNAseq)] and genetic linkage analysis approach to identify the rph1 gene. rph1 variants are responsible for resistance to the fumigant phosphine (PH3) that is used to control insect pests of stored grain. In each of the four major species of pest insect of grain we have investigated, there are two major resistance genes, rph1 and rph2, which interact synergistically to produce strongly phosphine-resistant insects. Using RNAseq and genetic linkage analyses, we identified candidate resistance (rph1) genes in phosphine-resistant strains of three species: Rhyzopertha dominica (129 candidates), Sitophilus oryzae (206 candidates), and Cryptolestes ferrugineus (645 candidates). We then compared these candidate genes to 17 candidate resistance genes previously mapped in Tribolium castaneum and found only one orthologous gene, a cytochrome b5 fatty acid desaturase (Cyt-b5-r), to be associated with the rph1 locus in all four species. This gene had either missense amino acid substitutions and/or insertion/deletions/frameshift variants in each of 18 phosphine-resistant strains that were not observed in the susceptible strains of the four species. We propose a model of phosphine action and resistance in which phosphine induces lipid peroxidation through reactive oxygen species generated by dihydrolipoamide dehydrogenase, whereas disruption of Cyt-b5-r in resistant insects decreases the polyunsaturated fatty acid content of membranes, thereby limiting the potential for lipid peroxidation.

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Project description:Phosphine (PH3) is a highly toxic, corrosive, flammable, heavier-than-air gas that is a commonly used fumigant. Although the mechanism of toxicity is unclear, PH3 is thought to be a metabolic poison. PH3 exposure induces multi-organ toxicity and no effective antidotes or therapeutics have been identified. To better characterize the mechanism(s) driving PH3-induced toxicity we have performed transcriptomic analysis on conscious adult male Sprague-Dawley rats following whole-body inhalation exposure to phosphine gas at three concentrations. PH3 exposure induced concentration- and time-dependent changes in gene expression across multiple tissues.

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Phosphine-Nitrogen-Phosphine chelated CoCl2 (Co68) is a novel therapeutic agent for pancreatic cancer [ATAC-seq]

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