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Heterorhabditis bacteriophora

ABSTRACT: Heterorhabditis bacteriophora

PROVIDER: PRJNA20357 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR005473.fastq.gz	Fastqsanger.gz
	SRR005474.fastq.gz	Fastqsanger.gz

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Project description:This research investigates the molecular mechanisms of trait deterioration of two experimental lines of entamopathogenic nematodes, an inbred line (L5M) and its original parental line (OHB), created by sub-culturing different experimental lines of the nematode-bacterium complex over 20 passages in insect hosts. These lines differed in their virulence, heat tolerance and fecundity . Transcriptional profiles of the two experimental lines were determined and select differentially expressed genes were validated by quantitative PCR. Samples from four biological replicates each of the parental strain (OHB) and the laboratory strain (L5M) were hybridized to the custom H. bacteriophora arrays.

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Project description:We report the application of next generation RNA sequencing to analyze the transcriptional response of Drosophila adult flies to infection by the insect pathogenic nematodes Heterorhabditis bacteriophora and their mutualistic bacteria Photorhabdus luminescens, either separately or together. We find that Heterorhabditis and Photorhabdus differentially modulate a large number of genes, many of which participate in metabolic functions, stress responses, repression of gene transcription and neuronal activities. We have also identified Drosophila genes with potential role in nematode recognition and others with putative anti-nematode properties. These findings generate novel insights into how the host immune function is shaped to respond against nematode parasites and their associated bacteria. Transcriptional profiles of Drosophila wild-type adult flies infected with Heterorhabditis bacteriophora carrying or lacking Photorhabdus or the bacteria alone were generated at 12 and 30 hours post infection using Illumina deep sequencing technology.

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Project description:Heterorhabditis bacteriophora transcriptome

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Improving the annotation of the Heterorhabditis bacteriophora genome.

Project description:Genome assembly and annotation remain exacting tasks. As the tools available for these tasks improve, it is useful to return to data produced with earlier techniques to assess their credibility and correctness. The entomopathogenic nematode Heterorhabditis bacteriophora is widely used to control insect pests in horticulture. The genome sequence for this species was reported to encode an unusually high proportion of unique proteins and a paucity of secreted proteins compared to other related nematodes. We revisited the H. bacteriophora genome assembly and gene predictions to determine whether these unusual characteristics were biological or methodological in origin. We mapped an independent resequencing dataset to the genome and used the blobtools pipeline to identify potential contaminants. While present (0.2% of the genome span, 0.4% of predicted proteins), assembly contamination was not significant. Re-prediction of the gene set using BRAKER1 and published transcriptome data generated a predicted proteome that was very different from the published one. The new gene set had a much reduced complement of unique proteins, better completeness values that were in line with other related species' genomes, and an increased number of proteins predicted to be secreted. It is thus likely that methodological issues drove the apparent uniqueness of the initial H. bacteriophora genome annotation and that similar contamination and misannotation issues affect other published genome assemblies.

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