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Hybrid assembly of the genome of the entomopathogenic nematode Steinernema carpocapsae identifies the X-chromosome.

ABSTRACT: Hybrid assembly of the genome of the entomopathogenic nematode Steinernema carpocapsae identifies the X-chromosome.

PROVIDER: PRJNA525461 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8667930_1.fastq.gz	Fastqsanger.gz
	SRR8667930_2.fastq.gz	Fastqsanger.gz
	SRR8667940_1.fastq.gz	Fastqsanger.gz
	SRR8667940_2.fastq.gz	Fastqsanger.gz
	SRR8667950_1.fastq.gz	Fastqsanger.gz

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Hybrid assembly of the genome of the entomopathogenic nematode Steinernema carpocapsae identifies the X-chromosome.

Project description:Entomopathogenic nematodes from the genus Steinernema are lethal insect parasites that quickly kill their insect hosts with the help of their symbiotic bacteria. Steinernema carpocapsae is one of the most studied entomopathogens due to its broad lethality to diverse insect species and its effective commercial use as a biological control agent for insect pests, as well as a genetic model for studying parasitism, pathogenesis, and symbiosis. In this study, we used long-reads from the Pacific Biosciences platform and BioNano Genomics Irys system to assemble the best genome of S. carpocapsae ALL strain to date, comprising 84.5 Mb in 16 scaffolds, with an N50 of 7.36Mb. The largest scaffold, with 20.9Mb, was identified as chromosome X based on sex-specific genome sequencing. The high level of contiguity allowed us to characterize gene density, repeat content, and GC content. RNA-seq data from 17 developmental stages, spanning from embryo to adult, were used to predict 30,957 gene models. Using this new genome, we performed a macrosyntenic analysis to Caenorhabditis elegans and Pristionchus pacificus and found S. carpocapsae’s chromosome X to be primarily orthologous to C. elegans’ and P. pacificus’ chromosome II and IV. We also investigated the expansion of protein families and gene expression differences between male and female stage nematodes. This new genome and more accurate set of annotations provide a foundation for new comparative genomic and gene expression studies within the Steinernema clade and across the Nematode phylum.

2019-03-06 | GSE127823 | GEO

Steinernema carpocapsae Breton small RNA sequencing insect in vitro simulation system, from "The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle"

Project description:We report small RNA sequencing of the entomopathogenic nematode Steinernema carpocapsae. The nematodes were grown in liquid culture in homogenates of pig kidney/fat and infective juveniles were gathered. Then Galleria mellonella insect haemolymph was added to simulate insect infection, control nematodes weren't added haemolymph. Nematodes were collected after two hours after haemolymph addition.

2016-09-05 | GSE85256 | GEO

2016-09-05 | E-GEOD-85256 | biostudies-arrayexpress

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Project description:Steinernema carpocapsae genomic variation

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Steinernema carpocapsae and Steinernema puntauvense

Project description:Transcriptomic data from infective juvenile of two entomopathogenic nematodes: Steinernema carpocapsae and Steinernema puntauvense

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Project description:Steinernema carpocapsae Raw sequence reads

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Activated entomopathogenic nematode infective juveniles release lethal venom proteins

Project description:Entomopathogenic nematodes (EPNs) are unique parasitic nematodes due to their symbiosis with entomopathogenic bacteria and their ability to kill insect hosts quickly after infection. Although it has been widely believed that EPNs rely on their bacterial partners for killing insect hosts, compelling evidence from previous studies challenges this model. We developed an improved method of activating millions of Steinernema carpocapsae infective juveniles (IJs) in vitro to harvest excreted/secreted (ES) proteins for bioactivity tests and proteomics analysis. We found that a low dose of the ES proteins from early activated nematodes is lethal to Drosophila melanogaster adults within 2-6 hours. We analyzed the protein composition of this venom using mass spectrometry and identified 472 proteins. Many of these venom proteins share high homology with those of vertebrate-parasitic nematodes. Among many different families of proteins found in the venom, proteases and protease inhibitors are especially abundant. Some toxin-related proteins such as Shk domain-containing proteins were also detected. We further analyzed the transcriptomes of individual non-activated IJs and nematodes that were activated in vitro and in vivo, which revealed a dramatic shift in gene expression during IJ activation. By comparing the whole transcriptomes and the genes encoding venom proteins between the in vitro and in vivo activated nematodes, we confirmed that the in vitro activation is a good approximation of the in vivo process. In summary, our findings strongly support a new model that S. carpocapsae and likely other Steinernema EPNs have a more active role in contributing to the pathogenicity of the nematode-bacterium complex than simply relying on their symbiotic bacteria. Furthermore, we propose that EPNs are a good model system for investigating vertebrate- and human-parasitic nematodes, especially regarding the function of ES products.

2017-03-27 | GSE89961 | GEO

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Project description:Steinernema carpocapsae Transcriptome or Gene expression

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Secreted proteins from activated infective juveniles of the entomopathogenic nematode Steinernema capocapsae

Project description:The infective juveniles (IJs) of entomopathogenic nematodes such as Steinernema carpocapsae are the only stage in their life cycle that is free living before infecting new hosts. When the IJs enter the host, they activate and secrete proteins to modulate the host immune system. The secreted proteins are identified by mass spectrometry in this study.

2016-11-01 | MSV000080306 | MassIVE

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Project description:Steinernema carpocapsae Breton small RNA sequencing insect in vitro simulation system, from "The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle"

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