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Steinernema carpocapsae

ABSTRACT: 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"

PROVIDER: PRJNA337956 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4005250.fastq.gz	Fastqsanger.gz
	SRR4005251.fastq.gz	Fastqsanger.gz
	SRR4005252.fastq.gz	Fastqsanger.gz
	SRR4005253.fastq.gz	Fastqsanger.gz
	SRR4005254.fastq.gz	Fastqsanger.gz

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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. infective juveniles S. carpocapsae were incubated with and without haemolymph, three replicates

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

2016-09-05 | GSE85256 | GEO

Steinernema carpocapsae

Project description:Steinernema carpocapsae genomic variation

| PRJNA351254 | ENA

Steinernema carpocapsae

Project description:Steinernema carpocapsae Transcriptome or Gene expression

| PRJNA525359 | ENA

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 strain:Breton

Project description:Steinernema carpocapsae genome sequencing project

| PRJNA39853 | ENA

Transcriptomic analysis of Steinernema nematodes highlights metabolic costs associated to Xenorhabdus endosymbiont association and rearing conditions

Project description:We investigate the potential metabolic costs for Steinernema nematode in relation to the maintenance and vectoring of their Xenorhabdus endosymbionts. we performed a comparative dual RNA-seq analysis of infective juveniles (IJs) of two symbiotic partners: S. carpocapsae-X. nematophila and S. puntauvense-X. bovienii.

2022-03-16 | GSE185177 | GEO

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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Steinernema carpocapsae strain:ALL

Project description:Steinernema carpocapsae strain:ALL Genome sequencing and assembly

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Comparative genomics of Steinernema reveals deeply conserved regulatory networks in nematodes

Project description:Parasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as pathogens, including deadly parasites of insects that are used in biological control. We have sequenced and analyzed the draft genomes and transcriptomes of the entomopathogenic nematode Steinernema carpocapsae and four congeners (S. scapterisci, S. monticolum, S. feltiae, S. glaseri) distantly related to Caenorhabditis elegans. We used these genomes to establish phylogenetic relationships, explore gene conservation across species, identify genes uniquely expanded in insect parasites, and to identify conserved non-coding regulatory motifs that influence similar biological processes. Protein domain analysis of these genomes reveals a striking expansion of numerous putative parasitism genes including certain protease and protease inhibitor families as well as fatty acid- and retinol-binding proteins. We identify rapid evolution and expansion of the important developmental Hox gene cluster and identify novel conserved non-coding regulatory motifs associated with orthologous genes in Steinernema and Caenorhabditis. The deep conservation of the network of non-coding DNA motifs between these two genera for a subset of orthologous genes involved in neurogenesis and embryonic development suggests that a kernel of protein-DNA relationships is conserved through nematode evolution. We analyzed the gene expression of a total of 24 RNA-seq samples from 3 nematode species( S. carpocapsae, S. feltiae, and C. elegans) for comparative analysis. We collected the RNA at four developmental time points (mixed embryo, L1, infective juvenile/dauer, young adult) for each species in replicates.

2015-06-05 | E-GEOD-68588 | biostudies-arrayexpress

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