Strongyloides RNA-seq Browser: a web-based software platform for on-demand bioinformatics analyses of Strongyloides species

Abstract

Soil-transmitted gastrointestinal parasitic nematodes infect approximately 1 billion people worldwide, predominantly in low-resource communities. Skin-penetrating gastrointestinal nematodes in the genus Strongyloides are emerging as model systems for mechanistic studies of soil-transmitted helminths due to the growing availability of functional genomics tools for these species. To facilitate future genomics studies of Strongyloides species, we have designed a web-based application, the Strongyloides RNA-seq Browser, that provides an open source, user-friendly portal for accessing and analyzing Strongyloides genomic expression data. Specifically, the Strongyloides RNA-seq Browser takes advantage of alignment-free read mapping tools and R-based transcriptomics tools to re-analyze publicly available RNA sequencing datasets from four Strongyloides species: Strongyloides stercoralis, Strongyloides ratti, Strongyloides papillosus, and Strongyloides venezuelensis. This application permits on-demand exploration and quantification of gene expression across life stages without requiring previous coding experience. Here, we describe this interactive application and demonstrate how it may be used by nematode researchers to conduct a standard set of bioinformatics queries.

Carbon dioxide shapes parasite-host interactions in a human-infective nematode

“…The Ss-gcy-9 gene encodes a protein with a domain structure resembling that of other rGC proteins – it includes an extracellular ligand-binding domain, a transmembrane domain, an intracellular kinase domain, and a guanylate cyclase domain (Figure S2A-B). To better characterize the Ss - gcy-9 gene, we first analyzed its expression levels across life stages using the available life-stage-specific transcriptomic dataset for S. stercoralis [29–31]. We found that this gene is expressed at low levels in post-parasitic L1/L2 larvae and free-living adults but is highly expressed in iL3s (Figure 2A).…”

“…Each data point represents a single biological replicate; lines indicate medians. Data were analyzed using the Strongyloides RNA-seq browser [29]. B.…”

The Wild Worm Codon Adapter: a web tool for automated codon adaptation of transgenes for expression in non-Caenorhabditis nematodes

“…For C. elegans and Strongyloides species, results were filtered to identify six functional subsets: the 2% of genes with highest and lowest S. ratti CAI values, the 2% of genes with the highest and lowest C. elegans CAI values, and the 2% of genes with highest and lowest RNA-seq expression in free-living females. Log 2 counts per million (CPM) expression in free-living adult females was downloaded from the Strongyloides RNA-seq Browser ( Bryant et al 2021 ). For statistical comparisons of the expression of the highest and lowest Strongyloides -codon-adapted genes, relative to all genes, a 2-way ANOVA (type III) with Tukey post-hoc tests was performed in R using the car package v3.0-8.…”

Advancing Strongyloides omics data: bridging the gap with Caenorhabditis elegans

“…This raises questions about how clinical steroids and other medication can affect parasite development and survival in endemic strongyloidiasis. As we continue to generate and collate Strongyloides transcriptome data, data repositories and software such as the Strongyloides RNA-seq Browser [76] will be useful in combining existing data from Strongyloides species and will facilitate easier comparative gene expression and enrichment analyses.…”