NemChR-DB: a database of parasitic nematode chemosensory G-protein coupled receptors

Langeland, Andrea; Hawdon, John M.; O'Halloran, Damien M.

doi:10.1016/j.ijpara.2020.09.007

“…Many nematode chemoreceptors are G protein-coupled receptors (GPCRs), and nematode genomes encode large numbers of predicted chemoreceptor GPCRs (Bargmann 2006; Wheeler et al . 2020; Langeland et al . 2020).…”

Section: Resultsmentioning

confidence: 99%

“…File S7 contains a list of chemoreceptor gene IDs for all Strongyloides species (Wheeler et al . 2020; Langeland et al . 2020).…”

Section: Methodsmentioning

confidence: 99%

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

Bryant¹,

DeMarco²,

Hallem³

2021

Preprint

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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.

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“…For example, S. stercoralis iL3s respond robustly to a number of human-associated odorants and have distinct olfactory preferences from those of other life stages ( Castelletto et al 2014 ; Gang et al 2020 ). Many nematode chemoreceptors are G protein-coupled receptors (GPCRs), and nematode genomes encode large numbers of predicted chemoreceptor GPCRs ( Bargmann 2006 ; Langeland et al 2020 ; Wheeler et al 2020 ). Putative chemosensory GPCR genes are highly divergent across nematode species ( Wheeler et al 2020 ), leading to the functional diversity that likely underlies species-specific differences in chemosensory behaviors ( Hallem et al 2011 ; Dillman et al 2012 ; Castelletto et al 2014 ; Lee et al 2016 ; Gang et al 2020 ).…”

Section: Resultsmentioning

confidence: 99%

“…Genes were extracted based on PCA variable scores using tidyverse package version 1.3.0. Supplementary File S5 contains a list of chemoreceptor gene IDs for all Strongyloides species ( Langeland et al 2020 ; Wheeler et al 2020 ). Supplementary File S6 is an example .xlsx results file generated by the Strongyloides RNA-seq Browser containing a DGE table listing 64 S. stercoralis chemoreceptors that are consistently upregulated in iL3s versus all other life stages.…”

Section: Methodsmentioning

confidence: 99%

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

Bryant

¹

,

DeMarco

²

,

Hallem

³

2021

G3 Genes|Genomes|Genetics

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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.

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“…WBPS15) ( Howe et al 2017 ). GluCl subunits were predicted from each genome using hidden Markov models (HMMs) as described previously ( Langeland et al 2020 , 2021 ; Wheeler et al 2020 ; Bode and O’Halloran 2021 ). The Pfam ( Finn et al 2014 ) HMM, PF02932 ( Neur_chan_memb ), was used alongside an HMM based on known GluCl proteins that was generated using hmmbuild ( Mistry et al 2013 ).…”

Section: Methodsmentioning

confidence: 99%

Database of glutamate-gated chloride (GluCl) subunits across 125 nematode species: patterns of gene accretion and sequence diversification

O'Halloran

¹

2021

G3 Genes|Genomes|Genetics

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Glutamate Gated Chloride (GluCl) channels belong to the Cys-loop receptor superfamily. GluCl channels are activated by glutamate (Glu) and form substrates for the anti-parasitic drugs from the avermectin family. GluCl channels are pentameric, and each subunit contains an N-terminal extracellular domain that binds Glu and four helical transmembrane domains (TMs), which contain binding sites for avermectin drugs. In order to provide more insight into phylum-wide patterns of GluCl subunit gene expansion and sequence diversity across nematodes, we have developed a database of predicted GluCl subunit genes from 125 nematode species. Our analysis into this dataset described assorted patterns of species-specific GluCl gene counts across different nematodes as well as sequence diversity in key residues thought to be involved in avermectin binding.

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NemChR-DB: a database of parasitic nematode chemosensory G-protein coupled receptors

Cited by 10 publications

References 23 publications

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

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

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

Database of glutamate-gated chloride (GluCl) subunits across 125 nematode species: patterns of gene accretion and sequence diversification

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