Dataset Information

Gain and Loss of Small RNA Classes-Characterization of Small RNAs in the Parasitic Nematode Family Strongyloididae.

ABSTRACT: The nematode family Strongyloididae is of particular interest because it contains important parasites of medical and veterinary relevance. In addition, species of this family can form parasitic and free-living generations and it also occupies an interesting phylogenetic position within the nematodes. Nematodes differ in several ways from other taxa with respect to their small noncoding RNAs. Recent comparative studies revealed that there is also considerable variability within the nematodes. However, no Strongyloididae species or close relative was included in these studies. We characterized the small RNAs of two developmental stages of three different Strongyloididae species and compared them with the well-studied free-living nematodes Caenorhabditis elegans and Pristionchus pacificus. Strongyloididae have conserved and taxon-specific microRNAs, many of which are differentially regulated between the two developmental stages. We identified a novel class of around 27-nucleotide-long RNAs starting with 5'G or A, of which a large fraction have the potential to target transposable elements. These RNAs most likely have triphosphates at their 5' ends and are therefore presumably synthesized by RNA-dependent RNA polymerases. In contrast to C. elegans but similarly to some other nematode taxa, Strongyloididae have no Piwi-interacting RNAs, nor do their genomes encode Argonaute proteins of the Piwi family. Finally, we attempted but failed to detect circulating parasite small RNAs in the blood of hosts.

SUBMITTER: Holz A

PROVIDER: S-EPMC5737618 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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Gain and Loss of Small RNA Classes-Characterization of Small RNAs in the Parasitic Nematode Family Strongyloididae.

Holz Anja A Streit Adrian A

Genome biology and evolution 20171001 10

The nematode family Strongyloididae is of particular interest because it contains important parasites of medical and veterinary relevance. In addition, species of this family can form parasitic and free-living generations and it also occupies an interesting phylogenetic position within the nematodes. Nematodes differ in several ways from other taxa with respect to their small noncoding RNAs. Recent comparative studies revealed that there is also considerable variability within the nematodes. How ...[more]

PMID: 29036592

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Project description:BackgroundAlternative splicing (AS) of mRNA is a vital mechanism for enhancing genomic complexity in eukaryotes. Spliced isoforms of the same gene can have diverse molecular and biological functions and are often differentially expressed across various tissues, times, and conditions. Thus, AS has important implications in the study of parasitic nematodes with complex life cycles. Transcriptomic datasets are available from many species, but data must be revisited with splice-aware assembly protocols to facilitate the study of AS in helminthes.MethodsWe sequenced cDNA from the model worm Caenorhabditis elegans using 454/Roche technology for use as an experimental dataset. Reads were assembled with Newbler software, invoking the cDNA option. Several combinations of parameters were tested and assembled transcripts were verified by comparison with previously reported C. elegans genes and transcript isoforms and with Illumina RNAseq data.ResultsThoughtful adjustment of program parameters increased the percentage of assembled transcripts that matched known C. elegans sequences, decreased mis-assembly rates (i.e., cis- and trans-chimeras), and improved the coverage of the geneset. The optimized protocol was used to update de novo transcriptome assemblies from nine parasitic nematode species, including important pathogens of humans and domestic animals. Our assemblies indicated AS rates in the range of 20-30%, typically with 2-3 transcripts per AS locus, depending on the species. Transcript isoforms from the nine species were translated and searched for similarity to known proteins and functional domains. Some 21 InterPro domains, including several involved in nucleotide and chromatin binding, were statistically correlated with AS genetic loci. In most cases, the Roche/454 data explored in this study are the only sequences available from the species in question; however, the recently published genome of the human hookworm Necator americanus provided an additional opportunity to validate our results.ConclusionsOur optimized assembly parameters facilitated the first survey of AS among parasitic nematodes. The nine transcriptome assemblies, their protein translations, and basic annotations are available from Nematode.net as a resource for the research community. These should be useful for studies of specific genes and gene families of interest as well as for curating draft genome assemblies as they become available.

Dataset Information

Gain and Loss of Small RNA Classes-Characterization of Small RNAs in the Parasitic Nematode Family Strongyloididae.

Publications

Gain and Loss of Small RNA Classes-Characterization of Small RNAs in the Parasitic Nematode Family Strongyloididae.

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