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Background Strongyloidiasis is a neglected tropical disease (NTD) that is caused mainly by Strongyloides stercoralis , with an estimated 600 million people infected worldwide, and in fewer cases by Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi . A number of studies have been conducted on the genetic diversity of S. stercoralis in East and Southeast Asia; however, there is very limited corresponding information from West Asian countries, including Iran. Methods For Strongyloides worms collected from patients in southwestern Iran, the hypervariable regions I (HVR-I) and IV (HVR-IV) of the nuclear 18S ribosomal DNA (rDNA) locus ( SSU ) and a fragment of the subunit 1 mitochondrial cytochrome c oxidase gene ( cox-1 ) were sequenced. For a subset of the worms, whole-genome sequencing data were generated. Results The cox-1 sequences of 136 worms isolated from 23 patients indicated that all isolates were S. stercoralis. Among the cox-1 sequences, 33 polymorphic sites and 13 haplotypes were found. The phylogenetic analysis demonstrated that some sequences clustered fairly closely with sequences from humans and dogs from other parts of the world, while others formed a separate, Iran-specific group. Among 64 S. stercoralis analyzed, we found three of the previously described SSU HVR-I haplotypes, with haplotype II being the most frequent haplotype. In contrast to Southeast Asia, where S. stercoralis heterozygous for different haplotypes at the HVR-I locus are rare, we found 20 worms to be heterozygous for two different HVR-I haplotypes, 18 of which fell into the Iran-specific cox-1 cluster. SSU -heterozygous worms also showed elevated heterozygosity at the whole-genome level. Conclusions We conclude that the S. stercoralis population from the Khuzestan province shares much of the genetic diversity with the population in Southeast Asia, but there is an indication of additional genetic input. There appears to be some population structure with different subpopulations, which however do interbreed at least occasionally. Graphical Abstract

About 600 million people are estimated to be infected with Strongyloides stercoralis, the species that causes most of the human strongyloidiasis cases. S. stercoralis can also infect non-human primates (NHPs), dogs and cats, rendering these animals putative sources for zoonotic human S. stercoralis infection. S. fuelleborni is normally found in old world NHPs but occasionally also infects humans, mainly in Africa. Dogs in southeast Asia carry at least two types of Strongyloides, only one of which appears to be shared with humans (\"dog only\" and \"human and dog\" types). For S. stercoralis with molecular taxonomic information, there is a strong sampling bias towards southeast and east Asia and Australia. In order to extend the geographic range of sampling, we collected human and dog derived Strongyloides spp. and hookworms from two locations in Bangladesh and subjected them to molecular taxonomic and genomic analysis based on nuclear and mitochondrial sequences. All hookworms found were Necator americanus. Contrary to earlier studies in Asia, we noticed a rather high incidence of S. fuelleborni in humans. Also in this study, we found the two types of S. stercoralis and no indication for genetic isolation from the southeast Asian populations. However, we found one genomically \"dog only\" type S. stercoralis in a human sample and we found two worms in a dog sample that had a nuclear genome of the \"dog only\" but a mitochondrial genome of the \"human and dog\" type. S. fuelleborni may play a more prominent role as a human parasite in certain places in Asia than previously thought. The introgression of a mitochondria haplotype into the \"dog only\" population suggests that rare interbreeding between the two S. stercoralis types does occur and that exchange of genetic properties, for example a drug resistance, between the two types is conceivable.

In the nematode Caenorhabditis elegans, the terminal transferase RDE-3 adds a poly(UG)-tail to the free 3’ end of RNA molecules generated by the action of primary siRNAs or piRNAs. The tailed RNA serves as a template for RNA-dependent RNA polymerases (RdRp) to generate secondary siRNAs, thereby reinforcing the RNAi effect. In this iterative process, progressively shorter tailed RNAs are formed. In C. elegans, injection of poly(UG)-tailed single-stranded RNA (ssRNA) leads to RNAi-mediated gene silencing, thereby bypassing the need for the processing of double-stranded RNA into siRNAs. We wondered if poly(UG)-tailed ssRNAs could also be used for experimental gene knockdown in nematodes where long dsRNA-mediated RNAi does not work reliably, such as the satellite model organism Pristionchus pacificus or parasitic nematodes of the genus Strongyloides. Here we show that injection of poly(UG)-tailed RNA leads to gene knock down in P. pacificus and that the injected RNA, as well as the corresponding endogenous RNA, serve as substrate for the formation of new poly(UG)-tailed RNAs. Different from C. elegans, in P. pacificus, the knockdown effect depends on the redundant activity of the three rde-1 paralogs present in this species. We detected endogenously occurring poly(UG)-tailed RNAs derived from thousands of genes, more than half of which belong to germline-specific co-expression clusters. Mutations in Ppa-rde-3, lead to sterility. In contrast, in Strongyloides spp., we found poly(UG)-tailed RNAs to be much less abundant, if not absent. Our results show that poly(UG)-tailed RNAs are not restricted to C. elegans and suggest that they play an important function in the germ line in P. pacificus.