title: RNAi effector diversity in nematodes.
abstract: While RNA interference (RNAi) has been deployed to facilitate gene function studies in diverse helminths, parasitic nematodes appear variably susceptible. To test if this is due to inter-species differences in RNAi effector complements, we performed a primary sequence similarity survey for orthologs of 77 Caenorhabditis elegans RNAi pathway proteins in 13 nematode species for which genomic or transcriptomic datasets were available, with all outputs subjected to domain-structure verification. Our dataset spanned transcriptomes of Ancylostoma caninum and Oesophagostomum dentatum, and genomes of Trichinella spiralis, Ascaris suum, Brugia malayi, Haemonchus contortus, Meloidogyne hapla, Meloidogyne incognita and Pristionchus pacificus, as well as the Caenorhabditis species C. brenneri, C. briggsae, C. japonica and C. remanei, and revealed that: (i) Most of the C. elegans proteins responsible for uptake and spread of exogenously applied double stranded (ds)RNA are absent from parasitic species, including RNAi-competent plant-nematodes; (ii) The Argonautes (AGOs) responsible for gene expression regulation in C. elegans are broadly conserved, unlike those recruited during the induction of RNAi by exogenous dsRNA; (iii) Secondary Argonautes (SAGOs) are poorly conserved, and the nuclear AGO NRDE-3 was not identified in any parasite; (iv) All five Caenorhabditis spp. possess an expanded RNAi effector repertoire relative to the parasitic nematodes, consistent with the propensity for gene loss in nematode parasites; (v) In spite of the quantitative differences in RNAi effector complements across nematode species, all displayed qualitatively similar coverage of functional protein groups. In summary, we could not identify RNAi effector deficiencies that associate with reduced susceptibility in parasitic nematodes. Indeed, similarities in the RNAi effector complements of RNAi refractory and competent nematode parasites support the broad applicability of this research genetic tool in nematodes.
authors.affiliation: Molecular Biosciences-Parasitology, School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom.
authors.forename: Johnathan J
authors.initials: JJ
authors.lastname: Dalzell
authors.forename: Paul
authors.initials: P
authors.lastname: McVeigh
authors.forename: Neil D
authors.initials: ND
authors.lastname: Warnock
authors.forename: Makedonka
authors.initials: M
authors.lastname: Mitreva
authors.forename: David McK
authors.initials: DM
authors.lastname: Bird
authors.forename: Pierre
authors.initials: P
authors.lastname: Abad
authors.forename: Colin C
authors.initials: CC
authors.lastname: Fleming
authors.forename: Tim A
authors.initials: TA
authors.lastname: Day
authors.forename: Angela
authors.initials: A
authors.lastname: Mousley
authors.forename: Nikki J
authors.initials: NJ
authors.lastname: Marks
authors.forename: Aaron G
authors.initials: AG
authors.lastname: Maule
mesh_terms: D000818:Animals; D017124:Conserved Sequence; D020869:Gene Expression Profiling; D015801:Helminth Proteins / Q000096:biosynthesis* / Q000235:genetics*; D009348:Nematoda / Q000235:genetics*; D034622:RNA Interference
chemical_list: D015801:Helminth Proteins