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The genome and transcriptome of Panagrellus redivivus is shaped by the harsh demands of a free-living lifestyle

ABSTRACT: Nematodes comprise an abundant and diverse invertebrate phylum with members inhabiting nearly every ecological niche. Panagrellus redivivus (the ’microworm’) is a free-living nematode frequently used to understand the evolution of developmental and behavioral processes given its phylogenetic distance to Caenorhabditis elegans. Here we report the de novo sequencing of the genome, transcriptome, and small RNAs of P. redivivus. Using a combination of automated gene finders and RNA‑seq data, we predict 24249 genes and 32676 transcripts. Small RNA analysis revealed 248 micro RNA hairpins, of which 63 had orthologs in other species. Fourteen miRNA clusters containing 42 miRNA precursors were found. P. redivivus has a full complement of genes for regulation of dauer formation despite the apparent absence of dauer juveniles in this species. The RNAi and programmed cell death pathways are largely conserved. Analysis of protein family domain abundance revealed that P. redivivus has experienced a striking expansion of BTB domain‑containing proteins and an unprecedented expansion of the cullin scaffold family of proteins involved in multi‑subunit ubiquitin ligases, suggesting proteolytic plasticity and/or tighter regulation of protein turnover. The eukaryotic release factor (eRF1) protein family has also been dramatically expanded and suggests an ongoing evolutionary arms race with viruses and transposons. The P. redivivus genome provides a resource to advance our understanding of nematode evolution and biology and to further elucidate the genomic architecture leading to free-living lineages, taking advantage of the many fascinating features of this worm revealed by comparative studies.

ORGANISM(S): Panagrellus redivivus

PROVIDER: GSE44020 | GEO | 2013/02/07

SECONDARY ACCESSION(S): PRJNA188692

REPOSITORIES: GEO

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Project description:Third-stage larvae (L3s) of the canine hookworm, Ancylostoma caninum, endure a period of arrested development preceding transmission to a host. Many of the mRNAs up-regulated at this stage are likely to encode proteins that act at the host-parasite interface and facilitate the transition from a free-living to a parasitic larva. The initial phase of the infection of a mammalian host by A. caninum L3s (herein termed “activation”) can be mimicked in vitro by culturing L3s in serum-containing medium. The mRNAs differentially transcribed between activated and non-activated L3s were identified by suppression subtractive hybridisation (SSH). The analysis of these mRNAs on a custom oligonucleotide microarray printed with the SSH ESTs and publicly available A. caninum ESTs (non-subtracted) yielded a total of 602 differentially expressed mRNAs, of which the most highly represented sequences (27) encoded products belonging to the pathogenesis-related protein (PRP) superfamily and different mechanistic classes of proteases. Comparison of these A. caninum mRNAs with those of Caenorhabditis elegans larvae exiting from developmental (dauer) arrest demonstrated unexpectedly large differences with respect to gene ontology profiles. C. elegans L3 exiting developmental arrest up-regulated the expression of collagens and other (mostly intracellular) molecules involved in growth and development. Such mRNAs are virtually absent from activated hookworm larvae, and instead are represented by an inordinately large number of mRNAs encoding extracellular proteins, suggesting that many of the activation-associated hookworm mRNAs are involved in host-parasite interactions. The near absence of mRNAs associated with reproduction, growth and development among activated hookworm L3s probably reflects their ability to further arrest (i.e. undergo hypobiosis) in tissues of non-permissive hosts or in the external environment when conditions for transmission are unfavourable. Although this should not necessarily invalidate C. elegans dauer exit as a model for hookworm activation, it provides substantial information on the limitations of this free-living nematode as a model organism for the transition of nematode larvae from a free-living to a parasitic state. Keywords: Comparative transcriptomic hybridisation

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The genome and transcriptome of Panagrellus redivivus is shaped by the harsh demands of a free-living lifestyle

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