Pristionchus pacificus: a well-rounded nematode

Starvation resistance in the nematode Pristionchus pacificus requires a conserved supplementary nuclear receptor

Nuclear hormone receptors (NHRs) are a deeply-conserved superfamily of metazoan transcription factors, which fine-tune the expression of their regulatory target genes in response to a plethora of sensory inputs. In nematodes, NHRs underwent an explosive expansion and many species have hundreds of nhr genes, most of which remain functionally uncharacterized. However, recent studies have reported that two sister receptors, Ppa-NHR-1 and Ppa-NHR-40, are crucial regulators of feeding-structure morphogenesis in the diplogastrid model nematode Pristionchus pacificus. In the present study, we functionally characterize Ppa-NHR-10, the sister paralog of Ppa-NHR-1 and Ppa-NHR-40, aiming to reveal whether it too regulates aspects of feeding-structure development. We used CRISPR/CAS9-mediated mutagenesis to create small frameshift mutations of this nuclear receptor gene and applied a combination of geometric morphometrics and unsupervised clustering to characterize potential mutant phenotypes. However, we found that Ppa-nhr-10 mutants do not show aberrant feeding-structure morphologies. Instead, multiple RNA-seq experiments revealed that many of the target genes of this receptor are involved in lipid catabolic processes. We hypothesized that their mis-regulation could affect the survival of mutant worms during starvation, where lipid catabolism is often essential. Indeed, using novel survival assays, we found that mutant worms show drastically decreased starvation resistance, both as young adults and as dauer larvae. We also characterized genome-wide changes to the transcriptional landscape in P. pacificus when exposed to 24 h of acute starvation, and found that Ppa-NHR-10 partially regulates some of these responses. Taken together, these results demonstrate that Ppa-NHR-10 is broadly required for starvation resistance and regulates different biological processes than its closest paralogs Ppa-NHR-1 and Ppa-NHR-40.

GCY-20 signaling controls suppression of Caenorhabditis elegans egg laying by moderate cold

Organisms sensing environmental cues and internal states and integrating the sensory information to control fecundity are essential for survival and proliferation. The present study finds that a moderate cold temperature of 11°C reduces egg laying in Caenorhabditis elegans. ASEL and AWC neurons sense the cold via GCY-20 signaling and act antagonistically on egg laying through the ASEL and AWC/AIA/HSN circuits. Upon cold stimulation, ASEL and AWC release glutamate to activate and inhibit AIA interneurons by acting on highly and lowly sensitive ionotropic GLR-2 and GLC-3 receptors, respectively. AIA inhibits HSN motor neuron activity via acetylcholinergic ACR-14 receptor signaling and suppresses egg laying. Thus, ASEL and AWC initiate and reduce the cold suppression of egg laying. ASEL's action on AIA and egg laying dominates AWC's action. The biased opposite actions of these neurons on egg laying provide animals with a precise adaptation of reproductive behavior to environmental temperatures.

The evolution of entomopathogeny in nematodes

Understanding how parasites evolved is crucial to understand the host and parasite interaction. The evolution of entomopathogenesis in rhabditid nematodes has traditionally been thought to have occurred twice within the phylum Nematoda: in Steinernematidae and Heterorhabditidae families, which are associated with the entomopathogenic bacteria Xenorhabdus and Photorhabdus, respectively. However, nematodes from other families that are associated with entomopathogenic bacteria have not been considered to meet the criteria for "entomopathogenic nematodes." The evolution of parasitism in nematodes suggests that ecological and evolutionary properties shared by families in the order Rhabditida favor the convergent evolution of the entomopathogenic trait in lineages with diverse lifestyles, such as saprotrophs, phoretic, and necromenic nematodes. For this reason, this paper proposes expanding the term "entomopathogenic nematode" considering the diverse modes of this attribute within Rhabditida. Despite studies are required to test the authenticity of the entomopathogenic trait in the reported species, they are valuable links that represent the early stages of specialized lineages to entomopathogenic lifestyle. An ecological and evolutionary exploration of these nematodes has the potential to deepen our comprehension of the evolution of entomopathogenesis as a convergent trait spanning across the Nematoda.

Nematodes: an overlooked tiny engineer of plant health

Nematodes are a crucial component of rhizosphere biodiversity, affecting plant health as the most abundant and functionally diverse soil animals. Plant-parasitic nematodes are generally considered harmful, which may overlook their potential benefits to plants when coexisting with free-living nematodes in soil. We provide new insights into nematodes as vital plant partners. Plant root damage by plant-parasitic nematodes creates opportunities for pathogens and beneficial microbiota to colonize the rhizosphere. Free-living nematodes coordinate microbiota to suppress plant diseases, but they are susceptible to mortality from plant pathogens, potentially favoring pathogen release in the root zone. We conclude that the nematode's role in regulating plant pathogens represents a missing link, constraining our ability to predict and control soil-borne diseases in healthy plants.

Exploring the Potential Hormonal Effects of Tire Polymers (TPs) on Different Species Based on a Theoretical Computational Approach

Tire polymers (TPs) are the most prevalent type of microplastics and are of great concern due to their potential environmental risks. This study aims to determine the toxicity of TPs with the help of molecular-dynamics simulations of their interactions with receptors and to highlight the differences in the toxicity characteristics of TPs in different environmental media (marine environment, freshwater environment, soil environment). For this purpose, five TPs—natural rubber, styrene–butadiene rubber (SBR), butadiene rubber, nitrile–butadiene rubber, and isobutylene–isoprene rubber—were analyzed. Molecular-dynamics calculations were conducted on their binding energies to neurotoxic, developmental, and reproductive receptors of various organisms to characterize the toxic effects of the five TPs. The organisms included freshwater species (freshwater nematodes, snails, shrimp, and freshwater fish), marine species (marine nematodes, mussels, crab, and marine fish), and soil species (soil nematodes, springtails, earthworms, and spiders). A multilevel empowerment method was used to determine the bio-toxicity of the TPs in various environmental media. A coupled-normalization method–principal-component analysis–factor-analysis weighting method—was used to calculate the weights of the TP toxicity (first level) categories. The results revealed that the TPs were the most biologically neurotoxic to three environmental media (20.79% and 10.57% higher compared with developmental and reproductive toxicity, respectively). Regarding the effects of TPs on organisms in various environmental media (second level), using a subjective empowerment approach, a gradual increase in toxicity was observed with increasing trophic levels due to the enrichment of TPs and the feeding behavior of organisms. TPs had the greatest influence in the freshwater-environment organisms according to the subjective empowerment approach employed to weight the three environmental media (third level). Therefore, using the minimum-value method coupled with the feature-aggregation method, the interval-deflation method coupled with the entropy-weighting method, and the standard-deviation normalization method, the three toxicity characteristics of SBR in three environmental media and four organisms were determined. SBR was found to have the greatest impact on the overall toxicity of the freshwater environment (12.38% and 9.33% higher than the marine and soil environments, respectively). The greatest contribution to neurotoxicity (26.01% and 15.95% higher than developmental and reproductive toxicity, respectively) and the greatest impact on snails and shrimp among organisms in the freshwater environment were observed. The causes of the heterogeneity of SBR’s toxicity were elucidated using amino-acid-residue analysis. SBR primarily interacted with toxic receptors through van der Waals, hydrophobic, π-π, and π-sigma interactions, and the more stable the binding, the more toxic the effect. The toxicity characteristics of TMPs to various organisms in different environments identified in this paper provide a theoretical basis for subsequent studies on the prevention and control of TMPs in the environment.

Nematode Pheromones: Structures and Functions

Pheromones are chemical signals secreted by one individual that can affect the behaviors of other individuals within the same species. Ascaroside is an evolutionarily conserved family of nematode pheromones that play an integral role in the development, lifespan, propagation, and stress response of nematodes. Their general structure comprises the dideoxysugar ascarylose and fatty-acid-like side chains. Ascarosides can vary structurally and functionally according to the lengths of their side chains and how they are derivatized with different moieties. In this review, we mainly describe the chemical structures of ascarosides and their different effects on the development, mating, and aggregation of nematodes, as well as how they are synthesized and regulated. In addition, we discuss their influences on other species in various aspects. This review provides a reference for the functions and structures of ascarosides and enables their better application.

Multidimensional competition of nematodes affects plastic traits in a beetle ecosystem

Resource competition has driven the evolution of novel polyphenisms in numerous organisms, enhancing fitness in constantly changing environmental conditions. In natural communities, the myriad interactions among diverse species are difficult to disentangle, but the multidimensional microscopic environment of a decaying insect teeming with bacteria and fighting nematodes provides pliable systems to investigate. Necromenic nematodes of the family Diplogastridae live on beetles worldwide, innocuously waiting for their hosts’ deaths to feast on the blooming bacteria. Often, more than one worm species either affiliates with the insect or joins the microbial meal; thus, competition over limited food ensues, and phenotypic plasticity provides perks for species capable of employing polyphenisms. The recently established system of cockchafer Gymnogaster bupthalma and its occasional co-infestation of Pristionchus mayeri and Acrostichus spp. has revealed that these worms will simultaneously utilize two polyphenisms to thrive in a competitive environment. While both genera maintain plastic capacities in mouth form (strictly bacterial-feeding and omnivorous predation) and developmental pathway (direct and arrested development, dauer), P. mayeri employs both when faced with competition from Acrostichus. Here, we took advantage of the malleable system and added a third competitor, model nematode Pristionchus pacificus. Intriguingly, with a third competitor, P. mayeri is quicker to exit dauer and devour available food, while Acrostichus hides in dauer, waiting for the two Pristionchus species to leave the immediate environment before resuming development. Thus, experimental manipulation of short-lived ecosystems can be used to study the roles of polyphenisms in organismal interactions and their potential significance for evolution.

Adaptation to environmental temperature in divergent clades of the nematode Pristionchus pacificus

Because of ongoing climate change, populations of organisms are being subjected to stressful temperatures more often. This is especially problematic for ectothermic organisms, which are likely to be more sensitive to changes in temperature. Therefore, we need to know if ectotherms have adapted to environmental temperature and, if so, what are the evolutionary mechanisms behind such adaptation. Here, we use the nematode Pristionchus pacificus as a case study to investigate thermal adaptation on the Indian Ocean island of La Réunion, which experiences a range of temperatures from coast to summit. We study the evolution of high-temperature tolerance by constructing a phylogenetic tree of strains collected from many different thermal niches. We show that populations of P. pacificus at low altitudes have higher fertility at warmer temperatures. Most likely, this phenotype has arisen recently and at least twice independently, consistent with parallel evolution. We also studied low-temperature tolerance and showed that populations from high altitudes have increased their fertility at cooler temperatures. Together, these data indicate that P. pacificus strains on La Réunion are subject to divergent selection, adapting to hot and cold niches at the coast and summit of the volcano. Precisely defining these thermal niches provides essential information for models that predict the impact of future climate change on these populations.

Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes

The birth of new genes is a major molecular innovation driving phenotypic diversity across all domains of life. Although repurposing of existing protein-coding material by duplication is considered the main process of new gene formation, recent studies have discovered thousands of transcriptionally active sequences as a rich source of new genes. However, differential loss rates have to be assumed to reconcile the high birth rates of these incipient de novo genes with the dominance of ancient gene families in individual genomes. Here, we test this rapid turnover hypothesis in the context of the nematode model organism Pristionchus pacificus We extended the existing species-level phylogenomic framework by sequencing the genomes of six divergent P. pacificus strains. We used these data to study the evolutionary dynamics of different age classes and categories of origin at a population level. Contrasting de novo candidates with new families that arose by duplication and divergence from known genes, we find that de novo candidates are typically shorter, show less expression, and are overrepresented on the sex chromosome. Although the contribution of de novo candidates increases toward young age classes, multiple comparisons within the same age class showed significantly higher attrition in de novo candidates than in known genes. Similarly, young genes remain under weak evolutionary constraints with de novo candidates representing the fastest evolving subcategory. Altogether, this study provides empirical evidence for the rapid turnover hypothesis and highlights the importance of the evolutionary timescale when quantifying the contribution of different mechanisms toward new gene formation.

Reproductive plasticity in response to food source in the fungal-feeding nematode Bursaphelenchus okinawaensis

Organisms use various strategies to cope with fluctuating environments. Some organisms express different phenotypes in alternative conditions through a process known as ‘phenotypic plasticity’, which is presumably an evolutionary adaptation to environmental variation. Nematodes adapt to various environments; it has been suggested that phenotypic plasticity is a contributing factor in their high level of environmental adaptability. We investigated the reproductive plasticity in response to a food source in the fungal-feeding nematode, Bursaphelenchus okinawaensis. Bursaphelenchus okinawaensis is known to reproduce primarily as a self-fertilising hermaphrodite on a filamentous fungus and yeast; here, we showed that newly isolated SH3 strain hermaphrodites produced a small number of progenies (⩽9 progenies per hermaphrodite) on the yeast test plate, while they laid similar numbers of eggs to the SH1 strain on the fungus test plate. Subsequent sperm observation by 4′,6-diamidino-2-phenylindole (DAPI) revealed that SH3 hermaphrodites could produce only a small number of sperm on the yeast test plate. Some hermaphrodites did not produce any eggs, indicating that they had become females rather than hermaphrodites. These results showed that the hermaphrodite or female status of SH3 nematodes was a plastic character, dependent on the food stimulus. An intra-strain crossing test between SH1 and SH3 suggested that the reproductive plasticity was controlled by a single recessive gene. This study provided an insight into a novel type of phenotypic plasticity in nematodes.

Synergistic interaction of gut microbiota enhances the growth of nematode through neuroendocrine signaling

Animals are associated with a diverse bacterial community that impacts host physiology. It is well known that nutrients and enzymes synthesized by bacteria largely expand host metabolic capacity. Bacteria also impact a wide range of animal physiology that solely depends on host genetics through direct interaction. However, studying the synergistic effects of the bacterial community remains challenging due to its complexity. The omnivorous nematode Pristionchus pacificus has limited digestive efficiency on bacteria. Therefore, we established a bacterial collection that represents the natural gut microbiota that are resistant to digestion. Using this collection, we show that the bacterium Lysinibacillus xylanilyticus by itself provides limited nutritional value, but in combination with Escherichia coli, it significantly promotes life-history traits of P. pacificus by regulating the neuroendocrine peptide in sensory neurons. This gut-to-brain communication depends on undigested L. xylanilyticus providing Pristionchus nematodes a specific fitness advantage to compete with nematodes that rupture bacteria efficiently. Using RNA-seq and CRISPR-induced mutants, we show that 1-h exposure to L. xylanilyticus is sufficient to stimulate the expression of daf-7-type TGF-β signaling ligands, which induce a global transcriptome change. In addition, several effects of L. xylanilyticus depend on TGF-β signaling, including olfaction, body size regulation, and a switch of energy allocation from lipid storage to reproduction. Our results reveal the beneficial effects of a gut bacterium to modify life-history traits and maximize nematode survival in natural habitats.

Efficient visual screening of CRISPR/Cas9 genome editing in the nematode Pristionchus pacificus

CRISPR/Cas9 genome editing has been applied to a wide variety of organisms, including nematodes such as Caenorhabditis elegans and Pristionchus pacificus. In these nematodes, genome editing is achieved by microinjection of Cas9 protein and guide RNA into the hermaphrodite gonads. However, P. pacificus is less efficient in CRISPR/Cas9 genome editing and exogenous gene expression. Therefore, it takes considerable time and effort to screen for target mutants if there are no visual markers that indicate successful injection. To overcome this problem, co-injection markers (gRNA for Ppa-prl-1, which induces the roller phenotype, and Ppa-egl-20p::turboRFP, a plasmid expressing a fluorescent protein) have been developed in P. pacificus. By selecting worms with the roller phenotype or turboRFP expression, screening efficiency is substantially increased to obtain worms with desired mutations. Here, we describe a step-by-step protocol for the visual screening system for CRISPR/Cas9 genome editing in P. pacificus. We also describe technical tips for microinjection, which is difficult for beginners. This protocol will facilitate genome editing in P. pacificus and may be applied to other nematode species.

Introduction to Pristionchus pacificus anatomy

Pristionchus pacificus has emerged as an important nematode species used to understand the evolution of development and behavior. While P. pacificus (Diplogasteridae) is only distantly related to Caenorhabditis elegans (Rhabditidae), both use an identical reproductive strategy, are easily reared on bacteria in Petri dishes and complete their life cycles within a few days. Over the past 25 years, several detailed light and electron microscopy studies have elucidated the anatomy of P. pacificus and have demonstrated clear homology to many cells in C. elegans. Despite this similarity, sufficient anatomical differences between C. elegans and P. pacificus have allowed the latter to be used in comparative evo-devo studies. For example, the stoma of P. pacificus contains a large dorsal tooth used during predation on other nematodes when supplementing its primarily bacterial diet. This review discusses the main anatomical features of P. pacificus with emphasis on comparison to C. elegans.

Analysis of meiosis in Pristionchus pacificus reveals plasticity in homolog pairing and synapsis in the nematode lineage

Meiosis is conserved across eukaryotes yet varies in the details of its execution. Here we describe a new comparative model system for molecular analysis of meiosis, the nematode Pristionchus pacificus, a distant relative of the widely studied model organism Caenorhabditis elegans. P. pacificus shares many anatomical and other features that facilitate analysis of meiosis in C. elegans. However, while C. elegans has lost the meiosis-specific recombinase Dmc1 and evolved a recombination-independent mechanism to synapse its chromosomes, P. pacificus expresses both DMC-1 and RAD-51. We find that SPO-11 and DMC-1 are required for stable homolog pairing, synapsis, and crossover formation, while RAD-51 is dispensable for these key meiotic processes. RAD-51 and DMC-1 localize sequentially to chromosomes during meiotic prophase and show nonoverlapping functions. We also present a new genetic map for P. pacificus that reveals a crossover landscape very similar to that of C. elegans, despite marked divergence in the regulation of synapsis and crossing-over between these lineages.

Improving Transgenesis Efficiency and CRISPR-Associated Tools Through Codon Optimization and Native Intron Addition in Pristionchus Nematodes

A lack of appropriate molecular tools is one obstacle that prevents in-depth mechanistic studies in many organisms. Transgenesis, clustered regularly interspaced short palindromic repeats (CRISPR)-associated engineering, and related tools are fundamental in the modern life sciences, but their applications are still limited to a few model organisms. In the phylum Nematoda, transgenesis can only be performed in a handful of species other than Caenorhabditis elegans, and additionally, other species suffer from significantly lower transgenesis efficiencies. We hypothesized that this may in part be due to incompatibilities of transgenes in the recipient organisms. Therefore, we investigated the genomic features of 10 nematode species from three of the major clades representing all different lifestyles. We found that these species show drastically different codon usage bias and intron composition. With these findings, we used the species Pristionchus pacificus as a proof of concept for codon optimization and native intron addition. Indeed, we were able to significantly improve transgenesis efficiency, a principle that may be usable in other nematode species. In addition, with the improved transgenes, we developed a fluorescent co-injection marker in P. pacificus for the detection of CRISPR-edited individuals, which helps considerably to reduce associated time and costs.

Phoresy in animals: review and synthesis of a common but understudied mode of dispersal

Phoresy is a type of interaction in which one species, the phoront, uses another species, the dispersal host, for transportation to new habitats or resources. Despite being a widespread behaviour, little is known about the ecology and evolution of phoresy. Our goal is to provide a comprehensive review of phoretic dispersal in animals and to bring renewed attention to this subject. We surveyed literature published between 1900 and 2020 to understand the extent of known higher-level taxonomic diversity (phyla, classes, and orders) and functional aspects of animals that use phoretic dispersal. Species dispersing phoretically have been observed in at least 13 animal phyla, 25 classes, and 60 orders. The majority of known phoronts are arthropods (Phylum Euarthropoda) in terrestrial habitats, but phoronts also occur in freshwater and marine environments. Marine phoronts may be severely under-represented in the literature due to the relative difficulty of studying these systems. Phoronts are generally small with low mobility and use habitats or resources that are ephemeral and/or widely dispersed. Many phoronts are also parasites. In general, animals that engage in phoresy use a wide variety of morphological and behavioural traits for locating, attaching to, and detaching from dispersal hosts, but the exact mechanisms behind these activities are largely unknown. In addition to diversity, we discuss the evolution of phoresy including the long-standing idea that it can be a precursor to parasitism and other forms of symbioses. Finally, we suggest several areas of future research to improve our understanding of phoresy and its ecological and evolutionary significance.

Intraguild predation between Pristionchus pacificus and Caenorhabditis elegans: a complex interaction with the potential for aggressive behaviour

The related nematodes Pristionchus pacificus and Caenorhabditis elegans both eat bacteria for nutrition and are therefore competitors when they exploit the same bacterial resource. In addition to competing with each other, P. pacificus is a predator of C. elegans larval prey. These two relationships together form intraguild predation, which is the killing and sometimes eating of potential competitors. In killing C. elegans, the intraguild predator P. pacificus may achieve dual benefits of immediate nutrition and reduced competition for bacteria. Recent studies of P. pacificus have characterized many aspects of its predatory biting behaviour as well as underlying molecular and genetic mechanisms. However, little has been explored regarding the potentially competitive aspect of P. pacificus biting C. elegans. Moreover, aggression may also be implicated if P. pacificus intentionally bites C. elegans with the goal of reducing competition for bacteria. The aim of this review is to broadly outline how aggression, predation, and intraguild predation relate to each other, as well as how these concepts may be applied to future studies of P. pacificus in its interactions with C. elegans.

Geometric morphometrics of microscopic animals as exemplified by model nematodes

While a host of molecular techniques are utilized by evolutionary developmental (evo-devo) biologists, tools for quantitative evaluation of morphology are still largely underappreciated, especially in studies on microscopic animals. Here, we provide a standardized protocol for geometric morphometric analyses of 2D landmark data sets using a combination of the geomorph and Morpho R packages. Furthermore, we integrate clustering approaches to identify group structures within such datasets. We demonstrate our protocol by performing exemplary analyses on stomatal shapes in the model nematodes Caenorhabditis and Pristionchus. Image acquisition for 80 worms takes 3-4 d, while the entire data analysis requires 10-30 min. In theory, this approach is adaptable to all microscopic model organisms to facilitate a thorough quantification of shape differences within and across species, adding to the methodological toolkit of evo-devo studies on morphological evolution and novelty.

Interspecific Variation in Nematode Responses to Metals

Performing toxicity testing on multiple species with differing degrees of evolutionary relatedness can provide important information on how chemical sensitivity varies among species and can help pinpoint the biological drivers of species sensitivity. Such knowledge could ultimately be used to design better multispecies predictive ecological risk assessment models and identify particularly sensitive species. However, laboratory toxicity tests involving multiple species can also be resource intensive, especially when each species has unique husbandry conditions. We performed lethality tests with 2 metals, copper chloride and zinc chloride, on 5 different nematode species, which are nested in their degree of evolutionary relatedness: Caenorhabditis briggsae, Caenorhabditis elegans, Oscheius myriophila, Oscheius tipulae, and Pristionchus pacificus. All species were successfully cultured and tested concurrently with limited resources, demonstrating that inexpensive, multispecies nematode toxicity testing systems are achievable. The results indicate that P. pacificus is the most sensitive to both metals. Conversely, C. elegans is the least sensitive species to copper, but the second most sensitive to zinc, indicating that species relationships do not necessarily predict species sensitivity. Toxicity testing with additional nematode species and types of chemicals is feasible and will help form more generalizable conclusions about relative species sensitivity. Environ Toxicol Chem 2020;39:1006-1016. © 2020 SETAC.

Predator-secreted sulfolipids induce defensive responses in C. elegans

Animals respond to predators by altering their behavior and physiological states, but the underlying signaling mechanisms are poorly understood. Using the interactions between Caenorhabditis elegans and its predator, Pristionchus pacificus, we show that neuronal perception by C. elegans of a predator-specific molecular signature induces instantaneous escape behavior and a prolonged reduction in oviposition. Chemical analysis revealed this predator-specific signature to consist of a class of sulfolipids, produced by a biochemical pathway required for developing predacious behavior and specifically induced by starvation. These sulfolipids are detected by four pairs of C. elegans amphid sensory neurons that act redundantly and recruit cyclic nucleotide-gated (CNG) or transient receptor potential (TRP) channels to drive both escape and reduced oviposition. Functional homology of the delineated signaling pathways and abolishment of predator-evoked C. elegans responses by the anti-anxiety drug sertraline suggests a likely conserved or convergent strategy for managing predator threats.

A Genome Resequencing-Based Genetic Map Reveals the Recombination Landscape of an Outbred Parasitic Nematode in the Presence of Polyploidy and Polyandry

The parasitic nematode Haemonchus contortus is an economically and clinically important pathogen of small ruminants, and a model system for understanding the mechanisms and evolution of traits such as anthelmintic resistance. Anthelmintic resistance is widespread and is a major threat to the sustainability of livestock agriculture globally; however, little is known about the genome architecture and parameters such as recombination that will ultimately influence the rate at which resistance may evolve and spread. Here, we performed a genetic cross between two divergent strains of H. contortus, and subsequently used whole-genome resequencing of a female worm and her brood to identify the distribution of genome-wide variation that characterizes these strains. Using a novel bioinformatic approach to identify variants that segregate as expected in a pseudotestcross, we characterized linkage groups and estimated genetic distances between markers to generate a chromosome-scale F1 genetic map. We exploited this map to reveal the recombination landscape, the first for any helminth species, demonstrating extensive variation in recombination rate within and between chromosomes. Analyses of these data also revealed the extent of polyandry, whereby at least eight males were found to have contributed to the genetic variation of the progeny analyzed. Triploid offspring were also identified, which we hypothesize are the result of nondisjunction during female meiosis or polyspermy. These results expand our knowledge of the genetics of parasitic helminths and the unusual life-history of H. contortus, and enhance ongoing efforts to understand the genetic basis of resistance to the drugs used to control these worms and for related species that infect livestock and humans throughout the world. This study also demonstrates the feasibility of using whole-genome resequencing data to directly construct a genetic map in a single generation cross from a noninbred nonmodel organism with a complex lifecycle.

Hybrid crosses and the genetic basis of interspecific divergence in lifespan in Pristionchus nematodes

Characterizing the genetic basis of among-species variation in lifespan is a major goal of evolutionary gerontology research, but the very feature that defines separate species - the inability to interbreed - makes achieving this goal impractical, if not impossible, for most taxa. Pristionchus nematodes provide an intriguing system for tackling this problem, as female lifespan varies among species that can be crossed to form viable (although infertile) hybrids. By conducting reciprocal crosses among three species - two dioecious (long-lived Pristionchus exspectatus and short-lived Pristionchus arcanus) and one androdioecious (short-lived Pristionchus pacificus) - we found that female lifespan was long for all hybrids, consistent with the hypothesis that the relatively short lifespans seen for P. pacificus hermaphrodites and P. arcanus females are caused by independent, recessive alleles that are masked in hybrid genomes. Cross-direction had a small effect on survivorship for crosses involving P. exspectatus, indicating that nuclear-mitochondrial interactions may also influence Pristionchus longevity. Our findings suggest that long lifespan in P. exspectatus reflects the realization of an ancestral potential for extended longevity in the P. pacificus species complex. This work demonstrates the utility of interspecific hybrids for ageing research and provides a foundation for future work on the genetic architecture of interspecific lifespan variation.

Life History Responses and Gene Expression Profiles of the Nematode Pristionchus pacificus Cultured on Cryptococcus Yeasts

Nematodes, the earth's most abundant metazoa are found in all ecosystems. In order to survive in diverse environments, they have evolved distinct feeding strategies and they can use different food sources. While some nematodes are specialists, including parasites of plants and animals, others such as Pristionchus pacificus are omnivorous feeders, which can live on a diet of bacteria, protozoans, fungi or yeast. In the wild, P. pacificus is often found in a necromenic association with beetles and is known to be able to feed on a variety of microbes as well as on nematode prey. However, in laboratory studies Escherichia coli OP50 has been used as standard food source, similar to investigations in Caenorhabditis elegans and it is unclear to what extent this biases the obtained results and how relevant findings are in real nature. To gain first insight into the variation in traits induced by a non-bacterial food source, we study Pristionchus-fungi interactions under laboratory conditions. After screening different yeast strains, we were able to maintain P. pacificus for at least 50-60 generations on Cryptococcus albidus and Cryptococcus curvatus. We describe life history traits of P. pacificus on both yeast strains, including developmental timing, survival and brood size. Despite a slight developmental delay and problems to digest yeast cells, which are both reflected at a transcriptomic level, all analyses support the potential of Cryptococcus strains as food source for P. pacificus. In summary, our work establishes two Cryptococcus strains as alternative food source for P. pacificus and shows change in various developmental, physiological and morphological traits, including the transcriptomic profiles.

Comparison of RP-HPLC modes to analyse the N-glycome of the free-living nematode Pristionchus pacificus

Pristionchus pacificus is a free-living nematode increasingly used as an organism for comparison to the more familiar model Caenorhabditis elegans. In this study, we examined the N-glycans of this organism isolated after serial release with peptide:N-glycosidases F and A; after fluorescent labelling with 2-aminopyridine, chromatographic fractionation by three types of RP-HPLC (with either classical C18, fused core C18 or alkylamide-bonded phases) followed by mass spectrometric analyses revealed key features of its N-glycome. In addition to paucimannosidic and oligomannosidic glycans typical of invertebrates, N-glycans with two core fucose residues were detected. Furthermore, a range of glycans carrying up to three phosphorylcholine residues was observed whereas, unlike C. elegans, no tetrafucosylated N-glycans were detected. Structures with three fucose residues, unusual methylation of core α1,3-fucose or with galactosylated fucose motifs were found in low amounts; these features may correlate with a different ensemble or expression of glycosyltransferase genes as compared to C. elegans. From an analytical perspective, both the alkylamide RP-amide and fused core C18 columns, as compared to a classical C18 material, offer advantages in terms of resolution and of elution properties, as some minor pyridylamino-labelled glycans (e.g. those carrying phosphorylcholine) appear in earlier fractions and so potential losses of such structures due to insufficient gradient length can be avoided.

Disentangling nematode-bacteria interactions using a modular soil model system and biochemical markers

Interactions between bacteria and nematode grazers are an important component of soil food webs yet, due to the cryptic habitat, they are almost exclusively investigated in artificial agar substrate. Transport, food choice and foraging experiments were performed in a modular microcosm system with the nematode Acrobeloides buetschlii and bacterial diets (Escherichia coli, Pseudomonas putida and Bacillus subtilis) in gamma-irradiated soil. Bacterial biomass was assessed by soil phospholipid fatty acids (PLFAs). Continuous random foraging of nematodes was affected by soil type. Food choice experiments revealed diet switch and time lag preference responses, suggesting that nematode population fluctuations are driven by multiple factors such as bacterial attractants, defence strategies or food quality. Application of PLFA markers revealed a strong nematode predation pressure, as biomass in P. putida declined by 50%, whereas no transport of bacteria through soil was indicated. Overall, semi-natural experimental systems are an essential prerequisite to gain a realistic picture in microbial-microfaunal interactions.

Rendering the Intractable More Tractable: Tools from Caenorhabditis elegans Ripe for Import into Parasitic Nematodes

Recent and rapid advances in genetic and molecular tools have brought spectacular tractability to Caenorhabditis elegans, a model that was initially prized because of its simple design and ease of imaging. C. elegans has long been a powerful model in biomedical research, and tools such as RNAi and the CRISPR/Cas9 system allow facile knockdown of genes and genome editing, respectively. These developments have created an additional opportunity to tackle one of the most debilitating burdens on global health and food security: parasitic nematodes. I review how development of nonparasitic nematodes as genetic models informs efforts to import tools into parasitic nematodes. Current tools in three commonly studied parasites (Strongyloides spp., Brugia malayi, and Ascaris suum) are described, as are tools from C. elegans that are ripe for adaptation and the benefits and barriers to doing so. These tools will enable dissection of a huge array of questions that have been all but completely impenetrable to date, allowing investigation into host-parasite and parasite-vector interactions, and the genetic basis of parasitism.

Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus

Background

The development of multicellular organisms is accompanied by gene expression changes in differentiating cells. Profiling stage-specific expression during development may reveal important insights into gene sets that contributed to the morphological diversity across the animal kingdom.

Results

We sequenced RNA-seq libraries throughout a developmental timecourse of the nematode Pristionchus pacificus. The transcriptomes reflect early larval stages, adult worms including late larvae, and growth-arrested dauer larvae and allowed the identification of developmentally regulated gene clusters. Our data reveals similar trends as previous transcriptome profiling of dauer worms and represents the first expression data for early larvae in P. pacificus. Gene expression clusters characterizing early larval stages show most significant enrichments of chaperones, while collagens are most significantly enriched in transcriptomes of late larvae and adult worms. By combining expression data with phylogenetic analysis, we found that developmentally regulated genes are found in paralogous clusters that have arisen through lineage-specific duplications after the split from the Caenorhabditis elegans branch.

Conclusions

We propose that gene duplications of developmentally regulated genes represent a plausible evolutionary mechanism to increase the dosage of stage-specific expression. Consequently, this may contribute to the substantial divergence in expression profiles that has been observed across larger evolutionary time scales.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0466-2) contains supplementary material, which is available to authorized users.

Life-History Traits of the Model Organism Pristionchus pacificus Recorded Using the Hanging Drop Method: Comparison with Caenorhabditis elegans

The nematode Pristionchus pacificus is of growing interest as a model organism in evolutionary biology. However, despite multiple studies of its genetics, developmental cues, and ecology, the basic life-history traits (LHTs) of P. pacificus remain unknown. In this study, we used the hanging drop method to follow P. pacificus at the individual level and thereby quantify its LHTs. This approach allowed direct comparisons with the LHTs of Caenorhabditis elegans recently determined using this method. When provided with 5×10(9) Escherichia coli cells ml(-1) at 20°C, the intrinsic rate of natural increase of P. pacificus was 1.125 (individually, per day); mean net production was 115 juveniles produced during the life-time of each individual, and each nematode laid an average of 270 eggs (both fertile and unfertile). The mean age of P. pacificus individuals at first reproduction was 65 h, and the average life span was 22 days. The life cycle of P. pacificus is therefore slightly longer than that of C. elegans, with a longer average life span and hatching time and the production of fewer progeny.

A host beetle pheromone regulates development and behavior in the nematode Pristionchus pacificus

Nematodes and insects are the two most speciose animal phyla and nematode–insect associations encompass widespread biological interactions. To dissect the chemical signals and the genes mediating this association, we investigated the effect of an oriental beetle sex pheromone on the development and behavior of the nematode Pristionchus pacificus. We found that while the beetle pheromone is attractive to P. pacificus adults, the pheromone arrests embryo development, paralyzes J2 larva, and inhibits exit of dauer larvae. To uncover the mechanism that regulates insect pheromone sensitivity, a newly identified mutant, Ppa-obi-1, is used to reveal the molecular links between altered attraction towards the beetle pheromone, as well as hypersensitivity to its paralyzing effects. Ppa-obi-1 encodes lipid-binding domains and reaches its highest expression in various cell types, including the amphid neuron sheath and excretory cells. Our data suggest that the beetle host pheromone may be a species-specific volatile synomone that co-evolved with necromeny.

DOI:http://dx.doi.org/10.7554/eLife.03229.001

The nematode worm Pristionchus pacificus can live as a parasite inside the oriental beetle, where it waits for the beetle to die so it can feed off the bacteria that live on the beetle's decomposing carcass. This ecologically important interaction is called necromeny. P. pacificus is attracted to a new host by a sex pheromone produced by the beetle, but the genes and biological mechanisms that enable this interaction to occur are not understood in much detail.

To identify the genetic basis of this interaction, Cinkornpumin et al. identified and examined a mutant form of P. pacificus that cannot sense the beetle sex pheromone. This revealed that although this pheromone attracts the adult nematodes, it stops P. pacificus embryos developing and can paralyze larvae. Cinkornpumin et al. suggest that the pheromone has likely evolved this ability in order to counteract the spread of the nematodes. This result implies that being invaded by P. pacificus makes life more difficult for the beetles than was previously thought.

Further investigation of the gene damaged in the P. pacificus mutants revealed that it encodes a protein that may bind to molecules called lipids, which are needed to form cell membranes and are used in cell signaling. As well as helping the nematodes to detect the sex pheromone, the lipid-binding protein also appears to help protect the worms from the pheromone's detrimental effects.

Cinkornpumin et al. observed that the gene for the lipid-binding protein is activated in several tissues, including the cells that form a sheath around some of the nerves that detect chemical signals. Whether this tissue is responsible for the chemical-sensing abilities of the lipid-binding protein, and whether these same tissues are responsible for protecting the nematodes from the damaging effects of the pheromone, remains to be discovered.

DOI:http://dx.doi.org/10.7554/eLife.03229.002

Conserved behavioral and genetic mechanisms in the pre-hatching molt of the nematode Pristionchus pacificus

Background

During development, juvenile nematodes undergo four molts. Although the number of molts appears to be constant within the Nematoda, the timing of the first molt can occur either before or after hatching. A previous study indicates that, as in some parasitic nematode lineages, a pre-hatching juvenile stage also exists in Diplogastrid nematodes. A detailed description of these sequence of events has yet to be shown for any single species.

Findings

To delineate the timing of the pre-hatching molt in the beetle-associated Pristionchus pacificus, we tracked individual mid-J1 stage worms inside the eggshell through the J1-J2 transition and hatching. We found that active movement ended 21 hours after egg-laying, followed by lethargus and hatching. We inferred that lethargus behavior represents the onset of the first molt, which precedes each post-hatching molt in C. elegans and P. pacificus. The onset of the J1-J2 molt was also marked by the upregulation of the P. pacificus molting marker Ppa-pnhr-1. We further corroborated the pre-hatching molt with the isolation of two genetic mutants that exhibited aberrant molting both inside the egg and after hatching, as characterized by protracted and often-aborted shedding of the old cuticle.

Conclusion

Our results describe in detail the pre-hatching juvenile molt in P. pacificus, provide strong visual evidence of a pre-hatching molt, and show support for common genetic mechanisms regulating molting in the pre-hatching and post-hatching developmental stages. Our findings support the hypothesis that the evolution of pre-hatching development in Diplogastrid nematodes is likely due to a heterochronic shift between the timing of the first molt and hatching.

Genome-wide analysis of trans-splicing in the nematode Pristionchus pacificus unravels conserved gene functions for germline and dauer development in divergent operons

Discovery of trans-splicing in multiple metazoan lineages led to the identification of operon-like gene organization in diverse organisms, including trypanosomes, tunicates, and nematodes, but the functional significance of such operons is not completely understood. To see whether the content or organization of operons serves similar roles across species, we experimentally defined operons in the nematode model Pristionchus pacificus. We performed affinity capture experiments on mRNA pools to specifically enrich for transcripts that are trans-spliced to either the SL1- or SL2-spliced leader, using spliced leader-specific probes. We obtained distinct trans-splicing patterns from the analysis of three mRNA pools (total mRNA, SL1 and SL2 fraction) by RNA-seq. This information was combined with a genome-wide analysis of gene orientation and spacing. We could confirm 2219 operons by RNA-seq data out of 6709 candidate operons, which were predicted by sequence information alone. Our gene order comparison of the Caenorhabditis elegans and P. pacificus genomes shows major changes in operon organization in the two species. Notably, only 128 out of 1288 operons in C. elegans are conserved in P. pacificus. However, analysis of gene-expression profiles identified conserved functions such as an enrichment of germline-expressed genes and higher expression levels of operonic genes during recovery from dauer arrest in both species. These results provide support for the model that a necessity for increased transcriptional efficiency in the context of certain developmental processes could be a selective constraint for operon evolution in metazoans. Our method is generally applicable to other metazoans to see if similar functional constraints regulate gene organization into operons.

Nuclear receptors in nematode development: Natural experiments made by a phylum

The development of complex multicellular organisms is dependent on regulatory decisions that are necessary for the establishment of specific differentiation and metabolic cellular states. Nuclear receptors (NRs) form a large family of transcription factors that play critical roles in the regulation of development and metabolism of Metazoa. Based on their DNA binding and ligand binding domains, NRs are divided into eight NR subfamilies from which representatives of six subfamilies are present in both deuterostomes and protostomes indicating their early evolutionary origin. In some nematode species, especially in Caenorhabditis, the family of NRs expanded to a large number of genes strikingly exceeding the number of NR genes in vertebrates or insects. Nematode NRs, including the multiplied Caenorhabditis genes, show clear relation to vertebrate and insect homologues belonging to six of the eight main NR subfamilies. This review summarizes advances in research of nematode NRs and their developmental functions. Nematode NRs can reveal evolutionarily conserved mechanisms that regulate specific developmental and metabolic processes as well as new regulatory adaptations. They represent the results of a large number of natural experiments with structural and functional potential of NRs for the evolution of the phylum. The conserved and divergent character of nematode NRs adds a new dimension to our understanding of the general biology of regulation by NRs. This article is part of a Special Issue entitled: Nuclear receptors in animal development.

Assaying environmental nickel toxicity using model nematodes

Although nickel exposure results in allergic reactions, respiratory conditions, and cancer in humans and rodents, the ramifications of excess nickel in the environment for animal and human health remain largely undescribed. Nickel and other cationic metals travel through waterways and bind to soils and sediments. To evaluate the potential toxic effects of nickel at environmental contaminant levels (8.9-7,600 µg Ni/g dry weight of sediment and 50-800 µg NiCl₂/L of water), we conducted assays using two cosmopolitan nematodes, Caenorhabditis elegans and Pristionchus pacificus. We assayed the effects of both sediment-bound and aqueous nickel upon animal growth, developmental survival, lifespan, and fecundity. Uncontaminated sediments were collected from sites in the Midwestern United States and spiked with a range of nickel concentrations. We found that nickel-spiked sediment substantially impairs both survival from larval to adult stages and adult longevity in a concentration-dependent manner. Further, while aqueous nickel showed no adverse effects on either survivorship or longevity, we observed a significant decrease in fecundity, indicating that aqueous nickel could have a negative impact on nematode physiology. Intriguingly, C. elegans and P. pacificus exhibit similar, but not identical, responses to nickel exposure. Moreover, P. pacificus could be tested successfully in sediments inhospitable to C. elegans. Our results add to a growing body of literature documenting the impact of nickel on animal physiology, and suggest that environmental toxicological studies could gain an advantage by widening their repertoire of nematode species.

The dauer hypothesis and the evolution of parasitism: 20 years on and still going strong

How any complex trait has evolved is a fascinating question, yet the evolution of parasitism among the nematodes is arguably one of the most arresting. How did free-living nematodes cross that seemingly insurmountable evolutionary chasm between soil dwelling and survival inside another organism? Which of the many finely honed responses to the varied and harsh environments of free-living nematodes provided the material upon which natural selection could act? Although several complementary theories explain this phenomenon, I will focus on the dauer hypothesis. The dauer hypothesis posits that the arrested third-stage dauer larvae of free-living nematodes such as Caenorhabditis elegans are, due to their many physiological similarities with infective third-stage larvae of parasitic nematodes, a pre-adaptation to parasitism. If so, then a logical extension of this hypothesis is that the molecular pathways which control entry into and recovery from dauer formation by free-living nematodes in response to environmental cues have been co-opted to control the processes of infective larval arrest and activation in parasitic nematodes. The molecular machinery that controls dauer entry and exit is present in a wide range of parasitic nematodes. However, the developmental outputs of the different pathways are both conserved and divergent, not only between populations of C. elegans or between C. elegans and parasitic nematodes but also between different species of parasitic nematodes. Thus the picture that emerges is more nuanced than originally predicted and may provide insights into the evolution of such an interesting and complex trait.

The nematode Pristionchus pacificus as a model system for integrative studies in evolutionary biology

Comprehensive studies of evolution have historically been hampered by the division among disciplines. Now, as biology moves towards an '-omics' era, it is more important than ever to tackle the evolution of function and form by considering all those research areas involved in the regulation of phenotypes. Here, we review recent attempts to establish the nematode Pristionchus pacificus as a model organism that allows integrative studies of development and evo-devo, with ecology and population genetics. Originally developed for comparative study with the nematode Caenorhabditis elegans, P. pacificus provided insight into developmental pathways including dauer formation, vulva and gonad development, chemosensation, innate immunity and neurobiology. Its subsequent discovery across a wide geographic distribution in association with scarab beetles enabled its evaluation in a biogeographic context. Development of an evolutionary field station on La Réunion Island, where P. pacificus is present in high abundance across a number of widespread habitat types, allows examination of the microfacets of evolution - processes of natural selection, adaptation and drift among populations can now be examined in this island setting. The combination of laboratory-based functional studies with fieldwork in P. pacificus has the long-term prospective to provide both proximate (mechanistic) and ultimate (evolutionary and ecological) causation and might therefore help to overcome the long-term divide between major areas in biology.

System-wide rewiring underlies behavioral differences in predatory and bacterial-feeding nematodes

The relationship between neural circuit function and patterns of synaptic connectivity is poorly understood, in part due to a lack of comparative data for larger complete systems. We compare system-wide maps of synaptic connectivity generated from serial transmission electron microscopy for the pharyngeal nervous systems of two nematodes with divergent feeding behavior: the microbivore Caenorhabditis elegans and the predatory nematode Pristionchus pacificus. We uncover a massive rewiring in a complex system of identified neurons, all of which are homologous based on neurite anatomy and cell body position. Comparative graph theoretical analysis reveals a striking pattern of neuronal wiring with increased connectional complexity in the anterior pharynx correlating with tooth-like denticles, a morphological feature in the mouth of P. pacificus. We apply focused centrality methods to identify neurons I1 and I2 as candidates for regulating predatory feeding and predict substantial divergence in the function of pharyngeal glands.

Unraveling the evolutionary history of the nematode Pristionchus pacificus: from lineage diversification to island colonization

The hermaphroditic nematode Pristionchus pacificus is a model organism with a range of fully developed genetic tools. The species is globally widespread and highly diverse genetically, consisting of four major independent lineages (lineages A, B, C, and D). Despite its young age (∼2.1 Ma), volcanic La Réunion Island harbors all four lineages. Ecological and population genetic research studies suggest that this diversity is due to repeated independent island colonizations by P. pacificus. Here, we use model-based statistical methods to rigorously test hypotheses regarding the evolutionary history of P. pacificus. First, we employ divergence analyses to date diversification events among the four “world” lineages. Next, we examine demographic properties of a subset of four populations (“a”, “b”, “c”, and “d”), present on La Réunion Island. Finally, we use the results of the divergence and demographic analyses to inform a modeling-based approximate Bayesian computation (ABC) approach, where we test hypotheses about the order and timing of establishment of the Réunion populations. Our dating estimates place the recent common ancestor of P. pacificus lineages at nearly 500,000 generations past. Our demographic analysis supports recent (<150,000 generations) spatial expansion for the island populations, and our ABC approach supports c>a>b>d as the most likely colonization order of the island populations. Collectively, our study comprehensively improves previous inferences about the evolutionary history of P. pacificus.

Description of Parasitodiplogaster pharmaconema n. sp. and redescription of P. maxinema from Ficus maxima Mill. (Moraceae)

Parasitodiplogaster species associated with Ficus maxima were surveyed at the Smithsonian Tropical Research Institute, Barro Colorado Island, Panama. Phase B-D syconia were collected from different trees and dissected in distilled water. Because there were different nematode stomatal and male morphotypes observed in a single sycone, nematodes isolated from each fig were observed to determine general morphotype class and stored individually in DNA extraction buffer for accurate morpho/molecular pairing. Additional voucher nematodes were gently heat-treated and fixed in formalin and processed into permanent mounts in dehydrated glycerin for more rigorous morphological examination. The survey yielded two different Parasitodiplogaster species: P. maxinema and P. pharmaconema n. sp. Several morphological characters, e.g., two long and stick-like teeth in the metastegostom, and stomatal dimorphism (presence of eurystomatous form) which were not previously described, were observed in P. maxinema and are ascribed hereto this species. Parasitodiplogaster pharmaconema n. sp. is morphologically similar to P. maxinema and P. yoponema but can be distinguished from these species based upon stomatal morphology, spicule and gubernaculum morphology, and number and arrangement of male genital papillae.

Complex small-molecule architectures regulate phenotypic plasticity in a nematode

Chemistry the worm's way: The nematode Pristionchus pacificus constructs elaborate small molecules from modified building blocks of primary metabolism, including an unusual xylopyranose-based nucleoside (see scheme). These compounds act as signaling molecules to control adult phenotypic plasticity and dauer development and provide examples of modular generation of structural diversity in metazoans.

System wide analysis of the evolution of innate immunity in the nematode model species Caenorhabditis elegans and Pristionchus pacificus

The evolution of genetic mechanisms used to combat bacterial infections is critical for the survival of animals and plants, yet how these genes evolved to produce a robust defense system is poorly understood. Studies of the nematode Caenorhabditis elegans have uncovered a plethora of genetic regulators and effectors responsible for surviving pathogens. However, comparative studies utilizing other free-living nematodes and therefore providing an insight into the evolution of innate immunity have been lacking. Here, we take a systems biology approach and use whole genome microarrays to profile the transcriptional response of C. elegans and the necromenic nematode Pristionchus pacificus after exposure to the four different pathogens Serratia marcescens, Xenorhabdus nematophila, Staphylococcus aureus and Bacillus thuringiensis DB27. C. elegans is susceptible to all four pathogens whilst P. pacificus is only susceptible to S. marcescens and X. nematophila. We show an unexpected level of specificity in host responses to distinct pathogens within and across species, revealing an enormous complexity of effectors of innate immunity. Functional domains enriched in the transcriptomes on different pathogens are similar within a nematode species but different across them, suggesting differences in pathogen sensing and response networks. We find translation inhibition to be a potentially conserved response to gram-negative pathogens in both the nematodes. Further computational analysis indicates that both nematodes when fed on pathogens up-regulate genes known to be involved in other stress responses like heat shock, oxidative and osmotic stress, and genes regulated by DAF-16/FOXO and TGF-beta pathways. This study presents a platform for comparative systems analysis of two nematode model species, and a catalog of genes involved in the evolution of nematode immunity and identifies both pathogen specific and pan-pathogen responses. We discuss the potential effects of ecology on evolution of downstream effectors and upstream regulators on evolution of nematode innate immunity.

Tandem-repeat patterns and mutation rates in microsatellites of the nematode model organism Pristionchus pacificus

Modern evolutionary biology requires integrative approaches that combine life history, population structure, ecology, and development. The nematode Pristionchus pacificus has been established as a model system in which these aspects can be studied in one organism. P. pacificus has well-developed genetic, genomic, and transgenic tools and its ecologic association with scarab beetles is well described. A recent study provided first mutation rate estimates based on mitochondrial genome sequencing and mutation accumulation line experiments that help resolve rather ancient evolutionary branches. Here, we analyzed the tandem-repeat pattern and studied spontaneous mutation rates for microsatellite markers by using the previously generated mutation accumulation lines. We found that 0.59%–3.83% of the genome is composed of short tandem repeats. We developed 41 microsatellite markers, randomly chosen throughout the genome and analyzed them in 82 mutation accumulation lines after 142 generations. A total of 31 mutations were identified in these lines. There was a strong correlation between allele size and mutation rate in P. pacificus, similar to Caenorhabditis elegans. In contrast to C. elegans, however, there is no evidence for a bias toward multistep mutations. The mutation spectrum of microsatellite loci in P. pacificus shows more insertions than deletions, indicating a tendency toward lengthening, a process that might have contributed to the increase in genome size. The mutation rates obtained for individual microsatellite markers provide guidelines for divergence time estimates that can be applied in P. pacificus next-generation sequencing approaches of wild isolates.

Pristionchus uniformis, should I stay or should I go? Recent host range expansion in a European nematode

Pristionchus pacificus has been developed as a model system in evolutionary developmental biology, evolutionary ecology, and population genetics. This species has a well-known ecological association with scarab beetles. Generally, Pristionchus nematodes have a necromenic association with their beetle hosts. Arrested dauer larvae invade the insect and wait for the host's death to resume development. Only one Pristionchus species is known to frequently associate with a non-scarab beetle. Pristionchus uniformis has been isolated from the chrysomelid Leptinotarsa decemlineata, also known as the Colorado potato beetle, in Europe and North America, but is also found on scarab beetles. This unusual pattern of association with two unrelated groups of beetles on two continents requires the involvement of geographical and host range expansion events. Here, we characterized a collection of 81 P. uniformis isolates from North America and Europe and from both scarab beetles and L. decemlineata. We used population genetic and phylogenetic analyses of the mitochondrial gene nd2 to reconstruct the genetic history of P. uniformis and its beetle association. Olfactory tests on beetles chemical extracts showed that P. uniformis has a unique chemoattractive profile toward its beetle hosts. Our results provide evidence for host range expansion through host-switching events in Europe where P. uniformis was originally associated with scarab beetles and the nematode's subsequent invasion of North America.

Phosphoproteome of Pristionchus pacificus provides insights into architecture of signaling networks in nematode models

Pristionchus pacificus is a nematode that is increasingly used as a model organism in evolutionary biology. The genome of P. pacificus differs markedly from that of C. elegans, with a high number of orphan genes that are restricted to P. pacificus and have no homologs in other species. To gain insight into the architecture of signal transduction networks in model nematodes, we performed a large-scale qualitative phosphoproteome analysis of P. pacificus. Using two-stage enrichment of phosphopeptides from a digest of P. pacificus proteins and their subsequent analysis via high accuracy MS, we detected and localized 6,809 phosphorylation events on 2,508 proteins. We compared the detected P. pacificus phosphoproteome to the recently published phosphoproteome of C. elegans. The overall numbers and functional classes of phosphoproteins were similar between the two organisms. Interestingly, the products of orphan genes were significantly underrepresented among the detected P. pacificus phosphoproteins. We defined the theoretical kinome of P. pacificus and compared it to that of C. elegans. While tyrosine kinases were slightly underrepresented in the kinome of P. pacificus, all major classes of kinases were present in both organisms. Application of our kinome annotation to a recent transcriptomic study of dauer and mixed stage populations showed that Ser/Thr and Tyr kinases show similar expression levels in P. pacificus but not in C. elegans. This study presents the first systematic comparison of phosphoproteomes and kinomes of two model nematodes and, as such, will be a useful resource for comparative studies of their signal transduction networks.