Transgenesis by microparticle bombardment for live imaging of fluorescent proteins in Pristionchus pacificus germline and early embryos

Microparticle Bombardment as a Method for Transgenesis in Auanema and Tokorhabditis

Functional gene analysis tools in Caenorhabditis elegans are often ineffective in other nematodes due to differences in gonadal morphology and transgene silencing. Here, we established a method to generate stable transgenic lines in the nematodes Auanema freiburgense and Tokorhabditis tufae using microparticle bombardment coupled with hygromycin B selection. Despite using non-codon-optimized GFP, transgenic strains expressing fluorescent markers were obtained in both species. Additionally, an Auanema codon-optimized RFP construct showed robust expression in all tissues. This method will be valuable for future studies into the unusual sex determination, viviparity, and stress resistance in Auanema and Tokorhabditis .

Visualization of gene expression in Pristionchus pacificus with smFISH and in situ HCR

Single molecule fluorescence in situ hybridization (smFISH) and in situ hybridization chain reaction (HCR) have become powerful tools to visualize gene expression in many different animal species. We show here that smFISH and in situ HCR can be put to effective use in the satellite nematode model organism Pristionchus pacificus . Examining the expression of a homeobox gene ( Ppa-unc-30) , we found that HCR is more sensitive than smFISH. We confirmed the robustness of HCR by visualization of the expression of several genes involved in neurotransmitter synthesis or transport ( Ppa-unc-25 /GAD, Ppa-unc-17/VAChT, Ppa-eat-4 /VGLUT). Combined with its relative cost-effectiveness compared to smFISH analysis, in situ HCR constitutes a useful addition to the toolbox for P. pacificus research .

Genomic integration of transgenes using UV irradiation in Pristionchus pacificus

Transgenes are widely used throughout molecular biology for numerous applications. In Caenorhabditis elegans, stable transgenes are usually generated by microinjection into the germline establishing extrachromosomal arrays. Furthermore, numerous technologies exist to integrate transgenes into the C. elegans genome. In the nematode Pristionchus pacificus, transgenes are possible, however, their establishment is less efficient and dependent on the formation of complex arrays containing the transgene of interest and host carrier DNA. Additionally, genomic integration has only been reported via biolistic methods. Here we describe a simple technique using UV irradiation to facilitate the integration of transgenes into the P. pacificus genome.

Transgenesis of the gonochoristic nematode Caenorhabditis inopinata by microparticle bombardment with hygromycin B selection

The gonochoristic nematode Caenorhabditis inopinata is the phylogenetically closest species to the well-studied nematode Caenorhabditis elegans (Kanzaki et al. , 2018). While C. inopinata has been expected to be a useful comparative model for C. elegans , efficient transgenesis methods have not been available. Here, we established a method to integrate transgenes into the C. inopinata genome by microparticle bombardment with hygromycin B selection. C. elegans- derived genetic elements tested in this study, including universal and germline-specific promoters, ORFs, and 3’UTRs, were all functional in C. inopinata. Using this method, transgenic C. inopinata strains that express fluorescent subcellular markers were established.

Antibody Staining for Nematodes with Heat-induced Antigen Retrieval (HIAR)

Immunocytochemistry remains a valuable and necessary tool for biologists working with nematodes, even those nematode model organisms with advanced molecular genetic tools and transgenics. Because of the highly idiosyncratic nature of successful immunostaining procedures, innovations can still be found for this long-established technique. Heat-induced antigen retrieval (HIAR) is well known from other systems, but seems not to have been applied to antibody staining in nematodes. For some antigens, adding HIAR to an established antibody staining protocol for nematodes can reveal strong and reliable staining that without HIAR is poor or completely absent.

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.

The first steps in the life of a worm: Themes and variations in asymmetric division in C. elegans and other nematodes

Starting with Boveri in the 1870s, microscopic investigation of early embryogenesis in a broad swath of nematode species revealed the central role of asymmetric cell division in embryonic axis specification, blastomere positioning, and cell fate specification. Notably, across the class Chromadorea, a conserved theme emerges-asymmetry is first established in the zygote and specifies its asymmetric division, giving rise to an anterior somatic daughter cell and a posterior germline daughter cell. Beginning in the 1980s, the emergence of Caenorhabditis elegans as a model organism saw the advent of genetic tools that enabled rapid progress in our understanding of the molecular mechanisms underlying asymmetric division, in many cases defining key paradigms that turn out to regulate asymmetric division in a wide range of systems. Yet, the consequence of this focus on C. elegans came at the expense of exploring the extant diversity of developmental variation exhibited across nematode species. Given the resurgent interest in evolutionary studies facilitated in part by new tools, here we revisit the diversity in this asymmetric first division, juxtaposing molecular insight into mechanisms of symmetry-breaking, spindle positioning and fate specification, with a consideration of plasticity and variability within and between species. In the process, we hope to highlight questions of evolutionary forces and molecular variation that may have shaped the extant diversity of developmental mechanisms observed across Nematoda.

Different combinations of serotonin receptors regulate predatory and bacterial feeding behaviors in the nematode Pristionchus pacificus

Feeding behavior is one of the most fundamental behaviors in animals, and regulation of this behavior is critical for proper food intake. The nematode Pristionchus pacificus exhibits dimorphism in feeding behavior, bacterial feeding and predatory feeding on other nematodes, and the latter behavior is assumed to be an evolutionarily novel behavior. Both types of feeding behavior are modulated by serotonin; however, the downstream mechanism that modulates these behaviors is still to be clarified. Here, we focused on serotonin receptors and examined their expression patterns in P. pacificus. We also generated knockout mutants of the serotonin receptors using the CRISPR/Cas9 system and examined feeding behaviors. We found that Ppa-ser-5 mutants and the Ppa-ser-1; Ppa-ser-7 double mutant decreased predation. Detailed observation of the pharyngeal movement revealed that the Ppa-ser-1; Ppa-ser-7 double mutant reduces tooth movement, which is required for efficient predatory feeding. Conversely, Ppa-ser-7 and Ppa-mod-1 mutants decreased bacterial feeding. This study revealed that specific combinations of serotonin receptors are essential for the modulation of these distinct feeding behaviors, providing insight into the evolution of neural pathways to regulate novel feeding behavior.

Screening for CRISPR/Cas9-induced mutations using a co-injection marker in the nematode Pristionchus pacificus

CRISPR/Cas9 genome-editing methods are used to reveal functions of genes and molecular mechanisms underlying biological processes in many species, including nematodes. In evolutionary biology, the nematode Pristionchus pacificus is a satellite model and has been used to understand interesting phenomena such as phenotypic plasticity and self-recognition. In P. pacificus, CRISPR/Cas9-mediated mutations are induced by microinjecting a guide RNA (gRNA) and Cas9 protein into the gonads. However, mutant screening is laborious and time-consuming due to the absence of visual markers. In this study, we established a Co-CRISPR strategy by using a dominant roller marker in P. pacificus. We found that heterozygous mutations in Ppa-prl-1 induced the roller phenotype, which can be used as an injection marker. After the co-injection of Ppa-prl-1 gRNA, target gRNA, and the Cas9 protein, roller progeny and their siblings were examined using the heteroduplex mobility assay and DNA sequencing. We found that some of the roller and non-roller siblings had mutations at the target site. We used varying Cas9 concentrations and found that a higher concentration of Cas9 did not increase genome-editing events. The Co-CRISPR strategy promotes the screening for genome-editing events and will facilitate the development of new genome-editing methods in P. pacificus.

Crowdsourcing and the feasibility of manual gene annotation: A pilot study in the nematode Pristionchus pacificus

Nematodes such as Caenorhabditis elegans are powerful systems to study basically all aspects of biology. Their species richness together with tremendous genetic knowledge from C. elegans facilitate the evolutionary study of biological functions using reverse genetics. However, the ability to identify orthologs of candidate genes in other species can be hampered by erroneous gene annotations. To improve gene annotation in the nematode model organism Pristionchus pacificus, we performed a genome-wide screen for C. elegans genes with potentially incorrectly annotated P. pacificus orthologs. We initiated a community-based project to manually inspect more than two thousand candidate loci and to propose new gene models based on recently generated Iso-seq and RNA-seq data. In most cases, misannotation of C. elegans orthologs was due to artificially fused gene predictions and completely missing gene models. The community-based curation raised the gene count from 25,517 to 28,036 and increased the single copy ortholog completeness level from 86% to 97%. This pilot study demonstrates how even small-scale crowdsourcing can drastically improve gene annotations. In future, similar approaches can be used for other species, gene sets, and even larger communities thus making manual annotation of large parts of the genome feasible.

From "the Worm" to "the Worms" and Back Again: The Evolutionary Developmental Biology of Nematodes

Since the earliest days of research on nematodes, scientists have noted the developmental and morphological variation that exists within and between species. As various cellular and developmental processes were revealed through intense focus on Caenorhabditis elegans, these comparative studies have expanded. Within the genus Caenorhabditis, they include characterization of intraspecific polymorphisms and comparisons of distinct species, all generally amenable to the same laboratory culture methods and supported by robust genomic and experimental tools. The C. elegans paradigm has also motivated studies with more distantly related nematodes and animals. Combined with improved phylogenies, this work has led to important insights about the evolution of nematode development. First, while many aspects of C. elegans development are representative of Caenorhabditis, and of terrestrial nematodes more generally, others vary in ways both obvious and cryptic. Second, the system has revealed several clear examples of developmental flexibility in achieving a particular trait. This includes developmental system drift, in which the developmental control of homologous traits has diverged in different lineages, and cases of convergent evolution. Overall, the wealth of information and experimental techniques developed in C. elegans is being leveraged to make nematodes a powerful system for evolutionary cellular and developmental biology.

Streptothricin acetyl transferase 2 (Sat2): A dominant selection marker for Caenorhabditis elegans genome editing

Studies on Caenorhabditis elegans would benefit from the introduction of new selectable markers to allow more complex types of experiments to be conducted with this model animal. We established a new antibiotic selection marker for C. elegans transformation based on nourseothricin (NTC) and its resistance-encoding gene, streptothricin-acetyl transferase 2 (Sat2). NTC was able to efficiently prevent worm development at very low concentrations, and the worms expressing Sat2 were able to survive on the selection plates without any developmental defects. Using CRISPR/Cas9 and NTC selection, we were able to easily insert a 13-kb expression cassette into a defined locus in C. elegans. The structure and spectrum of NTC differs from other antibiotics like hygromycin B and geneticin, making it possible to use NTC alongside them. Indeed, we confirmed NTC-sat2 selection could work with the hygromycin B selection system simultaneously. Thus, the new NTC–Sat2 system can act as a useful dominant marker for gene transfer and genome editing in C. elegans.