Goldstein P et al. (1982) Chromosoma "The synaptonemal complexes of caenorhabditis elegans: comparison of wild-type and mutant strains and pachytene karyotype analysis of wild-type."

Goldstein P, Slaton DE

[Chromosoma, 1982]

Normal synaptonemal complexes (SCs), consisting of two lateral elements and a central element, are present in wild-type, him-4 and him-8 mutant strains in both hermaphrodites and males of caenorhabditis elegans. Thus, the increase in rate of nondisjunction in the him mutants is not related to aberrant SC morphology. The wild- type hermaphrodite has six SCs, as determined from 3-D reconstruction analysis of serial section from electron microscopy. Thus, n=6 and this confirms early reports based on cytological studies with the light microscope. Only one end of the SC is attached to the nuclear envelope while the other end is free in the nucleoplasm and there is no apparent bouquet formation. Either end of the SC can attach to the nuclear envelope. The pairing behavior of the XX bivalent is normal and occurs synchronously with the autosomes. Electron dense bodies, or knobs, are associated with the SC via the central element and displace the chromatin for a distance of 200 nm. Each pachytene nucleus of the wild-type hermaphrodite has six such structures that are randomly dispersed along the bivalents such that some SCs have one or two knobs while others have none. Their function is unknown.

Benedetto A et al. (2019) Autophagy "Autophagy promotes visceral aging in wild-type C. elegans."

Gems D, Benedetto A

[Autophagy, 2019]

A plethora of studies over several decades has demonstrated the importance of autophagy in aging and age-related neurodegenerative disease. The role of autophagy in damage clearance and cell survival is well established, and supports a prevailing view that increasing autophagic activity can be broadly beneficial, and could form the basis of anti-aging interventions. However, macroautophagy/autophagy also promotes some elements of senescence. For example, in C. elegans hermaphrodites it facilitates conversion of intestinal biomass into yolk, leading to sex-specific gut atrophy and senescent steatosis.

Ramani AK et al. (2012) Cell "The majority of animal genes are required for wild-type fitness."

Jiao A, Fraser AG, Na H, Wannissorn N, Pelte N, Ramani AK, Vu V, Chuluunbaatar T, Verster AJ

[Cell, 2012]

Almost all eukaryotic genes are conserved, suggesting that they have essential functions. However, only a minority of genes have detectable loss-of-function phenotypes in experimental assays, and multiple theories have been proposed to explain this discrepancy. Here, we use RNA-mediated interference in C. elegans to examine how knockdown of any gene affects the overall fitness of worm populations. Whereas previous studies typically assess phenotypes that are detectable by eye after a single generation, we monitored growth quantitatively over several generations. In contrast to previous estimates, we find that, in these multigeneration population assays, the majority of genes affect fitness, and this suggests that genetic networks are not robust to mutation. Our results demonstrate that, in a single environmental condition, most animal genes play essential roles. This is a higher proportion than for yeast genes, and we suggest that the source of negative selection is different in animals and in unicellular eukaryotes.

Heaton A et al. (2022) Chemosphere "Variation in copper sensitivity between laboratory and wild strains of Caenorhabditis elegans."

Allen A, Heaton A, Nguyen T, Faulconer E, Milligan E, Weir SM, Glaberman S

[Chemosphere, 2022]

Ecological risk assessments of chemicals are frequently based on laboratory toxicity data from a small number of model species that may be reared in labs for years or decades. These populations can undergo many processes in the lab including artificial selection, founder effect, and genetic drift, and may not adequately represent their wild counterparts, potentially undermining the goal of protecting natural populations. Here we measure variation in lethality to copper chloride among strains of an emerging model species in toxicology, Caenorhabditis elegans. We tested four wild strains from Chile, Germany, Kenya, and Madeira (Portugal) against several versions of the standard laboratory N2 strain from Bristol, UK used in molecular biology. The four wild strains were more sensitive than any of the N2 strains tested with copper. We also found that the standard N2 strain cultured in the laboratory for >1 year was less sensitive than a recently cultured N2 strain as well as a cataloged ancestral version of the N2 strain. These results suggest that toxicologists should be cognizant of performing toxicity testing with long-held animal cultures, and should perhaps use multiple strains as well as renew cultures periodically in the laboratory. This study also shows that multi-strain toxicity testing with nematodes is highly achievable and useful for understanding variation in intra- and interspecific chemical sensitivity.

Tintori SC et al. (2022) J Vis Exp "Rapid Isolation of Wild Nematodes by Baermann Funnel."

Rockman MV, Sloat SA, Tintori SC

[J Vis Exp, 2022]

Beyond being robust experimental model organisms, Caenorhabditis elegans and its relatives are also real animals that live in nature. Studies of wild nematodes in their natural environments are valuable for understanding many aspects of biology, including the selective regimes in which distinctive genomic and phenotypic characters evolve, the genetic basis for complex trait variation, and the natural genetic diversity fundamental to all animal populations. This manuscript describes a simple and efficient method for extracting nematodes from their natural substrates, including rotting fruits, flowers, fungi, leaf litter, and soil. The Baermann funnel method, a classical nematology technique, selectively isolates active nematodes from their substrates. Because it recovers nearly all active worms from the sample, the Baermann funnel technique allows for the recovery of rare and slow-growing genotypes that co-occur with abundant and fast-growing genotypes, which might be missed in extraction methods that involve multiple generations of reproduction. The technique is also well suited to addressing metagenetic, population-genetic, and ecological questions. It captures the entire population in a sample simultaneously, allowing an unbiased view of the natural distribution of ages, sexes, and genotypes. The protocol allows for deployment at scale in the field, rapidly converting substrates into worm plates, and the authors have validated it through fieldwork on multiple continents.

Cutter AD (2006) Genetics "Nucleotide polymorphism and linkage disequilibrium in wild populations of the partial selfer Caenorhabditis elegans."

Cutter AD

[Genetics, 2006]

An understanding of the relative contributions of different evolutionary forces on an organism''s genome requires an accurate description of the patterns of genetic variation within and between natural populations. To this end, I report a survey of nucleotide polymorphism in six loci from 118 strains of the nematode Caenorhabditis elegans. These strains derive from wild populations of several regions within France, Germany, and new localities in Scotland, in addition to stock center isolates. Overall levels of silent-site diversity are low within and between populations of this self-fertile species, averaging 0.2% in European samples and 0.3% worldwide. Population structure is present despite a lack of association of sequences with geography, and migration appears to occur at all geographic scales. Linkage disequilibrium is extensive in the C. elegans genome, even extending between chromosomes. Nevertheless, recombination is clearly present in the pattern of polymorphisms, indicating that outcrossing is an infrequent, but important, feature in this species ancestry. The range of outcrossing rates consistent with the data is inferred from linkage disequilibrium, using "scattered" samples representing the collecting phase of the coalescent process in a subdivided population. I propose that genetic variation in this species is largely shaped by population subdivision due to self-fertilization coupled with long- and short-range migration between subpopulations.

Koch R et al. (2000) Genome Res "Single nucleotide polymorphisms in wild isolates of Caenorhabditis elegans."

Thijssen KL, Plasterk RHA, van Luenen HGAM, Koch R, van der Horst M

[Genome Res, 2000]

Caenorhabditis elegans (isolate N2 from Bristol, UK) is the first animal of which the complete genome sequence was available. We sampled genomic DNA of natural isolates of C. elegans from four different locations (Australia, Germany, California, and Wisconsin) and found single nucleotide polymorphisms (SNPs) by comparing with the Bristol strain. SNPs are under-represented in coding regions, and many were found to be third base silent codon mutations. We tested 19 additional natural isolates for the presence and distribution of SNPs originally found in one of the four strains. Most SNPs are present in isolates from around the globe and thus are older than the latest contact between these strains. An exception is formed by an isolate from an island (Hawaii) that contains many unique SNPs, absent in the tested isolates from the rest of the world. It has been noticed previously that conserved genes (as defined by homology to genes in Saccharomyces cerevisiae) cluster in the chromosome centers. We found that the SNP frequency outside these regions is 4.5 times higher, supporting the notion of a higher rate of evolution of genes on the chromosome arms.

Paaby AB et al. (2015) Elife "Wild worm embryogenesis harbors ubiquitous polygenic modifier variation."

Riccardi DD, Gunsalus KC, White AG, Rockman MV, Paaby AB, Piano F

[Elife, 2015]

Embryogenesis is an essential and stereotypic process that nevertheless evolves among species. Its essentiality may favor the accumulation of cryptic genetic variation (CGV) that has no effect in the wild-type but that enhances or suppresses the effects of rare disruptions to gene function. Here, we adapted a classical modifier screen to interrogate the alleles segregating in natural populations of Caenorhabditis elegans: we induced gene knockdowns and used quantitative genetic methodology to examine how segregating variants modify the penetrance of embryonic lethality. Each perturbation revealed CGV, indicating that wild-type genomes harbor myriad genetic modifiers that may have little effect individually but which in aggregate can dramatically influence penetrance. Phenotypes were mediated by many modifiers, indicating high polygenicity, but the alleles tend to act very specifically, indicating low pleiotropy. Our findings demonstrate the extent of conditional functionality in complex trait architecture.

Lamelza P et al. (2017) G3 (Bethesda) "Cytoplasmic-Nuclear Incompatibility Between Wild Isolates of Caenorhabditis nouraguensis."

Lamelza P, Ailion M

[G3 (Bethesda), 2017]

How species arise is a fundamental question in biology. Species can be defined as populations of interbreeding individuals that are reproductively isolated from other such populations. Therefore, understanding how reproductive barriers evolve between populations is essential for understanding the process of speciation. Hybrid incompatibility (for example, hybrid sterility or lethality) is a common and strong reproductive barrier in nature. Here we report a lethal incompatibility between two wild isolates of the nematode Caenorhabditis nouraguensis. Hybrid inviability results from the incompatibility between a maternally inherited cytoplasmic factor from each strain and a recessive nuclear locus from the other. We have excluded the possibility that maternally inherited endosymbiotic bacteria cause the incompatibility by treating both strains with tetracycline and show that hybrid death is unaffected. Furthermore, cytoplasmic-nuclear incompatibility commonly occurs between other wild isolates, indicating that this is a significant reproductive barrier within C. nouraguensis. We hypothesize that the maternally inherited cytoplasmic factor is the mitochondrial genome and that mitochondrial dysfunction underlies hybrid death. This system has the potential to shed light on the dynamics of divergent mitochondrial-nuclear coevolution and its role in promoting speciation.

Blaxter ML (1993) J Biol Chem "Cuticle surface proteins of wild type and mutant Caenorhabditis elegans."

Blaxter ML

[J Biol Chem, 1993]

The molecular components of the surface of the free-living nematode Caenorhabditis elegans have been identified by surface-specific radioiodination. Four compartments were defined by fractionation of labeled wild type (N2 strain) adult hermaphrodites. Organic solvents extracted cuticular lipids. Homogenization in detergents released a single, non-collagenous, hydrophobic protein. This is not glycosylated and is a heterodimer of 6.5- and 12-kDa subunits. The third compartment, proteins solubilized by reducing agents, included both the cuticular collagens and the heterodimer. Residual material corresponds to the cuticlin fraction. Larval stages showed a similar pattern, except that the dauer larva had an additional 37-kDa detergent-soluble protein. Other species of rhabditid nematodes displayed similar profiles, and comparison with parasitic species suggests that this simple pattern may be primitive in the Nematoda. A C. elegans strain mutant in cuticular collagen (rol-6) had a pattern identical to that of wild type, but another morphological mutant (dpy-3) [corrected] and several mutants that differ in surface reactivity to antibody and lectins (srf mutants) also had striking differences in surface labeling patterns.