Researchers led by a team at the Universidad Nacional Autónoma de México isolated a new wild C. elegans strain, designated VJV2, from rotting pear fruit buried in gardens in Mexico City in June 2023. Species identity was confirmed by PCR amplification and Sanger sequencing of the ITS2 ribosomal DNA region, and further validated by backcrossing with males of a fluorescent reporter strain. The team then compared this Mexican isolate with two laboratory lineages obtained from the Caenorhabditis Genetics Center: the contemporary N2 Bristol strain, referred to as N2 Lab, and the so-called N2 Ancestral strain, derived from material cryopreserved in 1969 and estimated to be fewer than six generations from that frozen stock. All experiments used worms within ten generations of frozen stocks, minimizing further laboratory drift.

The three strains turned out to differ substantially in core life-history traits. Under standard laboratory conditions of 20 degrees Celsius and an E. coli diet, the Mexican strain had a median lifespan of just 10 days, compared with 12 days for N2 Lab and 13 days for the Ancestral strain, a statistically significant reduction. Fertility told a similar story: total offspring production over six days was highest in N2 Lab at roughly 282 larvae, followed by the Ancestral strain at about 264, while the Mexican strain produced only about 204, the lowest of the three. Daily fertility analysis showed the Mexican strain lagging from the second day of adulthood onward, and the Ancestral strain also produced fewer offspring than N2 Lab on day three, hinting that even the two N2 lineages have quietly diverged during their separate laboratory histories.

Stress-resistance assays revealed a mosaic of strain-specific strengths and weaknesses rather than a uniform hierarchy. When exposed to the bacterial pathogen Pseudomonas aeruginosa strain PA14, the Mexican worm proved the hardiest, with 50 percent lethality occurring at 43 hours post-infection compared with 37 hours for both N2 lineages. Yet under oxidative stress induced by paraquat, the picture reversed: the Mexican strain succumbed fastest, with a median lethal time of 4.7 hours, while the Ancestral strain was the most resistant at 7.8 hours and N2 Lab intermediate at 6.6 hours. Heat stress at 35 degrees Celsius showed yet another pattern, with the Mexican and N2 Lab strains equally tolerant at 7.5 hours and the Ancestral strain more vulnerable at 6.5 hours. Notably, the Mexican strain carries the npr-1 215F allele and displays the characteristic social feeding behavior of wild isolates, aggregating at the low-oxygen edges of bacterial lawns, while both N2 strains feed solitarily.

Transcriptomic profiling by RNA-sequencing under standard conditions provided a molecular explanation for these phenotypic contrasts. Principal component analysis showed that the N2 Lab strain separated cleanly from the other two along the first principal component, which accounted for 78 percent of total variance, while the Mexican and Ancestral strains diverged from each other only along the second axis. Differential expression analysis identified roughly 3,400 genes differing between the wild-type comparisons and N2 Lab, and 55 percent of these were shared between the Mexican and Ancestral strains, an overlap far exceeding chance. In other words, the laboratory-adapted reference strain has drifted furthest from the wild-type transcriptional state, and the Ancestral lineage, despite decades of lab propagation, remains closer to the newly isolated Mexican worm than to its own modern descendant.

Functional enrichment analysis connected these expression differences to observable phenotypes. Genes upregulated uniquely in the Mexican strain were enriched for pathogen-response and lysozyme categories, including lys-7, a lysozyme gene that P. aeruginosa actively suppresses during infection and whose restoration rescues worms from mortality. The Mexican strain also showed reduced expression of spl-2, a sphingosine phosphate lyase whose hyperactivation increases pathogen susceptibility. Conversely, the Ancestral strain, the most paraquat-resistant, showed elevated baseline expression of antioxidant genes including sod-3, gst-4, and gpx-5, while the oxidative-sensitive Mexican strain uniquely downregulated ctl-1, a catalase critical for hydrogen peroxide detoxification. The Ancestral strain’s reduced thermotolerance was mirrored by downregulation of several heat shock genes, including hsp-1, hsp-6, and hsp-60.

One of the most intriguing shared signatures involved the cuticle. More than 60 collagen transcripts were upregulated in both the Mexican and Ancestral strains relative to N2 Lab, alongside the transcription factor elt-3, which regulates collagen expression in response to environmental stress. Because the collagen-rich cuticle serves as the worm’s primary protective barrier, and because prior work has shown that cuticle-related traits differ between ancestral and laboratory backgrounds, the authors suggest that laboratory adaptation may have reshaped cuticle biology in the reference strain. Shared downregulated genes, meanwhile, were enriched for DNA repair, chromatin modification, and small noncoding RNA functions, pointing to chromatin-level regulatory differences as a promising avenue for future study.

When the team exposed all three strains to acute heat stress, two hours at 35 degrees Celsius, every strain mounted a massive transcriptional response involving roughly 2,400 to 2,900 differentially expressed genes. Yet the overlap was remarkably narrow: only 27 upregulated and 54 downregulated genes were shared across all three strains. The conserved core centered on the canonical heat-inducible genes hsp-16.2, hsp-16.41, and hsp-70, each induced approximately eight-fold in every background. Beyond that shared core, the Mexican and Ancestral strains again clustered together, sharing nearly a quarter of upregulated and a third of downregulated heat-responsive genes, while N2 Lab followed its own program. RT-qPCR validation confirmed these patterns for hsf-1, hsp-6, hsp-16.2, and daf-18, which were upregulated in the Mexican and Ancestral strains but reduced or unchanged in N2 Lab.

The authors are careful to frame these findings as associations rather than proof of causation. The Mexican strain represents a single isolate, so its traits cannot be generalized to the species’ full diversity, and all RNA-seq reads were mapped to the N2 reference genome, a limitation the team acknowledges by noting that mapping metrics showed no major bias and that strain-specific genomic references would refine future analyses. Standard laboratory conditions, including atmospheric oxygen and a monobacterial diet, may themselves constitute an altered environment for non-domesticated strains, meaning some transcriptional differences could reflect environmental response rather than fixed genetic divergence. The reduced lifespan and fertility of the Mexican worm under lab conditions may likewise reflect a trade-off between traits that enhance survival in nature, such as pathogen defense, and traits favored by stable laboratory culture, such as maximal reproductive output.

Nevertheless, the study carries a practical warning for the thousands of laboratories that rely on C. elegans daily. Strain background, laboratory history, and even the choice between the contemporary N2 and its 1969 ancestor can measurably alter lifespan, fertility, stress resistance, and global gene expression, meaning that experimental outcomes may depend on which version of the reference worm sits in the incubator. As the Caenorhabditis Genetics Center’s Natural Diversity Resource now catalogs over 2,000 wild isolates from every continent except Antarctica, this work underscores that the wild relatives of our laboratory workhorses are not mere curiosities but essential yardsticks for measuring how domestication has quietly rewritten one of biology’s most trusted model systems.

Subject of Research: Phenotypic and transcriptomic comparison of a wild Mexican C. elegans isolate with contemporary and ancestral N2 laboratory lineages

Article Title: Life‐History, Stress‐Resistance, and Transcriptomic Variation Among a Mexican Caenorhabditis elegans Isolate and Contemporary and Ancestral N2 Lineages

Article References: Life‐History, Stress‐Resistance, and Transcriptomic Variation Among a Mexican Caenorhabditis elegans Isolate and Contemporary and Ancestral N2 Lineages. (n.d.). https://doi.org/10.1002/ece3.74378

Image Credits: AI Generated

DOI: 10.1002/ece3.74378

Keywords: Caenorhabditis elegans, N2 Bristol, laboratory adaptation, wild isolate, lifespan, fertility, stress resistance, transcriptomics, heat shock response, Pseudomonas aeruginosa, oxidative stress, Mexico City