Single worm transcriptomics identifies a developmental core network of oscillating genes with deep conservation across nematodes

Abstract

High-resolution spatial and temporal maps of gene expression have facilitated a comprehensive understanding of animal development and evolution. In nematodes, the small body size represented a major challenge for such studies, but recent advancements have helped overcome this limitation. Here, we have implemented single worm transcriptomics (SWT) in the nematode model organism Pristionchus pacificus to provide a high-resolution map of the developmental transcriptome. We selected 38 time points from hatching of the J2 larvae to young adults to perform transcriptome analysis over 60 h of postembryonic development. A mean sequencing depth of 4.5 million read pairs allowed the detection of more than 23,135 (80%) of all genes. Nearly 3000 (10%) genes showed oscillatory expression with discrete expression levels, phases, and amplitudes. Gene age analysis revealed an overrepresentation of ancient gene classes among oscillating genes, and around one-third of them have 1:1 orthologs in C. elegans. One important gene family overrepresented among oscillating genes is collagens. Several of these collagen genes are regulated by the developmental switch gene eud-1, indicating a potential function in the regulation of mouth-form plasticity, a key developmental process in this facultative predatory nematode. Together, our analysis provides (1) an updated protocol for SWT in nematodes that is applicable to many microscopic species, (2) a 1- to 2-h high-resolution catalog of P. pacificus gene expression throughout postembryonic development, and (3) a comparative analysis of oscillatory gene expression between the two model organisms P. pacificus and C. elegans and associated evolutionary dynamics.

Experimental and theoretical support for costs of plasticity and phenotype in a nematode cannibalistic trait

“…The first column of the fundamental matrix for these strains on OP50 is[24.1,18.2,11.8,14.3,10,24,24,24,24,24,200], implying that an egg spends on average 24.1 hours in the egg stage, 18.2 in J2, 11.8 in J3, 14.3 in J4, 10 in YA, 24 in each of the five breeding adult stages, and 200 hours (roughly 8.5 days) in the old adult stage before dying. These values are in line with the laboratory measurements of developmental speed[57,58]. We adjusted the probability of YA → BA1 such that the duration of YA stage on Novosphigobium would reduce to ≈ 8 and ≈ 6 hours for RSC017 and RS5405, respectively.…”

“…S1b). The time point of 75hrs was chosen to capture the transition rate from juvenile stages to adulthood [57,58].…”

Genomic landscape of drug response reveals mediators of anthelmintic resistance

“…The ability to do so would enable more sophisticated genetic approaches to unravel the role of the minor signatures of selection we observe in this experiment and improve our understanding of the molecular basis of drug resistance phenotypes. Recent advances in single larvae whole-genome sequencing ( Doyle et al., 2019b ) and low-input RNA-seq ( Sun et al., 2021 ), even at single-cell resolution ( Diaz Soria et al., 2020 ), now provide the tools to allow a more precise understanding of molecular and cellular phenotypes for drug response and may help to understand the role of cky-1 fully. The identification of cky-1 as a putative candidate offers new plausible hypotheses relevant to a resistant phenotype, whereby cky-1 may act (1) during development to establish a neuronal architecture that is more tolerant to hyperexcitability, such as that caused by ivermectin, and/or (2) in response to ivermectin exposure by initiating transcription of downstream genes to modulate the excessive excitation/inhibition imbalance, thereby mitigating the lethal effect.…”

Genomic landscape of drug response reveals novel mediators of anthelmintic resistance

“…The ability to do so would improve our understanding of the molecular basis of drug resistance phenotypes and enable more sophisticated genetic approaches to unravel the role of the minor signatures of selection we observe in this experiment. Recent advances in single larvae whole-genome sequencing ( 69 ) and low-input RNA sequencing ( 70 ), even at single-cell resolution ( 71 ), now provide the tools to allow a more precise understanding of molecular and cellular phenotypes for drug response and may help to fully understand the role of cky-1 . The identification of cky-1 as a putative candidate offers new plausible hypotheses relevant to a resistant phenotype, whereby cky-1 may act: (i) during development to establish a neuronal architecture that is more tolerant to hyperexcitability such as that caused by ivermectin, and/or (ii) in response to ivermectin exposure by initiating transcription of downstream genes to modulate the excessive excitation/inhibition imbalance, thereby mitigating the lethal effect.…”