High-resolution single-worm transcriptomics and the function of oscillating genes in mouth-form development in Pristionchus pacificus

Abstract

Development is largely under the control of genes. Specific spatiotemporal gene expression can modify the development and the final phenotype of an organism. To obtain a high-resolution catalog of the developmental transcriptome in Pristionchus pacificus, I developed and implemented a single worm transcriptomic approach for the nematode model organism P. pacificus, and performed temporal transcriptome analysis over the entire postembryonic development with 38 time points. I focused on investigating oscillating gene expression patterns and found that i) nearly 3000 oscillating genes are periodically expressed during postembryonic development, ii) there is an overrepresentation of ancient gene classes among oscillatory genes, and iii) the developmental switch gene eud-1 mediates numerous oscillatory genes including collagens, indicating the potential roles of these oscillating collagens in regulating mouth-form plasticity. Mouth-form dimorphism in P. pacificus provides an ideal example to study the mechanisms of phenotype plasticity. Many previous studies focused on the regulation of mouth-form development and identified environmental influences, developmental switches, the gene regulatory network involved in mouth-form plasticity, and the associated evolutionary processes. However, the molecular and structural basis of the teeth in P. pacificus remains poorly understood. To address this fundamental question, I used two complementary approaches. First, I performed a large-scale genetic screen and obtained six mutants displaying morphological changes in both stomatal structures and body shape. Using whole genome sequencing and genome editing (CRISPR/Cas9 system) technologies, I identified Ppa-dpy-6, which encodes a mucin-type protein, as the first structural component of the nematode stoma involved in the specification of the cheilostom and cuticle. Second, I investigated the function of two chitin synthase genes (chs) in P. pacificus. Phylogenetic analysis revealed that two chitin synthase genes are highly conserved across nematodes. Mutations in the C- terminus of chs-2 in P. pacificus result in a viable but teethless phenotype. Moreover, animals with this teethless phenotype were observed after injection of the chitin-synthase inhibitor Nikkomycin Z. These results suggest that the conserved Ppa-chs-2 is essential for P. pacificus teeth formation. In addition, such teethless mutants can feed on various bacterial food sources, yet they are incapable of predation.