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

Area of Science:

• Developmental Biology
• Genomics
• Evolutionary Biology

Background:

• High-resolution gene expression mapping is vital for understanding development and evolution.
• Nematode studies were limited by small body size, but new techniques overcome this.
• Single worm transcriptomics (SWT) enables detailed analysis in microscopic organisms.

Purpose of the Study:

• To create a high-resolution developmental transcriptome map in *Pristionchus pacificus* using SWT.
• To analyze gene expression dynamics over 60 hours of postembryonic development.
• To compare oscillatory gene expression patterns with *C. elegans*.

Main Methods:

• Implemented single worm transcriptomics (SWT) across 38 time points from J2 larvae to young adults.
• Achieved high sequencing depth (4.5 million read pairs) to detect over 23,135 genes.
• Conducted gene age analysis and comparative genomics with *C. elegans*.

Main Results:

• Generated a 1- to 2-hour resolution gene expression catalog for *P. pacificus* development.
• Identified nearly 3000 (10%) oscillating genes with distinct expression patterns.
• Found overrepresentation of ancient genes and collagens among oscillating genes, with some linked to *eud-1* and mouth-form plasticity.

Conclusions:

• Developed an updated SWT protocol applicable to various microscopic species.
• Provided a comprehensive developmental transcriptome map for *P. pacificus*.
• Offered insights into the evolution of gene expression and developmental processes in nematodes.