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Media type:
E-Article
Title:
Single worm transcriptomics identifies a developmental core network of oscillating genes with deep conservation across nematodes
Contributor:
Sun, Shuai;
Rödelsperger, Christian;
Sommer, Ralf J.
Published:
Cold Spring Harbor Laboratory, 2021
Published in:
Genome Research, 31 (2021) 9, Seite 1590-1601
Language:
English
DOI:
10.1101/gr.275303.121
ISSN:
1088-9051;
1549-5469
Origination:
Footnote:
Description:
<jats:p>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 <jats:italic>Pristionchus pacificus</jats:italic> 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 <jats:italic>C. elegans</jats:italic>. One important gene family overrepresented among oscillating genes is collagens. Several of these collagen genes are regulated by the developmental switch gene <jats:italic>eud-1</jats:italic>, 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 <jats:italic>P. pacificus</jats:italic> gene expression throughout postembryonic development, and (3) a comparative analysis of oscillatory gene expression between the two model organisms <jats:italic>P. pacificus</jats:italic> and <jats:italic>C. elegans</jats:italic> and associated evolutionary dynamics.</jats:p>