A novel approach to comparative RNA-Seq does not support a conserved set of genes underlying animal regeneration
Abstract
Molecular studies of animal regeneration typically focus on conserved genes and signaling pathways that underlie morphogenesis. To date, a holistic analysis of gene expression across animals has not been attempted, as it presents a suite of problems related to differences in experimental design and gene homology. By combining orthology analysis with a novel statistical method for testing gene enrichment across large datasets, we are able to test whether biological processes across organisms share transcriptional regulation. We applied this method to six publicly available RNA-seq datasets from diverse examples of animal regeneration. We recovered 160 conserved orthologous gene clusters, which are enriched in structural genes as opposed to those regulating morphogenesis. A breakdown of gene presence/absence provides only limited support for the conservation of pathways typically implicated in regeneration, such as Wnt signaling and cell pluripotency. Specifically, these pathways are only conserved if we allow gene paralogs to be interchangeable through evolution. Overall, our analysis does not support the hypothesis that a shared set of ancestral genes underlie regeneration mechanisms in animals. The methods described in this paper will be broadly applicable for studying the genetic underpinnings of traits across distantly related organisms.
Additional Information
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. This version posted March 23, 2021. The authors have declared no competing interest.Attached Files
Submitted - 2021.03.22.434850v1.full.pdf
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Additional details
- Eprint ID
- 108540
- Resolver ID
- CaltechAUTHORS:20210324-071454082
- Created
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2021-03-24Created from EPrint's datestamp field
- Updated
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2021-04-19Created from EPrint's last_modified field
- Caltech groups
- Division of Biology and Biological Engineering, Division of Biology and Biological Engineering