Harnessing Single Cell RNA Sequencing to Uncover Developmental Genetic Underpinnings of Syngnathid Fishes’ Derived Traits
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Date
2025-02-24
Authors
Healey, Hope
Journal Title
Journal ISSN
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Publisher
University of Oregon
Abstract
Syngnathid fishes are extraordinary creatures with highly derived features. Notably, thesefishes have elongated, toothless snouts, male pregnancy, and exoskeletons. In addition to their
highly altered morphologies, syngnathids have lost highly conserved signaling genes (fgf3 and
4), transcription factors (eve1), and tooth mineralization genes (scpp genes). Although these
genomic changes are predicted to contribute to the development, or lack thereof, of syngnathid’s
derived traits, it is unknown whether this is the case. To investigate developmental origins of
syngnathid’s highly altered traits, I harnessed single cell RNA sequencing (scRNAseq) methods
for my dissertation research. First, I identified limitations for completing scRNAseq analysis in
non-traditional model organisms, then overcame these challenges using scISOseq to improve
gene annotations. Then, I used these methods to study syngnathid’s unique craniofacial
morphology (elongate head and loss of teeth). I identified the cell types present and signaling
genes expressed at the start of craniofacial elongation in Gulf pipefish. Additionally, I found
unique changes in signaling gene expression patterns during early craniofacial development of
Gulf pipefish. This thesis discovered local modifications (select Fgf, Wnt, and Bmp genes) in
pipefish craniofacial development, but found no evidence for global gene network re-wiring.
Overall, this study suggests that syngnathid’s highly derived heads evolved from local network
re-wiring.
This dissertation includes previously published and unpublished co-authored material.
Description
Keywords
evolutionary novelties, scRNAseq, syngnathid