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Article
The genome of the bowfin (Amia calva) illuminates the developmental evolution of ray-finned fishes
Ingo Braasch
Michigan State University
Corresponding Author
ORCiD: https://orcid.org/0000-0003-4766-611X
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This work is licensed under a CC BY 4.0 License. Read Full License
The bowfin fish (Amia calva) diverged before the genome duplication in teleost fishes, and its archetypical body plan and slow rate of molecular evolution make it a key species for genomic exploration as a basal representative of the neopterygian fishes. To investigate the evolution and development of ray-finned fishes, we generated a chromosome-level genome assembly for bowfin that enables gene-order analyses which settle its long-debated, phylogenetic relationship with gars. We analyze the genomic underpinnings of the bowfin’s unique combination of derived and ancestral phenotypes involving the immune system as well as scale, respiratory organ, and skeletal development. By detailing chromatin accessibility and gene expression through bowfin development, we connect developmental gene regulatory loci across vertebrates. We illustrate the utility of these genomic resources to connect developmental evolution across bony fishes, showing the importance of bowfin in understanding vertebrate biology and diversity.
Keywords
bowfin (Amia calva) genome, developmental evolution of ray-finned fishes, neopterygian fishes
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This is a list of supplementary files associated with this preprint. Click to download.
- BowfinSupplementsNG201013.pdf
Supplementary Material
- SupplFile1BowfinScppGenesv3.pdf
Supplementary File 1 - Bowfin Scpp gene predictions
- SupplFile2BowfinHoxv3.txt
Supplementary File 2 - Bowfin hox gene transcripts
- SupplTab6BowfinMHCgenes.pdf
Supplementary Table 6 - Bowfin MHC genes
- SupplTab7GarMHCgenes.xlsx
Supplementary Table 7 - Gar MHC genes
- SupplTab812ImmuneGeneAccessions.pdf
Supplementary Tables 8-12 - Immune gene accessions
- SupplTab19VISTAenhancersbowfinOCRs.xls
Supplementary Table 19 - Human VISTA enhancers in bowfin OCRs
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This preprint is under consideration at a Nature Portfolio Journal. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Nature journals have partnered with Research Square to offer In Review, a journal-integrated preprint deposition service.
Article
The genome of the bowfin (Amia calva) illuminates the developmental evolution of ray-finned fishes
Ingo Braasch
Michigan State University
Corresponding Author
ORCiD: https://orcid.org/0000-0003-4766-611X
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 1
Posted 27 Oct, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
The bowfin fish (Amia calva) diverged before the genome duplication in teleost fishes, and its archetypical body plan and slow rate of molecular evolution make it a key species for genomic exploration as a basal representative of the neopterygian fishes. To investigate the evolution and development of ray-finned fishes, we generated a chromosome-level genome assembly for bowfin that enables gene-order analyses which settle its long-debated, phylogenetic relationship with gars. We analyze the genomic underpinnings of the bowfin’s unique combination of derived and ancestral phenotypes involving the immune system as well as scale, respiratory organ, and skeletal development. By detailing chromatin accessibility and gene expression through bowfin development, we connect developmental gene regulatory loci across vertebrates. We illustrate the utility of these genomic resources to connect developmental evolution across bony fishes, showing the importance of bowfin in understanding vertebrate biology and diversity.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6