The genome of the bowfin (Amia calva) illuminates the developmental evolution of ray-finned fishes
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.
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This is a list of supplementary files associated with this preprint. Click to download.
Supplementary Material
Supplementary File 1 - Bowfin Scpp gene predictions
Supplementary File 2 - Bowfin hox gene transcripts
Supplementary Table 6 - Bowfin MHC genes
Supplementary Table 7 - Gar MHC genes
Supplementary Tables 8-12 - Immune gene accessions
Supplementary Table 19 - Human VISTA enhancers in bowfin OCRs
Posted 27 Oct, 2020
The genome of the bowfin (Amia calva) illuminates the developmental evolution of ray-finned fishes
Posted 27 Oct, 2020
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