Bioproject ID: PRJNA659268

bioproject id PRJNA659268      to NCBI
key word baseline;APICAL ECTODERMAL RIDGE;TOLL-LIKE RECEPTORS;SPOTTED GAR;TRANSCRIPTION FACTORS;READ ALIGNMENT;SCPP GENES;VERTEBRATE;TRANSITION;EXPRESSION;CHROMATIN
experiment type baseline
publication Thompson, A. , et al. "The genome of the bowfin (Amia calva) illuminates the developmental evolution of ray-finned fishes." Nature Genetics.
description Amia calva developmental genomics
abstract Analysis of a chromosome-level bowfin genome assembly sheds light into neopterygian fish evolution. Chromatin accessibility and gene expression profiling provides insight into bowfin embryonic development.The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin's importance for illuminating vertebrate biology and diversity in the genomic era.

Sample Information

sample id sample name tissue strain treatment description
1. SRR12613066 Amia_stage_26_fin_bud_mRNA_Pool_1 fin bud nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1986).)
2. SRR12613069 Amia_stage_25_fin_bud_mRNA_Pool_1 fin bud nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1987).)
3. SRR12613070 Amia_stage_24_fin_bud_mRNA_Pool_3 fin bud nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1988).)
4. SRR12613073 Amia_stage_23_fin_bud_mRNA_Pool_3 fin bud nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1989).)
5. SRR12613082 Amia_stage_30-31_embryo_mRNA whole embryo nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1990).)
6. SRR12613083 Amia_stage_28-29_embryo_mRNA whole embryo nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1991).)
7. SRR12613084 Amia_stage_26-27_embryo_mRNA whole embryo nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1992).)
8. SRR12613085 Amia_stage_24-25_embryo_mRNA whole embryo nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1993).)
9. SRR12613088 Amia_stage_23-24_embryo_mRNA whole embryo nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1994).)
10. SRR12613089 Amia_stage_22-23_embryo_mRNA whole embryo nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1986).)