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The little skate genome and the evolutionary emergence of wing-like fin appendages

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Leucoraja erinaceus

PROVIDER: GSE188980 | GEO | 2023/01/12

REPOSITORIES: GEO

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The little skate genome and the evolutionary emergence of wing-like fin appendages [HiChIP]

Project description:While retaining ancestral morphological and genomic traits, skates evolved a novel body plan with remarkably enlarged wing-like fins that allowed skates to thrive in benthic environments, but their molecular underpinnings remain elusive. Here we investigate the origin of this phenotypical innovation by assembling a high-quality chromosome-scale genome sequence for the little skate Leucoraja erinacea and by generating extensive regulatory profiling datasets in developing fins (gene expression, chromatin occupancy and conformation). We show that despite their derived morphology, the skate genome retains multiple features of the ancestral jawed vertebrate genome.

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The little skate genome and the evolutionary emergence of wing-like fins.

Project description:Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments1,2. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins-including gene expression, chromatin occupancy and three-dimensional conformation-we find skate-specific genomic rearrangements that alter the three-dimensional regulatory landscape of genes that are involved in the planar cell polarity pathway. Functional inhibition of planar cell polarity signalling resulted in a reduction in anterior fin size, confirming that this pathway is a major contributor to batoid fin morphology. We also identified a fin-specific enhancer that interacts with several hoxa genes, consistent with the redeployment of hox gene expression in anterior pectoral fins, and confirmed its potential to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganization and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait.

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The little skate genome and the evolutionary emergence of wing-like fin appendages

Project description:The little skate genome and the evolutionary emergence of wing-like fin appendages

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Project description:The little skate genome and the evolutionary emergence of wing-like fin appendages [HiChIP]

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Project description:The little skate genome and the evolutionary emergence of wing-like fin appendages [ATAC-seq]

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