Little skate genome provides insights into genetic programs essential for limb-based locomotion

Area of Science:

• Evolutionary biology
• Neuroscience
• Genomics

Background:

• The little skate (Leucoraja erinacea), a cartilaginous fish, exhibits walking-like behaviors driven by pelvic fins, utilizing genetic and neuronal pathways similar to terrestrial vertebrates.
• Mechanistic studies of motor circuit development in skates have been hindered by the absence of a high-quality reference genome.

Purpose of the Study:

• To generate a high-quality genome assembly and gene annotation for the little skate.
• To enable post-genomic analyses of spinal motor neurons (MNs) crucial for locomotion.
• To investigate conserved and divergent molecular mechanisms underlying vertebrate motor system evolution.

Main Methods:

• Genome assembly and annotation of Leucoraja erinacea.
• Comparative analysis of mouse, skate, and chicken spinal motor neuron transcriptomes.
• Interspecies comparison of accessible chromatin regions in mouse and skate motor neurons to predict transcription factor (TF) binding motifs.

Main Results:

• A high-quality genome assembly and gene annotation for the little skate were successfully generated.
• Comparative transcriptomic analysis identified shared and distinct gene expression profiles in spinal motor neurons across species.
• Analysis of chromatin accessibility revealed conserved and divergent TF motifs regulating gene expression in motor neurons, with more predicted TF binding sites in mouse MNs.

Conclusions:

• The study provides a foundational genomic resource for the little skate, facilitating future research on motor control.
• Conserved and divergent molecular mechanisms in motor neuron development were identified, shedding light on vertebrate evolution.
• These findings suggest that variations in gene regulatory networks, influenced by transcription factors, contribute to the evolution of complex motor systems in tetrapods.