Developing a High-Quality Linkage Map for the Atlantic Killifish Fundulus heteroclitus

Area of Science:

• Genomics
• Evolutionary Biology
• Aquatic Ecology

Background:

• Killifish (Fundulus heteroclitus) exhibit remarkable phenotypic plasticity and local adaptation across diverse aquatic environments.
• High-throughput sequencing aids in understanding genotype-phenotype relationships and evolutionary history.
• Existing scaffolded genome assemblies lack the contiguity needed for advanced genotype-phenotype analyses.

Purpose of the Study:

• To improve the contiguity of the killifish genome assembly.
• To establish a high-density genetic map for Fundulus heteroclitus.
• To provide a more robust genomic resource for population and comparative genomics.

Main Methods:

• Utilized 5,685 high-quality RAD-Seq markers from a single mapping family.
• Ordered 84% of the scaffolded genome assembly to 24 chromosomes.
• Investigated the impact of sequence data filtration thresholds on scaffold placement.

Main Results:

• Generated a high-density genetic map, significantly improving genome assembly contiguity.
• Estimated genome-wide recombination rates.
• Confirmed conserved synteny with other fish species and identified chromosomal rearrangements.

Conclusions:

• The improved genome map enhances the toolkit for killifish research.
• Highlights the importance of data filtration in linkage mapping.
• Suggests further optical mapping is needed for fine-scale genome structure resolution.
• Emphasizes the necessity of a quality mapped genome for future genomic studies.