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A genome assembly of the speckled dace, Rhinichthys Osculus
H K Baker1, M Escalona2, A P Kinziger3
1Department of Ecology, Behavior, and Evolution, University of California, San Diego, CA, United States.
The Journal of Heredity
|May 26, 2026
Summary
This study presents the first scaffold-level genome assembly for the speckled dace (Rhinichthys osculus), a widespread North American fish. This valuable genomic resource will aid in understanding its evolution and inform conservation efforts for imperiled populations.
Area of Science:
- Genomics
- Ichthyology
- Conservation Biology
Background:
- The speckled dace (Rhinichthys osculus) is a species complex with wide distribution in western North America.
- Significant morphological and genetic variation exists across its range.
- Several endemic speckled dace taxa are imperiled and protected under the US Endangered Species Act.
Purpose of the Study:
- To generate a high-quality, annotated, scaffold-level genome assembly for the speckled dace (Rhinichthys osculus).
- To provide a foundational genomic resource for research on speckled dace phylogeography, evolution, and conservation.
Main Methods:
- Utilized Pacific Biosciences HiFi long reads and Omni-C data for de novo genome assembly.
- Performed genome annotation using the NCBI Eukaryotic Genome Annotation Pipeline with species-specific RNA-Seq data.
- Assembled a genome of approximately 1.15 Gb with high contiguity and completeness (BUSCO score 97.7%).
Main Results:
- Generated a scaffold-level genome assembly of 490 scaffolds with a scaffold N50 of 44.5 Mb.
- Annotated 39,919 genes with high completeness (BUSCO score 98.3%).
- The speckled dace genome is estimated to comprise 25 chromosomes.
Conclusions:
- This represents the first scaffold-level genome assembly for the genus Rhinichthys.
- The annotated genome provides a critical resource for future studies on speckled dace.
- This genomic data will directly support conservation strategies for this species complex.
