A genome assembly of the speckled dace, Rhinichthys Osculus.

Abstract

The speckled dace, Rhinichtyhs osculus, is a cyprinoid fish species complex (family: Leuciscidae) with one of the widest native ranges of any freshwater fish in western North America. It occupies a variety of freshwater habitats and exhibits considerable morphological and genetic variation across its range. Several endemic taxa within the species complex are imperiled, four of which are protected under the US Endangered Species Act, with two more proposed for listing. Here, we present an annotated, scaffold-level assembly of the speckled dace genome as part of the California Conservation Genomics Project (CCGP). Consistent with the CCGP genome assembly strategy, we used Pacific Biosciences HiFi long reads and Omni-C data for our de novo genome assembly and performed genome annotations on NCBI Eukaryotic Genome Annotation Pipeline using novel, species-specific RNA-Seq reads generated from five tissue types. The assembly consists of 490 scaffolds totaling approximately 1.15 Gb, with a contig N50 of 10.9 Mb and a scaffold N50 of 44.5 Mb. A BUSCO score of 97.7% reflects the assembly's strong completeness. The genome of Rhinichthys osculus is estimated to consist of 25 chromosomes. This is the first scaffold-level genome assembly within the genus Rhinichthys. We annotated a total of 39,919 genes with a BUSCO completeness score of 98.3%. This reference genome will be a valuable resource for understanding the phylogeography and evolution of speckled dace and informing its conservation.