Abstract We present genome assemblies for two cyprinoid fishes, the tui chub (Siphateles bicolor) and the arroyo chub (Gila orcuttii). These fishes are ecologically important representatives of native fish assemblages in the western United States and are both species of conservation concern. The two species hybridize where introductions bring them into contact, with potentially important ecological and evolutionary implications that have not yet been thoroughly examined from a genomic perspective. We present de novo assemblies for both species, representing the first scaffold-level genomes within their respective genera, which were developed as part of the California Conservation Genomics Project (CCGP) using Pacific Biosciences HiFi and Omni-C data. Our tui chub assembly consists of 258 scaffolds spanning 1 148 084 093 base pairs, has a scaffold N50 of 45.9 Mb, a contig N50 of 23.7 Mb, and a BUSCO completeness score of 98.1%. Our arroyo chub assembly consists of 179 scaffolds spanning 1 263 410 250 base pairs, has a scaffold N50 of 50.5 Mb, a contig N50 of 13.1 Mb, and a BUSCO completeness score of 97.8%. A comparative analysis of the two species revealed relatively conserved genomes, with the exception of two inversions at chromosome 20. We annotated a total of 34 090 genes with a BUSCO completeness score of 98.1% for the tui chub, and 28 193 genes with a score of 97.4% for the arroyo chub. These assemblies will be valuable resources for characterizing the species’ phylogeographic histories and delineating the role of hybridization in their evolution.
Baker et al. (Fri,) studied this question.