A high-quality reference genome for the common creek chub, Semotilus atromaculatus.

Creek chub (Semotilus atromaculatus) is a leuciscid minnow species commonly found in anthropogenically disturbed environments, making it an excellent model organism to study human impacts on aquatic systems. Genomic resources for creek chub and other leuciscid species are currently limited. However, advancements in DNA sequencing now allow us to create genomic resources at a historically low cost. Here, we present a high quality, 239 contig reference genome for the common creek chub, created with PacBio HiFi sequencing. We compared the assembly quality of two pipelines: Pacific Biosciences' Improved Phase Assembly (873 contigs) and Hifiasm (239 contigs). Quality and completeness of this genome is comparable to the zebrafish (Danioninae) and fathead minnow (Leuciscidae) genomes. The creek chub genome is highly syntenic to the zebrafish and fathead minnow genomes, and while our assembly does not resolve into the expected 25 chromosomes, synteny with zebrafish suggests that each creek chub chromosome is likely represented by 1-4 large contigs in our assembly. This reference genome is a valuable resource that will enhance genomic biodiversity studies of creek chub and other nonmodel leuciscid species common to disturbed environments.

Limited evidence of a genetic basis for sex determination in the common creek chub, Semotilus atromaculatus.

Sexual reproduction is almost universal in vertebrates; therefore, each animal species which uses it must have a mechanism for designating sex as male or female. Fish, especially, have a wide range of sex determining systems. In the present study, we aimed to identify a genetic basis for sex determination in the common creek chub (Semotilus atromaculatus) using genotyping-by-sequencing data. No sex-associated markers were found by RADSex or a GWAS using GEMMA; however, Weir and Cockerham locus-specific FST analysis and discriminant analysis of principal components revealed genetic differentiation between the sexes at several loci. While no explicit sex determination mechanism has been yet discovered in creek chub, these loci are potential candidates for future studies. Incompatible systems are thought to increase reproductive isolation but interspecific hybridization is common among groups such as cyprinid minnows; thus, studies such as ours can provide insight into hybridization and evolutionary diversification of this clade. We also highlight technical challenges involved in studying sex determination in evolutionary groups with extremely variable mechanisms and without heteromorphic sex chromosomes.