Assembly and annotation of a chromosome-level reference genome for the endangered Colorado pikeminnow Ptychocheilus lucius

Abstract

Advancements in genome sequencing technology have brought unprecedented accessibility of high-throughput sequencing to species of conservation interest. The potential knowledge gained from application of these techniques is maximized by availability of high-quality, annotated reference genomes for endangered species. However, these vital resources are often lacking for endangered minnows of North America (Cypriniformes: Leuciscidae). One such endangered species, Colorado pikeminnow (Ptychocheilus lucius) is the largest North American minnow and the top-level native aquatic predator in the Colorado River Basin of the southwestern United States and northwestern Mexico. Over the past century Colorado pikeminnow has suffered habitat loss and population declines due to anthropogenic habitat modifications and invasive species introductions. The lack of genetic resources for Colorado pikeminnow has hindered conservation genomic study of this unique organism. This study seeks to remedy this issue by presenting a high-quality reference genome for Colorado pikeminnow developed from Pacific Biosciences HiFi sequencing and Hi-C scaffolding. The final assembly was a 1.1 Gb genome comprised of 305 contigs including 25 chromosome-sized scaffolds. Measures of quality, contiguity, and completeness met or exceeded those observed for Danio rerio (Danionidae) and two other Colorado River Basin leuciscids (Meda fulgida and Tiaroga cobitis). Comparative genomic analyses identified enrichment of gene families for growth, development, immune activity, and gene transcription; all of which are important for a large-bodied piscivorous fish living in a dynamic environment. This reference genome will provide a basis for important conservation genomic study of Colorado pikeminnow and help efforts to better understand the evolution of desert fishes.