A genome assembly of the American black bear, Ursus americanus, from California

Abstract

The American black bear, Ursus americanus, is a widespread and ecologically important species in North America. In California, the black bear plays an important role in a variety of ecosystems and serves as an important species for recreational hunting. While research suggests that the populations in California are currently healthy, continued monitoring is critical, with genomic analyses providing an important surveillance tool. Here we report a high-quality, near chromosome-level genome assembly from a U. americanus sample from California. The primary assembly has a total length of 2.5 Gb contained in 316 scaffolds, a contig N50 of 58.9 Mb, a scaffold N50 of 67.6 Mb, and a BUSCO completeness score of 96%. This U. americanus genome assembly will provide an important resource for the targeted management of black bear populations in California, with the goal of achieving an appropriate balance between the recreational value of black bears and the maintenance of viable populations. The high quality of this genome assembly will also make it a valuable resource for comparative genomic analyses among black bear populations and among bear species.

Keywords: CCGP; California Conservation Genomics Project; Conservation Genomics; wildlife management.

Fig. 1.

The American black bear, Ursus americanus, is a widespread species that can be found in a variety of habitats, from dense forests to open grasslands. Photos from California Department of Fish and Wildlife (left, CC BY 2.0), Florida Fish and Wildlife Conservation Commission (top right, public domain), and David Wasserman (bottom right, CC BY-SA 4.0).

Fig. 2.

Visualization of assembly metrics. (A) K-mer frequencies from the adapter-trimmed PacBio HiFi data used to estimate genome size, sequencing error rate, and heterozygosity. The main peak at ~37× coverage corresponds to homozygous regions of the genome, while the slight peak at ~18× corresponds to heterozygous regions of the genome. The peak around zero corresponds to probable sequencing errors. (B) The omni-C contact map for the primary assembly after manual curation shows the 3D organization of the genome, with darker areas indicating closer proximity. (C) Snail plot displaying assembly metrics for the primary assembly.