A De Novo Chromosome-Level Genome Assembly of the White-Tailed Deer, Odocoileus Virginianus

Abstract

Cervids are distinguished by the shedding and regrowth of antlers. Furthermore, they provide insights into prion and other diseases. Genomic resources can facilitate studies of the genetic underpinnings of deer phenotypes, behavior, and disease resistance. Widely distributed in North America, the white-tailed deer (Odocoileus virginianus) has recreational, commercial, and food source value for many households. We present a genome generated using DNA from a single Illinois white-tailed sequenced on the PacBio Sequel II platform and assembled using Wtdbg2. Omni-C chromatin conformation capture sequencing was used to scaffold the genome contigs. The final assembly was 2.42 Gb, consisting of 508 scaffolds with a contig N50 of 21.7 Mb, a scaffold N50 of 52.4 Mb, and a BUSCO complete score of 93.1%. Thirty-six chromosome pseudomolecules comprised 93% of the entire sequenced genome length. A total of 20 651 predicted genes using the BRAKER pipeline were validated using InterProScan. Chromosome length assembly sequences were aligned to the genomes of related species to reveal corresponding chromosomes.

Keywords: Illumina; Omni-C; Pacific Biosciences; annotation; haploid; non-model species.

Figure 1.

Contig, scaffold, and chromosome-level assemblies of the white-tailed deer genome. (A) Scaffolds are arranged by size (bottom) and their component contigs are arranged by scaffold (top). The largest scaffolds representing 50% (orange) and 90% (orange + red) of the assembly are indicated with color, leaving the remaining 10% of the assembly (black + gray). Scaffolds below 3 Mb (gray) are not visually separated. The number of contigs per scaffold is presented in Table 3. (B) Scaffold contact map generated from chromatin conformation capture Omni-C sequencing and visualized with HiCExplorer. Scaffold-scaffold contacts are shown increasing from blue to white, to red, and the strong diagonal signal represents scaffold self-association based on nuclear proximity. (C) Contact map for chromosome-sized pseudomolecules sequences manually curated into chromosomes.