A Highly Contiguous and Annotated Genome Assembly of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus)

Abstract

The Lesser Prairie-Chicken (Tympanuchus pallidicinctus; LEPC) is an iconic North American prairie grouse, renowned for ornate and spectacular breeding season displays. Unfortunately, the species has disappeared across much of its historical range, with corresponding precipitous declines in contemporary population abundance, largely due to climatic and anthropogenic factors. These declines led to a 2022 US Fish and Wildlife decision to identify and list two distinct population segments (DPSs; i.e., northern and southern DPSs) as threatened or endangered under the 1973 Endangered Species Act. Herein, we describe an annotated reference genome that was generated from a LEPC sample collected from the southern DPS. We chose a representative from the southern DPS because of the potential for introgression in the northern DPS, where some populations hybridize with the Greater Prairie-Chicken (Tympanuchus cupido). This new LEPC reference assembly consists of 206 scaffolds, an N50 of 45 Mb, and 15,563 predicted protein-coding genes. We demonstrate the utility of this new genome assembly by estimating genome-wide heterozygosity in a representative LEPC and in related species. Heterozygosity in a LEPC sample was 0.0024, near the middle of the range (0.0003-0.0050) of related species. Overall, this new assembly provides a valuable resource that will enhance evolutionary and conservation genetic research in prairie grouse.

Keywords: Pacific Biosciences; TELL-seq; conservation; de novo assembly; haploid; prairie grouse.

Fig. 1.

Genome statistics for the new LEPC genome (bold) and related avian species (Phasianidae) with publicly available reference genome assemblies and associated Illumina sequence data. (A) Genome contiguity (N50) for the most current accession of each species, with assembly build (chromosome or scaffold level) and Avian BUSCO % signified in symbol shape and color, respectively. (B) Genome-wide heterozygosity (H) derived from the alignment of Illumina shotgun data (N = 15 species). The LEPC and GRPC samples were sequenced in the current study for estimates of H. (C) Relationship between estimated genome size and assembly size for species in the Family Phasianidae where both haploid nuclear DNA content and genome assemblies are available from the Animal Genome Size Database and NCBI, respectfully, as of 27 February 2023. Genome Size (Gb) was estimated by multiplying the C-value of each species by 0.978 (Gregory 2023). In cases where a particular species had more than one C-value, a mean value was used. Assembly size (Gb) was obtained from the total genome length (including gaps) of the most current assembly for each species. The dashed black line represents a (theoretical) perfect correlation between C-value length and genome assembly size. In all cases, the assembly size was substantially smaller than the genome size derived from haploid nuclear DNA content.