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Title: Annotated draft genome assemblies for the northern bobwhite (Colinus virginianus) and the scaled quail (Callipepla squamata) reveal disparate estimates of modern genome diversity and historic effective population size

Author
item OLDESCHULTE, DAVID - Texas A&M University
item HALLEY, YVETTE - Texas A&M University
item WILSON, MIRANDA - Texas A&M University
item BHATTARAI, ERIC - Texas A&M University
item BRASHEAR, WESLEY - Texas A&M University
item HILL, JOSHUA - Texas A&M University
item METZ, RICHARD - Texas A&M University
item JOHNSON, CHARLES - Texas A&M University
item ROLLINS, DALE - Rolling Plains Quail Research Foundation
item PETERSON, MARKUS - University Of Texas - El Paso
item Bickhart, Derek
item DECKER, JARED - University Of Missouri
item SEWELL, JOHN - Harris Ranch
item SEABURY, CHRISTOPHER - Texas A&M University

Submitted to: Genes, Genomes, and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/10/2017
Publication Date: 9/1/2017
Citation: Oldeschulte, D.L., Halley, Y.A., Wilson, M.L., Bhattarai, E.K., Brashear, W., Hill, J., Metz, R.P., Johnson, C.D., Rollins, D., Peterson, M.J., Bickhart, D.M., Decker, J.E., Sewell, J.F., Seabury, C.M. 2017. Annotated draft genome assemblies for the northern bobwhite (Colinus virginianus) and the scaled quail (Callipepla squamata) reveal disparate estimates of modern genome diversity and historic effective population size. Genes, Genomes, and Genomics. https://doi.org/10.1534/g3.117.043083.
DOI: https://doi.org/10.1534/g3.117.043083

Interpretive Summary: The northern bobwhite and scaled quail are two native U.S. range fowl that are slowly losing ground to urbanization in their native habitats. This study is the first characterization of their DNA genomes in order to understand differences in their genetic makeup and their unique evolutionary history. Due to increased predation and loss of habitat, the scaled quail was found to have less genetic diversity than the bobwhite, suggesting that the species may further decline due to a new genetic bottleneck.

Technical Abstract: Northern bobwhite (Colinus virginianus; hereafter bobwhite) and scaled quail (Callipepla squamata) populations have suffered precipitous declines across most of their U.S. ranges. Illumina-based first- (v1.0) and second-generation (v2.0) draft genome assemblies for the scaled quail and the bobwhite produced N50 scaffold sizes of 1.035 Mb and 2.042 Mb, thereby producing a 45-fold improvement in contiguity over the existing bobwhite assembly. More than 90% of the assembled genomes were captured within 1,313 and 8,990 scaffolds, respectively. The scaled quail assembly (v1.0 = 1.045 Gb) was approximately 20% smaller than the bobwhite (v2.0 = 1.254 Gb), which was supported by kmer-based estimates of genome size. Nevertheless, estimates of GC content (41.72%; 42.66%), genome-wide repetitive content (10.40%; 10.43%), and MAKER-predicted protein coding genes (17,131; 17,165) were similar for the scaled quail (v1.0) and bobwhite (v2.0) assemblies, respectively. BUSCO analyses utilizing 3,023 single-copy orthologs revealed a high level of assembly completeness for the scaled quail (v1.0; 84.8%) and the bobwhite (v2.0; 82.5%), as verified by comparison with well-established avian genomes. We also detected 273 putative segmental duplications in the scaled quail genome (v1.0), and 711 in the bobwhite genome (v2.0), including some that were shared among both species. Autosomal variant prediction revealed approximately 2.48 and 4.17 heterozygous variants per Kb within the scaled quail (v1.0) and bobwhite (v2.0) genomes, respectively. Estimates of historic effective population size were uniformly higher for the bobwhite across all time points in a coalescent model. However, large-scale declines were predicted for both species, beginning at approximately 15-20 kya.