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Discovery and preliminary multi-species evaluation of single nucleotide polymorphism resources for genus Buteo developed from restriction site-associated DNA paired-end data

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Abstract

Just a few years ago, genomic studies of non-model organisms were extremely time and cost prohibitive, but recent advances in next-generation sequencing have made it possible to generate hundreds to thousands of informative single nucleotide polymorphisms (SNPs) for non-model organisms. We generated a SNP panel using restriction site-associated DNA (RAD) sequencing for species of the genus Buteo (Falconiformes: Accipitridae) with the aim of creating genomic resources in the absence of a reference genome. Using blood and feather samples from three different Buteo species, we used HiSeq Illumina sequencing to generate raw reads. We built 29 162 contigs and discovered 89 921 SNPs using paired-end single-digest RAD data. Using Bayesian clustering and principal componenets analysis, this SNP panel successfully assigned individuals of three Buteo (B. swainsoni, B. jamaicensis, B. lagopus) species correctly to species. We then scanned the SNPs for association with variation in coloration within the three species. This de novo reference will have broad application to the study of Buteo genomic diversity, analysis of population structure within species, identification of hybrids, and other applied studies of the avian genome.

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Acknowledgments

We would like to thank those who contributed samples to this study, including the Golden Gate Raptor Observatory, Christopher Briggs, and Frank Nicoletti. We would also like to acknowledge the Genomic Variation Laboratory and Alisha Goodblah for her guidance in laboratory procedures, and Ismael Saglam and the Miller lab for training in next-generation sequencing bioinformatics. Financial support came from the National Science Foundation Graduate Research Fellowship Program (Grant Number 1148897) and the Jastro Sheilds fellowship through the University of California, Davis.

Data accessibility

The 89,921 SNP data set used in this study is available from GenBank accession KX722542-KX751703.

Author contributions

M. A. M. designed the study, conducted laboratory work including extractions and library preparation, conducted the bioinformatics analyses, and wrote the manuscript. J. M. H. conceived the study and was involved in study design, provided technical supervision and guidance, and contributed to manuscript writing.

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Authors and Affiliations

  1. Department of Animal Science, University of California, Davis, CA, 95616, USA

    Megan A. Mayo & Joshua M. Hull

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  1. Megan A. Mayo
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  2. Joshua M. Hull
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Correspondence to Megan A. Mayo.

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Mayo, M.A., Hull, J.M. Discovery and preliminary multi-species evaluation of single nucleotide polymorphism resources for genus Buteo developed from restriction site-associated DNA paired-end data. Conservation Genet Resour 9, 151–156 (2017). https://doi.org/10.1007/s12686-016-0619-7

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  • DOI: https://doi.org/10.1007/s12686-016-0619-7

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