Abstract
Samples from avian species of high conservation concern are often low in total genomic DNA (gDNA). Feathers are collected more frequently than blood, yet they contain low total gDNA which can present challenges in using them for genomics. Whole Genome Sequencing (WGS) can provide many insights that can be used to aid in species conservation, but current methods for working with feathers are cost prohibitive for population level genomic analyses. Thus, there is a need for a cost-effective method of preparing WGS libraries from feathers. To bridge the gap between sampling techniques commonly used in avian conservation genetics that yield low total gDNA and the powerful tool of WGS, we developed a method that successfully produces WGS libraries from feather gDNA with as low input as 0.48 ng of DNA and an average final library size of 300–500 base pairs. Sequencing results suggest high sequencing quality using our protocol with feather DNA. We conclude that our method will facilitate high-throughput WGS on low total gDNA samples, like feathers, thus expanding the power of genomic tools in critical avian conservation research.
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Data availability
Sequence files and scripts is archived on Dryad: https://doi.org/10.5061/dryad.j6q573nf5. Full laboratory protocol will be submitted as Online Resource 1.
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Acknowledgements
This work was made possible by an National Science Foundation CAREER award (008933-00002), an NSF Grant Rules of Life Grant (007604-00002), and a National Geographic Grant (WW-202R-170) awarded to Dr. Kristen Ruegg as well as the Extreme Science and Engineering Discovery Environment (XSEDE) computer cluster, which is supported by National Science Foundation Grant ACI-1548562. Thank you to Dr. Kristen Ruegg for providing resources and guidance that made this publication possible. Thank you to Dr. Nina Therkildsen for sharing her WGS method, Harmony B. Borchardt-Wier for early guidance on trouble-shooting Dr. Therkildsen’s protocol, and Dr. Cristian Gruppi for his technical advising. We thank the UC Davis Genome Center for their help with the sequencing.
Funding
This work was made possible by an NSF CAREER award (008933-00002), an NSF Grant Rules of Life Grant (007604-00002), and a National Geographic Grant (WW-202R-170) awarded to Dr. Kristen Ruegg as well as the Extreme Science and Engineering Discovery Environment (XSEDE) computer cluster, which is supported by National Science Foundation Grant ACI-1548562.
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TMS designed and carried out the experiments. MGDeS analyzed data. TMS and MGDeS, wrote the manuscript and have approved the final version.
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Schweizer, T.M., DeSaix, M.G. Cost-effective library preparation for whole genome sequencing with feather DNA. Conservation Genet Resour 15, 21–28 (2023). https://doi.org/10.1007/s12686-023-01299-2
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DOI: https://doi.org/10.1007/s12686-023-01299-2