Cost-effective library preparation for whole genome sequencing with feather DNA
DeSaix, Matthew; Schweizer, Teia (2023), Cost-effective library preparation for whole genome sequencing with feather DNA, Dryad, Dataset, https://doi.org/10.5061/dryad.j6q573nf5
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.
See manuscript for modified method for library preparation of samples.
The BAM files are binary files of the Sequence Alignment/Map format for sequence data. The BAM files can be viewed and analyzed with open-source software such as Samtools (http://www.htslib.org/) and Picard Tools (https://broadinstitute.github.io/picard/).