Description
Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in a genotyping-by-sequencing (GBS) protocol. We focus on data from two species of Populus, because this genus has a relatively small genome and is emerging as a target for population genomic studies. We estimate the proportions and patterns of genomic sampling by examining the Populus trichocarpa genome (Nisqually-1), and demonstrate a pronounced bias towards coding regions when using the methylation-sensitive ApeKI restriction enzyme in this species. Using population-level data from a closely related species (P. tremuloides), we also investigate various approaches for filtering GBS data to retain high-depth, informative SNPs that can be used for population genetic analyses. We find a data filter that includes the designation of ambiguous alleles resulted in metrics of population structure and Hardy-Weinberg equilibrium that were most consistent with previous studies of the same populations based on other genetic markers. Analyses of the filtered data (27,910 SNPs) also resulted in patterns of heterozygosity and population structure similar to a previous study using microsatellites. Our application demonstrates that technically and analytically simple approaches can readily be developed for population genomics of natural populations.
Author ORCID Identifier
Paul G. Wolf https://orcid.org/0000-0002-4317-6976
Aaron M. Duffy https://orcid.org/0000-0003-0530-6191
OCLC
985526082
Document Type
Dataset
DCMI Type
Dataset
File Format
.txt, .pdf
Viewing Instructions
***A zipped version of this dataset is available. Contact RDMS (researchdata@usu.edu) for more details.***
Publication Date
4-18-2014
Publisher
Utah State University
Referenced by
Schilling, M.P., Wolf, P.G., Duffy, A.M., Rai, H.S., Rowe, C.A., Richardson, B.A., Mock, K.E. Genotyping-by-sequencing for Populus population genomics: An assessment of genome sampling patterns and filtering approaches (2014) PLoS ONE, 9 (4), art. no. e95292. Available at 10.1371/journal.pone.0095292
Language
eng
Disciplines
Genomics
License
This work is licensed under a Creative Commons Attribution 4.0 License.
Recommended Citation
Wolf, P. G., Schilling, M. P., Duffy, A. M., Rai, H. S., Rowe, C. A., Mock, K. E., & Richardson, B. A. (2014). Data from: Genotyping-by-Sequencing for Populus Population Genomics: An Assessment of Genome Sampling Patterns and Filtering Approaches. Utah State University. https://doi.org/10.15142/T33882
Checksum
http://di.lib.usu.edu/DATA_Wolf_20140418_ALL.zip
Additional Files
Schilling_et_al_Article_2014.pdf (406 kB)f59b1969876cee8dfb29cf8c0afbe2ed
H_Rai_Plate_1.txt (1 kB)
MD5: b6e03eda414296e907c469c0addad4f4
H_Rai_Plate_2.txt (1 kB)
MD5: 94b497424a45c8534ff7c7c6808f9886
2051-GSR-1_sequence.txt.bz2 (11008672 kB)
MD5: bd70772a7995747c50ed52d0ea0385ec
2051-GSR-2_sequence.txt.bz2 (7707994 kB)
MD5: 2343c761b91b41a1d26149c1d200e8aa