Illinois Data Bank - Dataset

A newer version of this dataset is available. View the latest version.
Population genetic structure of Miscanthus sacchariflorus
Cite this dataset:
Clark, Lindsay V.; Jin, Xiaoli; Petersen, Karen K.; Anzoua, Kossanou G.; Bagmet, Larissa; Chebukin, Pavel; Deuter, Martin; Dzyubenko, Elena; Dzyubenko, Nicolay; Heo, Kweon; Johnson, Douglas A.; Jørgensen, Uffe; Kjeldsen, Jens B.; Nagano, Hironori; Peng, Junhua; Sabitov, Andrey; Yamada, Toshihiko; Yoo, Ji Hye; Yu, Chang Yeon; Long, Stephen P.; Sacks, Erik J. (2018): Population genetic structure of Miscanthus sacchariflorus. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0170190_V1
Dataset Description

This repository contains datasets and R scripts that were used in a study of the population structure of Miscanthus sacchariflorus in its native range across East Asia. Notably, genotypes of 764 individuals at 34,605 SNPs, called from reduced-representation DNA sequencing using a non-reference bioinformatics pipeline, are provided. Two similar SNP datasets, used for identifying clonal duplicates and for determining the ancestry of ornamental and hybrid Miscanthus plants identified in previous studies respectively, are also provided. There is also a spreadsheet listing the provenance and ploidy of all individuals along with their plastid (chloroplast) haplotypes. Software output for Structure, Treemix, and DIYABC is also included. See README.txt for more information about individual files. Results of this study are described in a manuscript in revision in Annals of Botany by the same authors, "Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid Miscanthus sinensis, and diversity centered around the Yellow Sea."
Subject Life Sciences
Keywords Miscanthus; restriction site-associated DNA sequencing (RAD-seq); single nucleotide polymorphism (SNP); population genetics; Miscanthus xgiganteus; Miscanthus sacchariflorus; R scripts; germplasm; plastid haplotype
License CC BY
Funder U.S. Department of Energy (DOE)-Grant:DE-SC0012379
Funder U.S. Department of Energy (DOE)-Grant:DE-SC0006634
Funder U.S. Department of Agriculture (USDA)-Grant:Cooperative Agreement #59-1275-1-338
Funder Energy Biosciences Institute
Corresponding Creator Erik J. Sacks
Downloaded 2550 times
Version DOI Comment Publication Date
3 10.13012/B2IDB-0170190_V3 The revised dataset includes new scripts for testing isolation-by-distance and justification of our SNP filtering criteria. There are also minor revisions to figures and a correction of the longitude of RU2012-104 2018-06-18
2 10.13012/B2IDB-0170190_V2 Added missing file "160511polyfreq.R", minor updated to the diversity_differentiation_stats file and the README 2018-03-26
1 10.13012/B2IDB-0170190_V1 2018-03-16

Open in Globus File Manager what's this?
8.68 KB File
2.75 KB File
10.9 KB File
111 MB File
602 Bytes File
12 KB File
8.58 KB File
108 KB File
12 KB File
58.8 KB File
59.6 KB File
9.3 KB File
4.93 KB File
4.61 KB File
4.18 KB File
722 KB File
13.4 KB File
7.31 KB File
8.18 KB File
22.4 KB File
70.9 MB File
7.55 KB File
134 KB File
9.34 KB File
63.9 MB File
148 MB File
2.73 KB File
4.61 KB File
3.95 MB File
43.3 MB File
43 MB File
40.8 MB File
3.49 MB File
21.6 KB File
3.36 KB File
2.17 KB File

Contact the Research Data Service for help interpreting this log.

RelatedMaterial update: {"uri"=>["10.13012/B2IDB-0170190_V1", "10.13012/B2IDB-0170190_V2"]} 2018-03-26T18:07:31Z
RelatedMaterial create: {"material_type"=>"Dataset", "availability"=>nil, "link"=>"https://doi.org/10.13012/B2IDB-0170190_V2", "uri"=>"10.13012/B2IDB-0170190_V1", "uri_type"=>"DOI", "citation"=>"", "dataset_id"=>505, "selected_type"=>"Dataset", "datacite_list"=>"IsPreviousVersionOf"} 2018-03-26T16:46:29Z
RelatedMaterial update: {"uri"=>[nil, "ncbi.nlm.nih.gov/bioproject/PRJNA294794"], "uri_type"=>[nil, "URN"], "datacite_list"=>[nil, "IsSupplementedBy"]} 2018-03-26T16:46:29Z
RelatedMaterial update: {"uri"=>[nil, "ncbi.nlm.nih.gov/bioproject/PRJNA261699"], "uri_type"=>[nil, "URN"], "datacite_list"=>[nil, "IsSupplementedBy"]} 2018-03-26T16:46:29Z
RelatedMaterial update: {"uri"=>[nil, "ncbi.nlm.nih.gov/bioproject/PRJNA342314"], "uri_type"=>[nil, "URN"], "datacite_list"=>[nil, "IsSupplementedBy"]} 2018-03-26T16:46:29Z
RelatedMaterial update: {"uri"=>[nil, "ncbi.nlm.nih.gov/bioproject/PRJNA207721"], "uri_type"=>[nil, "URN"], "datacite_list"=>[nil, "IsSupplementedBy"]} 2018-03-26T16:46:29Z
RelatedMaterial update: {"uri"=>[nil, "10.5281/zenodo.1194279"], "uri_type"=>[nil, "DOI"], "datacite_list"=>[nil, "IsSupplementedBy"]} 2018-03-26T16:46:29Z
RelatedMaterial update: {"uri"=>[nil, "10.5281/zenodo.594215"], "uri_type"=>[nil, "DOI"], "datacite_list"=>[nil, "IsSupplementedBy"]} 2018-03-26T16:46:29Z
Dataset update: {"version_comment"=>[nil, ""]} 2018-03-26T16:46:29Z