Genotype variant files for: Harnessing citizen science to contextualize adaptation mechanism discovery

Summary: Genome-wide polymorphisms called from publicly-available switchgrass genotype data. These variants are used in a publication under review, Harnessing citizen science to contextualize adaptation mechanism discovery by Tibbs-Cortes et al. The source genotype data was described in Lovell et al. 2021 (https://doi.org/10.1038/s41586-020-03127-1) and is available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA622568.Genotype data collection: See Lovell et al. 2021 for full description. Briefly, rhizome plug samples from 789 diverse tetraploid switchgrass accessions were sequenced using Illumina HiSeq X10 and Illumina NovaSeq 6000 paired-end sequencing (2 × 150 bp) at HudsonAlpha Institute for Biotechnology and the Joint Genome Institute.Variant calling: The paired-end sequence reads were downloaded from the NCBI SRA. Reads were aligned to the AP13 v5 reference genome with BWA-mem and biallelic polymorphisms were called with bcftools. Polymorphisms with minor allele frequency above 0.05 and missing rate below 20% were retained.Funding acknowledgement: This research used resources provided by the SCINet project and/or the AI Center of Excellence of the USDA Agricultural Research Service, ARS project numbers 0201-88888-003-000D and 0201-88888-002-000D.数据集概要：本数据集包含基于公开可获取的柳枝稷（switchgrass）基因型数据所调用的全基因组多态性位点。上述变异位点已用于Tibbs-Cortes等人已投稿待刊论文《利用公民科学为适应性机制发现提供研究背景》（Harnessing citizen science to contextualize adaptation mechanism discovery）的相关研究。原始基因型数据的详细描述见Lovell等人2021年发表的研究（https://doi.org/10.1038/s41586-020-03127-1），数据可从https://www.ncbi.nlm.nih.gov/bioproject/PRJNA622568获取。 基因型数据采集：完整说明详见Lovell等人2021年的研究。简言之，研究团队从789份具有遗传多样性的四倍体柳枝稷种质资源中获取根茎块样品，由哈德逊阿尔法生物技术研究所（HudsonAlpha Institute for Biotechnology）与联合基因组研究所（Joint Genome Institute）采用Illumina HiSeq X10及Illumina NovaSeq 6000平台进行双端测序（2×150 bp）。 变异位点调用：从美国国家生物技术信息中心序列读取档案（National Center for Biotechnology Information Sequence Read Archive, NCBI SRA）下载双端测序读段，利用BWA-mem将读段比对至AP13 v5参考基因组，再通过bcftools工具调用双等位基因多态性位点。最终保留次要等位基因频率（minor allele frequency）大于0.05、缺失率（missing rate）低于20%的多态性位点。 资助声明：本研究使用了美国农业部农业研究服务局（United States Department of Agriculture Agricultural Research Service, USDA ARS）SCINet项目及/或人工智能卓越中心提供的计算资源，相关项目编号为0201-88888-003-000D与0201-88888-002-000D。