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

Résumé fourni par la source

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.

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