Filtered SNPs for wild Paspalum vaginatum and Paspalum distichum
Goad, David (2020), Filtered SNPs for wild Paspalum vaginatum and Paspalum distichum, Dryad, Dataset, https://doi.org/10.5061/dryad.vt4b8gtqh
Filtered SNP calls in .ped format from "Hybridization, polyploidy and clonality influence geographic patterns of diversity and salt tolerance in the model halophyte seashore paspalum (Paspalum vaginatum)". We used GBS to genotype 218 P. vaginatum and P. distichum accessions collected from the US Gulf and Atlantic coasts plus available USDA germplasm. We confirm that P. vaginatum and P. distichum are genetically distinct and that the coarse-textured ecotype of P. vaginatum is composed of hybrids between fine-textured accessions and an unidentified paspalum species. These hybrids vary in ploidy and subgenome composition which may influence their geographic patterns of adaptation to saline environments.
Read processing and variant calling were performed using the Fast-GBS pipeline with default parameters (Torkamaneh, Laroche, Bastien, Abed, & Belzile, 2017), which demultiplexes with sabre v1.000 (Joshi, 2011), trims with cutadapt v1.14 (Martin, 2011), maps with BWA MEM v0.7.12-r1039 (Li & Durbin, 2009) and calls variants with Platypus v0.8.1 (Rimmer et al., 2014). This produced a large SNP dataset which was then further filtered with plink v1.90b4.6 (Purcell et al. 2007). Sites were removed if there were missing calls for more than 10% of the samples or had less than 0.01 minor allele frequency. Individuals that were missing calls at 50% or more sites were also removed.
Pv_Pd_GBS_all.ped contains all accessions used in analyses. Pv_Pd_GBS_unique.ped contains only one accession for each unique genotype.