DOI: 10.5061/dryad.7h44j0zs7
title: GBS SNP datasets from "Genotyping-by-sequencing resolves relationships in Polygonaceae tribe Eriogoneae", TAXON

description: The data come from genotyping-by-sequencing (GBS) of samples from plants
 in the tribe Eriogoneae (Polygonaceae).  The data were used in
 evolutionary and population genomic analyses that can be found in Pearman
 et. al. "Genotyping-by-sequencing resolves relationships in
 Polygonaceae tribe Eriogoneae", published in TAXON.  The
 analyses reported data from 51 species from the genera Chorizanthe,
 Eriogonum and Sidotheca.  The data are organized by the analyses
 in which they were used.  In most cases, README files and R
 scripts are included that detail the filtering that was conducted to
 produce the SNP data sets used in each case.
description: Whole genomic DNA was isolated with
 the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany) by SGIKer genomic
 services at the University of the Basque Country, Leioa, Spain. Samples
 were first homogenized using 1.4 mm ceramic beads in a Percellys 24
 (Bertin Instruments, Montigny-le-Bretonneux, France) and then extracted
 following kit instructions. Libraries for GBS (Elshire & al.,
 2011) were prepared at the Centro Nacional de d-Anàlisi Genòmica (CNAG,
 Barcelona, Spain). A single restriction enzyme, ApeKI, was used to cut
 genomic DNA during library construction. ApeKI recognizes a 5-base pair
 degenerative sequence (GCWGC). Barcodes were designed to allow for two
 sequencing errors without confusion of samples. Paired-end sequencing of
 678 samples representing the genera Eriogonum, Chorizanthe and
 Sidotheca was
 conducted on Illumina HiSeq machines with a read length of 101
 base-pairs. Sequences from each run were parsed based
 on presence of the enzyme remnant cut site and in-line barcodes with
 GBS-SNP-CROP v.4.0 (Melo & al., 2016), and
 trimming based on quality and adapters was performed with GBS-SNP-CROP and
 Trimmomatic v.0.36 (Bolger & al., 2000). We
 accepted reads with a minimum Phred quality score of 20. These parsed and
 quality-filtered reads were demultiplexed according to their in-line
 barcode, and a pair of FASTQ files were produced for each sample with
 GBS-SNP-CROP. A mock reference was built with a de novo assembly method
 based on sequence similarity using Pear v.0.9.6 and Vsearch v.1.1.3 (Zhang
 & al., 2014; Rognes & al., 2016). Reads were aligned
 against this reference using BWA-MEM v.0.7.12 and mapped reads were
 filtered with SAMtools v.1.2 (Li & Durbin,
 2009; Li & al., 2009). The properly paired, primary aligned reads
 were kept to produce an mpileup file for each sample. Variant calling was
 done using GBS-SNP-CROP pipeline, including a series of filters. We
 discarded SNPs with more than two alleles and all loci with read depths
 less than 6 and greater than 100 (to reduce the potential for confounding
 of non-orthologous loci). The resulting data on 699,331 SNPs and 678
 samples were exported to PLINK v.1.9 (Chang & al., 2015) files for
 further filtering. SNPs with greater than 50% missingness across samples
 were removed, as were individuals with greater than 50% missing genotype
 data at the remaining SNPs.   Additional details are provided in readme
 files and RStudio scripts.
description: The data are an assortment of ready-to-use files and ones that
 will need filtering.  On-line files associated with the publication will
 be useful for working with the data sets.