Nucleotide Diversity Estimates of Tomatillo (Physalis Philadelphica) Accessions Including

Nucleotide diversity estimates of tomatillo (Physalis philadelphica) accessions including nine new inbred lines, Molecular Breeding,

Joanne A. Labate and Larry D. Robertson, Plant Genetic Resources Unit, United States Department of Agriculture, Agricultural

Research Service, 630 W. North St., Geneva, NY 14456 USA, email: [email protected]

Online Resource ESM_4. Implementation of TASSEL 3.0 Universal Network Enabled Analysis Kit (UNEAK) pipeline for tomatillo

(Physalis philadelphica) raw data collected in 96-plex format in two Illumina HiSeq 2000 flow cells.

Step in GBS pipeline Key arguments Results FastqToTagCountPlugin -e ApeKI Enzyme used to create GBS library File C28DTACXX_8_fastq.gz 202,621,424 total reads

179,777,205 reads with

barcode and cut site

overhang

File C270BACXX_1_fastq.gz 211,857,054 total reads

157,949,958 reads with

barcode and cut site

overhang UMergeTaxaTagCountPlugin -c 5 Tags must appear at least 5 times 6,186,997 tags covered by 234,926,621 matching reads

across 190 barcoded samples to be

-m 100,000,000 output

Maximum tag number in merged

TagCount file UTagCount ToTagPairPlugin -e 0.03 Error tolerance rate 242,204 reciprocal TagPairs (i.e., SNPs) found Step in GBS pipeline Key arguments Results UTagPairToTBTPlugin 484,408 tags output to TagsByTaxa file UTBTToMapInfoPlugin 242,204 HapMap records written to MapInfo file UMapInfoToHapMapPlugin -mnMAF 0.02 Minimum minor allele frequency An allele must be present in at least four of 190 samples

-mxMAF 0.50 Maximum minor allele frequency to be retained

-mnC 0.0 Proportion of taxa covered by at 240,056 SNPs written to HapMap file

-mxC 1.0 least one tag Filter sites using graphical minimum count = 19 taxa SNP must cover at least 10% of 190 77,340 filtered SNPs in 190 taxa version of TASSEL 4.0 samples to be retained

minimum proportion of sites

present = 0.10 Sample must have at least 10% of 77,340 filtered SNPs in 179 filtered taxa

SNPs present to be retained