Whole-genome sequencing of 37 Phaseolus vulgaris accessions (PE 150, 12x)

Whole-genome shotgun sequencing was conducted on the collection of 37 diverse accessions with diverse seed color patterns and other characteristics. DNA was extracted from seed embryonic axes of each variety using the Qiagen DNeasy Plant Minikit. Concentration and quality were checked by gel electrophoresis and Nanodrop, and the extracted DNA was sequenced by Illumina paired-end 150 bp sequencing at the UC Davis Genome Center. 270 Gb of sequence data were generated using a NovaSeq 6000 instrument, yielding an average of 12x sequencing depth per sample. Sequence quality was checked with FASTQC (Andrews, 2010), and adapters and barcodes were trimmed using the Trimmomatic v0.39 (Bolger et al. 2014) ILLUMINACLIP function. Low-quality sequence was removed using the SLIDINGWINDOW:4:20 MINLEN:50 settings.