ddRAD sequencing data of 27 tomato genotypes
Description
The genomic data of the 27 tomato genotypes were obtained using ddRAD sequencing technology. Total genomic DNA was extracted from 100 mg of young leaf tissue from genotypes using the DNeasy plant mini kit (Qiagen, Hilden, Germany). For DNA sequencing, samples were used to prepare libraries for the ddRAD sequencing, as described in Peterson et al. 2012, PLoS ONE 7, e37135 with minor modifications. MboI and SphI enzymes were used for restriction digestion and fragments sequenced with the V4 chemistry paired end 125 bp mode on the HiSeq2500 Illumina instrument.
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Raw FASTQ files were quality-filtered and trimmed using Trimmomatic v.0.39 (http://www.usadellab.org/cms/?page=trimmomatic) with default parameters. Paired trimmed reads were aligned with the Solanum lycopersicum reference genome (Tomato Genome version SL4.0, available at the Solgenomics Network, www.solgenomics.net) using Bowtie-2 with default parameters. The resulting SAM and BAM files were sorted, de-duplicated and indexed with Samtools. Finally, the variant calling step was performed by BCFtools mpileup with default parameters. Only the positions showing no missing data for all the 27 genotypes were considered to generate the final VCF file. Finally, it was filtered by using VCFtools setting the parameters as follows: minQ = 10 and minimum mean of depth of coverage (min–mean DP) = 10.