Genome Sequencing and T-DNA Insertion Mapping

Genomic DNA was extracted from 7-DPA tomato fruits using a Plant Genomic DNA Kit (TIANGEN; #DP305) and sequenced on Illumina HiSeq2000 platform at Novogene (Beijing, China). For obtaining clean, high-quality data, quality control of raw data from the Illumina HiSeq 2000 platform was checked using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc). The reads were fed into fastp v0.22.0^{32 (link)} to adapter trimming, low-quality reads removals and short-reads deletion. Next, the clean data was aligned to the tomato reference genome (SL4.0, https://solgenomics.net/ftp/genomes/Solanum_lycopersicum/assembly/build_4.00/S_lycopersicum_chromosomes.4.00.fa) and the pBI121-AGL66-FLAG vector sequence using BWA 0.7.17^{33 (link)}, respectively, to identify junction reads. Subsequently, the location information of the T-DNA insertion site was determined by the junction reads that aligned simultaneously with both the reference genome sequence and the vector sequence.