Nanopore sequencing data and structural variants identified in Prunus avium seedlings derived through mutagenesis

Abstract

DNA from four sweet cherry seedlings derived from gamma-irradiated female parents was sequenced via nanopore technology (Oxford Nanopore MinION). Total data yield was 8.07 Gb, ranging from 0.92 to 3.36 Gb per sample, with the average length of mapped reads ranging from 22 Kbp-24 Kbp. Sequence data was then analysed to identify and characterize variants using a published sweet cherry reference genome. Small and medium-sized indels (55-135 bp), as well as structural variants, including several large indels and complex variants were detected. Of these, 20 variants were localized within protein-coding gene sequences, including those encoding a putative F-box protein, an ADP-ribose glyxohydrolase protein, a predicted 26S protease regulatory subunit, an E3 ubiquitin protein ligase, a UDP-galactose/UDP-blucose transporter, an alpha/beta hydrolase domain-containing protein, a rhodanese-like domain-containing protein, a cytochrome p450 protein, phosphoinositide phosphatase, cysteine synthase-like, phosphoenolpyruvate carboxylase 4, and several uncharacterized proteins. These variations could have functional and phenotypic consequences that are useful in basic research and breeding.

Keywords: Long-read sequencing; Mutation breeding; Prunus avium; Rosaceae; Structural genomics.