Genome report: Genome sequence of 1S1, a transformable and highly regenerable diploid potato for use as a model for gene editing and genetic engineering

Generation of a genomic resource for a readily transformable diploid potato would provide a resource for high throughput functional analysis in potato. The heterozygous Solanum tuberosum Group Phureja clone 1S1 has a high regeneration rate, self-fertility, desirable tuber traits and is amenable to Agrobacterium-mediated transformation. To create a contiguous genome assembly, a homozygous doubled monoploid of 1S1 (DM1S1) was sequenced using 44 Gbp of long reads generated from Oxford Nanopore Technologies (ONT), yielding a 736 Mb assembly that encoded 31,145 protein-coding genes. The final assembly for DM1S1 represents a nearly complete genic space, shown by the presence of 99.6% (C:99.5%[S:97.8%, D:1.7%],F:0.1%,M:0.4%,n:1614) of the Benchmarking Universal Single Copy Orthologs. Variant analysis with Illumina reads from 1S1 was used to deduce its alternate haplotype using the variant calling tools Strelka2 (v2.9.10), GATK’s Haplotypecaller (v4.1.4.1), and Freebayes (v1.3.2). These variant..., DNA isolation and library preparation
Genomic DNA for Oxford Nanopore Technologies (ONT) sequencing was isolated, purified and size selected, from greenhouse-grown leaves of DM1S1 as described previously (Vaillancourt and Buell 2019). Short sequences were removed using the Ciruclomic’s Short Read Eliminator Kit (Circulomics, Baltimore, MD, Cat #SS-100-101-01). Eleven ONT DNA libraries were prepared using the ONT SQK-LSK109 Ligation Sequencing kit and sequenced on six R9 ONT FLO-MIN106 Rev D flow cells. Five of these R9 ONT flow cells were washed and reused according to the Flow Cell Wash kit and protocol (EXP-WSH003, version: WFC_9088_v1_revB_18Sept2019). Sequencing was performed using default settings on an ONT (Oxford, UK) MinION (MinIon 19.12.5 or 19.10.1) using MinKNOW default settings (MinKNOW v3.5.5, v3.6.0, v3.6.5).
Genomic DNA for whole-genome shotgun sequencing (WGS) was isolated from young leaves of tissue culture-grown DM1S1 and 1S1 clones using the DNeasy Plant Mini Kit (Qia...,