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 variants were used to create consensus fasta sequences with the
DM1S1 assembly using bcftools (v1.9.64).