Genome assembly of a commercial tomato hybrid (Funtelle) for haplotyping an introgression that confers TMV resistance

Plant crop genome assemblies facilitate the characterization of
genetically diverse cultivated and wild germplasm.  The
cultivated tomato (Solanum lycopersicum) has been improved through the
introgression of genetic material from related wild species, including
genetic resistance to pandemic strains of Tobacco Mosaic virus (TMV) and
tomato mosaic virus (ToMV) originating from Solanum peruvianum. The exact
size and the structure of the introgression from Solanum peruvianum
containing the TMV/ToMV resistance gene (Tm-2^2 gene) has remained
unknown, although it was known to include at least half of the physical
length of chromosome 9. We selected a commercial cultivated tomato
cultivar called Funtelle, which contains the Tm-2^2 resistance
introgression in a hemizygous state, and generated Oxford Nanopore
sequencing reads. Using Flye, a genome assembly tool, we assembled the
reads. The assembled DNA sequences (contigs) from the Flye assembly are
made available here. Subsequently, as described in detail in the
associated manuscript, we made use of the assembled contigs for
comprehensive haplotyping of the chromosome 9 introgression region in this
commercial hybrid. The raw Oxford Nanopore sequencing reads of the
Funtelle variety are available via the European Nucleotide Archive under
project number PRJEB44956.