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

Citation

van Rengs, Willem M. J.; Underwood, Charles J.; Schmidt, Maximilian H. W.; Usadel, Björn (2022), Genome assembly of a commercial tomato hybrid (Funtelle) for haplotyping an introgression that confers TMV resistance, Dryad, Dataset, https://doi.org/10.5061/dryad.3j9kd51kn

Abstract

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.

Methods

S. lycopersicum cv. Funtelle F1 (Date tomato) was produced by Syngenta.

Young unexpanded leaves were collected from 5-week-old plants and snap frozen in liquid nitrogen before interim storage at -80 degrees.

DNA from the S. lycopersicum cv. ‘Funtelle’ was extracted using the Machery Nagel Nucleobond HMW DNA Kit.

High molecular weight DNA was size selected using the Circulomics Short-Read Eliminator XL Kit (Circulomics Cat# SKU SS-100-111-01) and used as input for a library preparation with the Oxford Nanopore LSK-110 ligation sequencing Kit. 

Four libraries from the same sample were loaded onto three PromethION PRO-002 Flowcells and one MinION Flowcell (all R9.4.1 pores) and sequenced. 

ONT Sequencing was performed on an Oxford Nanopore P24 PromethION and a MinION MK1B at the Forschungszentrum Jülich using MinKNOW version 21.02.7 without live basecalling. 

Basecalling of the Oxford Nanopore read data was done using guppy basecaller version 5.0.11 using the R9.4.1 PromethION super-high-accuracy model (dna_r9.4.1_450bps_sup_prom) and the R9.4.1 MinION super-high-accuracy model (dna_r9.4.1_450bps_sup).

Flye v2.8.2 (Kolmogorov et al., 2019) was used to assemble the ONT reads with the option --nano-raw for unpolished Nanopore reads.