Solanum lycopersicum cv. Moneyberg
A gap-free tomato genome from complementary PacBio and nanopore long DNA sequences provides insights into linkage drag during breeding
The assembly and scaffolding of plant crop genomes is an essential step in the characterization of genetic diversity of cultivated and wild germplasm in classical, or genome editing led, plant breeding. Modern tomato breeding has introduced genetic material from multiple related wild species to provide genetically encoded resistance to abiotic and biotic stresses, including pandemic strains of Tobacco Mosaic virus (TMV). Here we applied PacBio HiFi and ONT nanopore sequencing to independently develop highly contiguous assemblies of an inbred TMV-resistant cultivated tomato variety. We merged the HiFi and ONT assemblies to generate a long read only assembly with an N50 value of 68.5 Mbp where all twelve chromosomes were assembled as single contigs. The merged assembly is validated by chromosome conformation capture data and is highly consistent with previous tomato assemblies that made use of genetic maps or HiC for scaffolding. Our long read only assemblies reveal that a complex series of structural variants in the TMV resistance locus likely contributed to linkage drag of a 64.1 megabase pair region of wild DNA from Solanum peruvianum during tomato breeding. We show that at least this minimal introgression size is present in six cultivated tomato hybrid varieties developed in three independent commercial breeding programs, underscoring the power of long reads to decode introgressions from wild crop relatives.
- MbTMV.fasta.gz is the final assembly that contains the quickmerged contigs from the Hifiasm+Canu amd NECAT+Flye assembly all oriented in accordance with the Heinz SL4.0 S. lycopersicum reference and all non chromsome contigs moved to Chromosome 0
- Moneyberg_Canu.fasta.gz is the assembly made from the HiFi-reads assembled with Canu v2.1.1 with HiCanu settings
- Moneyberg_Flye.fasta.gz is the assembly made from the Nanopore-reads assembled with Flye v2.8.2 on default settings
- Moneyberg_Hifiasm+Canu.fasta.gz is the assembly made by merging the contigs from Hifiasm and Canu with quickmerge
- Moneyberg_Hifiasm.fasta.gz is the assembly made from the HiFi-reads assembled with Hifiasm 0.14.2 on default settings
- Moneyberg_NECAT.fasta.gz is the assembly made from the Nanopore-reads assembled with NECAT 0.0.1_update20200803 with coverage increased to 40x
- Moneyberg_NECAT+Flye.fasta.gz is the assembly made by merging the contigs from NECAT and Flye with quickmerge.