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100 tomato genomes in 100 days

100 tomato genomes in 100 days

The tomato is one of the most valuable agricultural crops in the world, with an annual production of over 175 million tonnes and a value of $85 billion. Tomatoes are also important from a model system perspective due to their extensive phenotypic variation with over 15,000 known varieties1.

Michael Schatz and colleagues are sequencing 12–16 samples per week at 40x depth of coverage, using the PromethION platform, to achieve a target of 100 genome sequences in 100 days1. Initial results from the first 12 sequenced genomes revealed substantial variation between samples, with between 25,000–45,000 structural variants per sample (Figure 1). For example, an 83 kb tandem duplication was identified in the gene EJ2; this was found to be associated with the higher fruit yields observed in some plants2. The majority of structural variants identified were sample-specific and many had been missed using short-read sequencing, which struggles to resolve large-scale genomic differences.

‘Short-read sequencing has proven valuable for single nucleotide polymorphism discovery, but lacks power for more complex structural variants’1

Such large-scale sequencing efforts will enable the rapid and high-throughput genome-wide characterisation of a wide variety of tomato species, and potentially provide the genetic information needed to enrich for desired genome traits and increase the efficiency of crop breeding in the future.

Figure 1: Nanopore sequencing results from 12 tomato genomes revealed (a) approximately 25,000–45,000 SVs per genome, the majority of which were deletions and insertions, and (b) most SVs were specific to each sample. Figures courtesy of Prof. Michael Schatz, Johns Hopkins University, USA.


  1. Schatz. M. 100 genomes in 100 days: The structural variant landscape in tomato genomes. Available at: https:// michael-schatz-100-genomes-100- days-structural-variantlandscapetomato-genomes [Accessed: 7 May 2019]
  2. Soyk, S et al. Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato. Nat. Plants. 5(5):471- 479 (2019).
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