Pusa Ruby (PR), which is particularly amenable to Agrobacterium mediated transformation and regeneration. This genomic data can be potentially used for large scale crop improvement programs as well as functional annotation studies.Ĭontinuous breeding and selection have led to a plethora of region-specific varieties with differing fruit size, shape, shelf life, nutritional quality, antioxidant capacity, plant growth habit, and other organoleptic properties. The PR genome has an Ovate mutation leading to round fruit shape, causing economically undesirable fruit cracking. Further, allele mining for fruit quality-related genes was also executed. PR was found to have a high regeneration rate (45.51%) and therefore, we performed allele mining for genes associated with regeneration and found that only AGAMOUS-LIKE15 has a null mutation. We then analyzed the regeneration efficiency of PR in comparison to another variety, Pusa Early Dwarf (PED). The similarity of the PR genome assembly to Heinz1706, M82, and Fla.8924 was measured and the results suggest PR has the lowest affinity towards the hybrid Fla.8924. The assembly was packaged according to PanSol guidelines (N50 = 60,396,827) with the largest scaffold measuring 85 megabases. The PR genome contains 34,075 genes and 423,288 variants, out of which 127,131 are intragenic and 1232 are of high impact. Here, we report a reference-guided genome assembly for PR, covering 97.6% of the total single-copy genes in the solanales order. Pusa Ruby (PR) is a superior tomato cultivar routinely used as a model tomato variety.
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