Reference Guided De Novo Genome Assembly of Transformation Pliable Solanum lycopersicum cv. Pusa Ruby
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Date
2023-02
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Abstract
Solanum lycopersicum cv. Pusa Ruby (PR) is a superior tomato cultivar routinely used as a
model tomato variety. Here, we report a reference-guided genome assembly for PR, covering 97.6%
of the total single-copy genes in the solanales order. The PR genome contains 34,075 genes and
423,288 variants, out of which 127,131 are intragenic and 1232 are of high impact. The assembly
was packaged according to PanSol guidelines (N50 = 60,396,827) with the largest scaffold measuring
85 megabases. 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. We then
analyzed the regeneration efficiency of PR in comparison to another variety, Pusa Early Dwarf (PED).
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.
Further, allele mining for fruit quality-related genes was also executed. The PR genome has an
Ovate mutation leading to round fruit shape, causing economically undesirable fruit cracking. This
genomic data can be potentially used for large scale crop improvement programs as well as functional
annotation studies.