Reference Guided De Novo Genome Assembly of Transformation Pliable Solanum lycopersicum cv. Pusa Ruby

Sanskriti Vats; Virender Kumar; Rushil Mandlik; Gunvant Patil; Humira Sonah; Joy Roy; Tilak Raj Sharma; Rupesh Deshmukh

doi:10.3390/genes14030570

Reference Guided De Novo Genome Assembly of Transformation Pliable Solanum lycopersicum cv. Pusa Ruby

Genes (Basel). 2023 Feb 24;14(3):570. doi: 10.3390/genes14030570.

Authors

Sanskriti Vats^{1

2}, Virender Kumar^{1

2}, Rushil Mandlik^{1

3}, Gunvant Patil⁴, Humira Sonah¹, Joy Roy¹, Tilak Raj Sharma⁵, Rupesh Deshmukh⁶

Affiliations

¹ National Agri-Food Biotechnology Institute (NABI), Mohali 140306, Punjab, India.
² Regional Centre for Biotechnology, Faridabad 121001, Haryana, India.
³ Department of Biotechnology, Panjab University, Chandigarh 160014, Punjab, India.
⁴ Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79410, USA.
⁵ Department of Crop Science, Indian Council of Agriculture Research (ICAR), Krishi Bhavan, New Delhi 110001, Delhi, India.
⁶ Department of Biotechnology, Central University of Haryana, Mahendragarh 123031, Haryana, India.

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.

Keywords: Agrobacterium tumefaciens; Pusa Ruby; Solanum lycopersicum; reference-guided assembly; tomato; transformation protocol; whole genome sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Fruit / genetics
Genomics
Mutation
Solanum lycopersicum* / genetics

Grants and funding

This research was funded by the Department of Biotechnology (DBT), Government of India (GoI), for the Ramalingaswami Fellowship Award to R.D. and H.S. and grants BT/PR32853/AGIII/103/1159/2019 and BT/PR38279/GET/119/351/2020 to R.D., H.S. and T.R.S.; The Science and Engineering Research Board (SERB), India, Department of Science and Technology (DST), Government of India (GoI), for the JC Bose Fellowship to T.R.S. and research grant CRG/2019/006599 awarded to R.D., H.S. and T.R.S.; and the University Grants Commission (UGC) for the Senior Research Fellowship to G.R.