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

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, o...

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Autores principales: Vats, Sanskriti, Kumar, Virender, Mandlik, Rushil, Patil, Gunvant, Sonah, Humira, Roy, Joy, Sharma, Tilak Raj, Deshmukh, Rupesh
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10047940/
https://www.ncbi.nlm.nih.gov/pubmed/36980842
http://dx.doi.org/10.3390/genes14030570
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author Vats, Sanskriti
Kumar, Virender
Mandlik, Rushil
Patil, Gunvant
Sonah, Humira
Roy, Joy
Sharma, Tilak Raj
Deshmukh, Rupesh
author_facet Vats, Sanskriti
Kumar, Virender
Mandlik, Rushil
Patil, Gunvant
Sonah, Humira
Roy, Joy
Sharma, Tilak Raj
Deshmukh, Rupesh
author_sort Vats, Sanskriti
collection PubMed
description 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.
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spelling pubmed-100479402023-03-29 Reference Guided De Novo Genome Assembly of Transformation Pliable Solanum lycopersicum cv. Pusa Ruby Vats, Sanskriti Kumar, Virender Mandlik, Rushil Patil, Gunvant Sonah, Humira Roy, Joy Sharma, Tilak Raj Deshmukh, Rupesh Genes (Basel) Article 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. MDPI 2023-02-24 /pmc/articles/PMC10047940/ /pubmed/36980842 http://dx.doi.org/10.3390/genes14030570 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Vats, Sanskriti
Kumar, Virender
Mandlik, Rushil
Patil, Gunvant
Sonah, Humira
Roy, Joy
Sharma, Tilak Raj
Deshmukh, Rupesh
Reference Guided De Novo Genome Assembly of Transformation Pliable Solanum lycopersicum cv. Pusa Ruby
title Reference Guided De Novo Genome Assembly of Transformation Pliable Solanum lycopersicum cv. Pusa Ruby
title_full Reference Guided De Novo Genome Assembly of Transformation Pliable Solanum lycopersicum cv. Pusa Ruby
title_fullStr Reference Guided De Novo Genome Assembly of Transformation Pliable Solanum lycopersicum cv. Pusa Ruby
title_full_unstemmed Reference Guided De Novo Genome Assembly of Transformation Pliable Solanum lycopersicum cv. Pusa Ruby
title_short Reference Guided De Novo Genome Assembly of Transformation Pliable Solanum lycopersicum cv. Pusa Ruby
title_sort reference guided de novo genome assembly of transformation pliable solanum lycopersicum cv. pusa ruby
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10047940/
https://www.ncbi.nlm.nih.gov/pubmed/36980842
http://dx.doi.org/10.3390/genes14030570
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