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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...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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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. |
format | Online Article Text |
id | pubmed-10047940 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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