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The genome sequence of tetraploid sweet basil, Ocimum basilicum L., provides tools for advanced genome editing and molecular breeding
Sweet basil, Ocimum basilicum L., is a well-known culinary herb grown worldwide, but its uses go beyond the kitchen to traditional medicine, cosmetics and gardening. To date, the lack of an available reference genome has limited the utilization of advanced molecular breeding methods. We present a dr...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7758295/ https://www.ncbi.nlm.nih.gov/pubmed/33340318 http://dx.doi.org/10.1093/dnares/dsaa027 |
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author | Gonda, Itay Faigenboim, Adi Adler, Chen Milavski, Renana Karp, Merrie-Jean Shachter, Alona Ronen, Gil Baruch, Kobi Chaimovitsh, David Dudai, Nativ |
author_facet | Gonda, Itay Faigenboim, Adi Adler, Chen Milavski, Renana Karp, Merrie-Jean Shachter, Alona Ronen, Gil Baruch, Kobi Chaimovitsh, David Dudai, Nativ |
author_sort | Gonda, Itay |
collection | PubMed |
description | Sweet basil, Ocimum basilicum L., is a well-known culinary herb grown worldwide, but its uses go beyond the kitchen to traditional medicine, cosmetics and gardening. To date, the lack of an available reference genome has limited the utilization of advanced molecular breeding methods. We present a draft version of the sweet basil genome of the cultivar ‘Perrie’, a fresh-cut Genovese-type basil. Genome sequencing showed basil to be a tetraploid organism with a genome size of 2.13 Gbp, assembled in 12,212 scaffolds, with > 90% of the assembly being composed of 107 scaffolds. About 76% of the genome is composed of repetitive elements, with the majority being long-terminal repeats. We constructed and annotated 62,067 protein-coding genes and determined their expression in different plant tissues. We analysed the currently known phenylpropanoid volatiles biosynthesis genes. We demonstrated the necessity of the reference genome for a comprehensive understanding of this important pathway in the context of tetraploidy and gene redundancy. A complete reference genome is essential to overcome this redundancy and to avoid off-targeting when designing a CRISPR: Cas9-based genome editing research. This work bears promise for developing fast and accurate breeding tools to provide better cultivars for farmers and improved products for consumers. |
format | Online Article Text |
id | pubmed-7758295 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-77582952020-12-31 The genome sequence of tetraploid sweet basil, Ocimum basilicum L., provides tools for advanced genome editing and molecular breeding Gonda, Itay Faigenboim, Adi Adler, Chen Milavski, Renana Karp, Merrie-Jean Shachter, Alona Ronen, Gil Baruch, Kobi Chaimovitsh, David Dudai, Nativ DNA Res Resource Article: Genomes Explored Sweet basil, Ocimum basilicum L., is a well-known culinary herb grown worldwide, but its uses go beyond the kitchen to traditional medicine, cosmetics and gardening. To date, the lack of an available reference genome has limited the utilization of advanced molecular breeding methods. We present a draft version of the sweet basil genome of the cultivar ‘Perrie’, a fresh-cut Genovese-type basil. Genome sequencing showed basil to be a tetraploid organism with a genome size of 2.13 Gbp, assembled in 12,212 scaffolds, with > 90% of the assembly being composed of 107 scaffolds. About 76% of the genome is composed of repetitive elements, with the majority being long-terminal repeats. We constructed and annotated 62,067 protein-coding genes and determined their expression in different plant tissues. We analysed the currently known phenylpropanoid volatiles biosynthesis genes. We demonstrated the necessity of the reference genome for a comprehensive understanding of this important pathway in the context of tetraploidy and gene redundancy. A complete reference genome is essential to overcome this redundancy and to avoid off-targeting when designing a CRISPR: Cas9-based genome editing research. This work bears promise for developing fast and accurate breeding tools to provide better cultivars for farmers and improved products for consumers. Oxford University Press 2020-12-19 /pmc/articles/PMC7758295/ /pubmed/33340318 http://dx.doi.org/10.1093/dnares/dsaa027 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_modelThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Resource Article: Genomes Explored Gonda, Itay Faigenboim, Adi Adler, Chen Milavski, Renana Karp, Merrie-Jean Shachter, Alona Ronen, Gil Baruch, Kobi Chaimovitsh, David Dudai, Nativ The genome sequence of tetraploid sweet basil, Ocimum basilicum L., provides tools for advanced genome editing and molecular breeding |
title | The genome sequence of tetraploid sweet basil, Ocimum basilicum L., provides tools for advanced genome editing and molecular breeding |
title_full | The genome sequence of tetraploid sweet basil, Ocimum basilicum L., provides tools for advanced genome editing and molecular breeding |
title_fullStr | The genome sequence of tetraploid sweet basil, Ocimum basilicum L., provides tools for advanced genome editing and molecular breeding |
title_full_unstemmed | The genome sequence of tetraploid sweet basil, Ocimum basilicum L., provides tools for advanced genome editing and molecular breeding |
title_short | The genome sequence of tetraploid sweet basil, Ocimum basilicum L., provides tools for advanced genome editing and molecular breeding |
title_sort | genome sequence of tetraploid sweet basil, ocimum basilicum l., provides tools for advanced genome editing and molecular breeding |
topic | Resource Article: Genomes Explored |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7758295/ https://www.ncbi.nlm.nih.gov/pubmed/33340318 http://dx.doi.org/10.1093/dnares/dsaa027 |
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