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Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’
‘Chambourcin’ is a French-American interspecific hybrid grape grown in the eastern and midwestern United States and used for making wine. Few genomic resources are available for hybrid grapevines like ‘Chambourcin’. Here, we assembled the genome of ‘Chambourcin’ using PacBio HiFi long-read, Bionano...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
GigaScience Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10318349/ https://www.ncbi.nlm.nih.gov/pubmed/37408731 http://dx.doi.org/10.46471/gigabyte.84 |
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author | Patel, Sagar Harris, Zachary N. Londo, Jason P. Miller, Allison Fennell, Anne |
author_facet | Patel, Sagar Harris, Zachary N. Londo, Jason P. Miller, Allison Fennell, Anne |
author_sort | Patel, Sagar |
collection | PubMed |
description | ‘Chambourcin’ is a French-American interspecific hybrid grape grown in the eastern and midwestern United States and used for making wine. Few genomic resources are available for hybrid grapevines like ‘Chambourcin’. Here, we assembled the genome of ‘Chambourcin’ using PacBio HiFi long-read, Bionano optical map, and Illumina short-read sequencing technologies. We generated an assembly for ‘Chambourcin’ with 26 scaffolds, with an N50 length of 23.3 Mb and an estimated BUSCO completeness of 97.9%. We predicted 33,791 gene models and identified 16,056 common orthologs between ‘Chambourcin’, V. vinifera ‘PN40024’ 12X.v2, VCOST.v3, Shine Muscat and V. riparia Gloire. We found 1,606 plant transcription factors from 58 gene families. Finally, we identified 304,571 simple sequence repeats (up to six base pairs long). Our work provides the genome assembly, annotation and the protein and coding sequences of ‘Chambourcin’. Our genome assembly is a valuable resource for genome comparisons, functional genomic analyses and genome-assisted breeding research. |
format | Online Article Text |
id | pubmed-10318349 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | GigaScience Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-103183492023-07-05 Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’ Patel, Sagar Harris, Zachary N. Londo, Jason P. Miller, Allison Fennell, Anne GigaByte Data Release ‘Chambourcin’ is a French-American interspecific hybrid grape grown in the eastern and midwestern United States and used for making wine. Few genomic resources are available for hybrid grapevines like ‘Chambourcin’. Here, we assembled the genome of ‘Chambourcin’ using PacBio HiFi long-read, Bionano optical map, and Illumina short-read sequencing technologies. We generated an assembly for ‘Chambourcin’ with 26 scaffolds, with an N50 length of 23.3 Mb and an estimated BUSCO completeness of 97.9%. We predicted 33,791 gene models and identified 16,056 common orthologs between ‘Chambourcin’, V. vinifera ‘PN40024’ 12X.v2, VCOST.v3, Shine Muscat and V. riparia Gloire. We found 1,606 plant transcription factors from 58 gene families. Finally, we identified 304,571 simple sequence repeats (up to six base pairs long). Our work provides the genome assembly, annotation and the protein and coding sequences of ‘Chambourcin’. Our genome assembly is a valuable resource for genome comparisons, functional genomic analyses and genome-assisted breeding research. GigaScience Press 2023-07-03 /pmc/articles/PMC10318349/ /pubmed/37408731 http://dx.doi.org/10.46471/gigabyte.84 Text en © The Author(s) 2023. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Data Release Patel, Sagar Harris, Zachary N. Londo, Jason P. Miller, Allison Fennell, Anne Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’ |
title | Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’ |
title_full | Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’ |
title_fullStr | Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’ |
title_full_unstemmed | Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’ |
title_short | Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’ |
title_sort | genome assembly of the hybrid grapevine vitis ‘chambourcin’ |
topic | Data Release |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10318349/ https://www.ncbi.nlm.nih.gov/pubmed/37408731 http://dx.doi.org/10.46471/gigabyte.84 |
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