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Chromosome-scale assembly of the Verbenaceae species Queen’s Wreath (Petrea volubilis L.)
OBJECTIVES: Petrea volubilis, a member of the Order Lamiales and the Verbenaceae family, is an important horticultural species that has been used in traditional folk medicine. To provide a genome sequence for comparative studies within the Order Lamiales that includes important families such as Lami...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9985249/ https://www.ncbi.nlm.nih.gov/pubmed/36869291 http://dx.doi.org/10.1186/s12863-023-01110-z |
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author | Hamilton, John P. Vaillancourt, Brieanne Wood, Joshua C. Buell, C. Robin |
author_facet | Hamilton, John P. Vaillancourt, Brieanne Wood, Joshua C. Buell, C. Robin |
author_sort | Hamilton, John P. |
collection | PubMed |
description | OBJECTIVES: Petrea volubilis, a member of the Order Lamiales and the Verbenaceae family, is an important horticultural species that has been used in traditional folk medicine. To provide a genome sequence for comparative studies within the Order Lamiales that includes important families such as Lamiaceae (mints), we generated a long-read, chromosome-scale genome assembly of this species. DATA DESCRIPTION: Using a total of 45.5 Gb of Pacific Biosciences long read sequence, we generated a 480.2 Mb assembly of P. volubilis, of which, 93% is chromosome anchored. Representation of genic regions was robust with 96.6% of the Benchmarking of Universal Single Copy Orthologs present in the genome assembly. A total of 57.8% of the genome was annotated as a repetitive sequence. Using a gene annotation pipeline that included refinement of gene models using transcript evidence, 30,982 high confidence genes were annotated. Access to the P. volubilis genome will facilitate evolutionary studies in the Lamiales, a key order of Asterids that includes significant crop and medicinal plant species. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12863-023-01110-z. |
format | Online Article Text |
id | pubmed-9985249 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-99852492023-03-05 Chromosome-scale assembly of the Verbenaceae species Queen’s Wreath (Petrea volubilis L.) Hamilton, John P. Vaillancourt, Brieanne Wood, Joshua C. Buell, C. Robin BMC Genom Data Data Note OBJECTIVES: Petrea volubilis, a member of the Order Lamiales and the Verbenaceae family, is an important horticultural species that has been used in traditional folk medicine. To provide a genome sequence for comparative studies within the Order Lamiales that includes important families such as Lamiaceae (mints), we generated a long-read, chromosome-scale genome assembly of this species. DATA DESCRIPTION: Using a total of 45.5 Gb of Pacific Biosciences long read sequence, we generated a 480.2 Mb assembly of P. volubilis, of which, 93% is chromosome anchored. Representation of genic regions was robust with 96.6% of the Benchmarking of Universal Single Copy Orthologs present in the genome assembly. A total of 57.8% of the genome was annotated as a repetitive sequence. Using a gene annotation pipeline that included refinement of gene models using transcript evidence, 30,982 high confidence genes were annotated. Access to the P. volubilis genome will facilitate evolutionary studies in the Lamiales, a key order of Asterids that includes significant crop and medicinal plant species. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12863-023-01110-z. BioMed Central 2023-03-03 /pmc/articles/PMC9985249/ /pubmed/36869291 http://dx.doi.org/10.1186/s12863-023-01110-z Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Data Note Hamilton, John P. Vaillancourt, Brieanne Wood, Joshua C. Buell, C. Robin Chromosome-scale assembly of the Verbenaceae species Queen’s Wreath (Petrea volubilis L.) |
title | Chromosome-scale assembly of the Verbenaceae species Queen’s Wreath (Petrea volubilis L.) |
title_full | Chromosome-scale assembly of the Verbenaceae species Queen’s Wreath (Petrea volubilis L.) |
title_fullStr | Chromosome-scale assembly of the Verbenaceae species Queen’s Wreath (Petrea volubilis L.) |
title_full_unstemmed | Chromosome-scale assembly of the Verbenaceae species Queen’s Wreath (Petrea volubilis L.) |
title_short | Chromosome-scale assembly of the Verbenaceae species Queen’s Wreath (Petrea volubilis L.) |
title_sort | chromosome-scale assembly of the verbenaceae species queen’s wreath (petrea volubilis l.) |
topic | Data Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9985249/ https://www.ncbi.nlm.nih.gov/pubmed/36869291 http://dx.doi.org/10.1186/s12863-023-01110-z |
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