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Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’
Vitis riparia, a critically important Native American grapevine species, is used globally in rootstock and scion breeding and contributed to the recovery of the French wine industry during the mid-19th century phylloxera epidemic. This species has abiotic and biotic stress tolerance and the largest...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7261805/ https://www.ncbi.nlm.nih.gov/pubmed/32528704 http://dx.doi.org/10.1038/s41438-020-0316-2 |
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author | Patel, Sagar Robben, Michael Fennell, Anne Londo, Jason P. Alahakoon, Dilmini Villegas-Diaz, Roberto Swaminathan, Padmapriya |
author_facet | Patel, Sagar Robben, Michael Fennell, Anne Londo, Jason P. Alahakoon, Dilmini Villegas-Diaz, Roberto Swaminathan, Padmapriya |
author_sort | Patel, Sagar |
collection | PubMed |
description | Vitis riparia, a critically important Native American grapevine species, is used globally in rootstock and scion breeding and contributed to the recovery of the French wine industry during the mid-19th century phylloxera epidemic. This species has abiotic and biotic stress tolerance and the largest natural geographic distribution of the North American grapevine species. Here we report an Illumina short-read 369X coverage, draft de novo heterozygous genome sequence of V. riparia Michx. ‘Manitoba 37’ with the size of ~495 Mb for 69,616 scaffolds and a N50 length of 518,740 bp. Using RNAseq data, 40,019 coding sequences were predicted and annotated. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models found 96% of the complete BUSCOs in this assembly. The assembly continuity and completeness were further validated using V. riparia ESTs, BACs, and three de novo transcriptome assemblies of three different V. riparia genotypes resulting in >98% of respective sequences/transcripts mapping with this assembly. Alignment of the V. riparia assembly and predicted CDS with the latest V. vinifera ‘PN40024’ CDS and genome assembly showed 99% CDS alignment and a high degree of synteny. An analysis of plant transcription factors indicates a high degree of homology with the V. vinifera transcription factors. QTL mapping to V. riparia ‘Manitoba 37’ and V. vinifera PN40024 has identified genetic relationships to phenotypic variation between species. This assembly provides reference sequences, gene models for marker development and understanding V. riparia’s genetic contributions in grape breeding and research. |
format | Online Article Text |
id | pubmed-7261805 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-72618052020-06-10 Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’ Patel, Sagar Robben, Michael Fennell, Anne Londo, Jason P. Alahakoon, Dilmini Villegas-Diaz, Roberto Swaminathan, Padmapriya Hortic Res Article Vitis riparia, a critically important Native American grapevine species, is used globally in rootstock and scion breeding and contributed to the recovery of the French wine industry during the mid-19th century phylloxera epidemic. This species has abiotic and biotic stress tolerance and the largest natural geographic distribution of the North American grapevine species. Here we report an Illumina short-read 369X coverage, draft de novo heterozygous genome sequence of V. riparia Michx. ‘Manitoba 37’ with the size of ~495 Mb for 69,616 scaffolds and a N50 length of 518,740 bp. Using RNAseq data, 40,019 coding sequences were predicted and annotated. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models found 96% of the complete BUSCOs in this assembly. The assembly continuity and completeness were further validated using V. riparia ESTs, BACs, and three de novo transcriptome assemblies of three different V. riparia genotypes resulting in >98% of respective sequences/transcripts mapping with this assembly. Alignment of the V. riparia assembly and predicted CDS with the latest V. vinifera ‘PN40024’ CDS and genome assembly showed 99% CDS alignment and a high degree of synteny. An analysis of plant transcription factors indicates a high degree of homology with the V. vinifera transcription factors. QTL mapping to V. riparia ‘Manitoba 37’ and V. vinifera PN40024 has identified genetic relationships to phenotypic variation between species. This assembly provides reference sequences, gene models for marker development and understanding V. riparia’s genetic contributions in grape breeding and research. Nature Publishing Group UK 2020-06-01 /pmc/articles/PMC7261805/ /pubmed/32528704 http://dx.doi.org/10.1038/s41438-020-0316-2 Text en © The Author(s) 2020 https://creativecommons.org/licenses/by/4.0/Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Patel, Sagar Robben, Michael Fennell, Anne Londo, Jason P. Alahakoon, Dilmini Villegas-Diaz, Roberto Swaminathan, Padmapriya Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’ |
title | Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’ |
title_full | Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’ |
title_fullStr | Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’ |
title_full_unstemmed | Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’ |
title_short | Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’ |
title_sort | draft genome of the native american cold hardy grapevine vitis riparia michx. ‘manitoba 37’ |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7261805/ https://www.ncbi.nlm.nih.gov/pubmed/32528704 http://dx.doi.org/10.1038/s41438-020-0316-2 |
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