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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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Autores principales: Patel, Sagar, Robben, Michael, Fennell, Anne, Londo, Jason P., Alahakoon, Dilmini, Villegas-Diaz, Roberto, Swaminathan, Padmapriya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
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.
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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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