Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. 'Manitoba 37'

Authors: PATEL, SAGAR - South Dakota State University; ROBBEN, MICHAEL - South Dakota State University; FENNELL, ANNE - South Dakota State University; Londo, Jason; ALAHAKOON, DILMINI - South Dakota State University; VILLEGAS-DIAZ, ROBERTO - South Dakota State University; SWAMINATHAN, PADMAPRIYA - South Dakota State University

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/31/2020
Publication Date: 6/1/2020
Publication URL: https://handle.nal.usda.gov/10113/7019850
Citation: Patel, S., Robben, M., Fennell, A., Londo, J.P., Alahakoon, D., Villegas-Diaz, R., Swaminathan, P. 2020. Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. 'Manitoba 37'. Horticulture Research. doi.org/10.1038/s41438-020-0316-2.
DOI: https://doi.org/10.1038/s41438-020-0316-2

Interpretive Summary: Wild grape species are important for the future of grapevine cultivation through their use as rootstocks and in the generation of climate adapted hybrid cultivars. Vitis riparia is a wild grapevine species native to eastern North America and is commonly used in breeding programs, specifically for the creation of cold hardy hybrid grapes. Key to identifying V. riparia varieties that would be of use in breeding programs is the generation of whole genome data for this species. This study represents a the production of a high quality draft genome of this species. This is the second V. riparia to be sequenced, but the first example of a variety selected specifically for scion breeding and cold hardiness. The draft genome was produced using short read technology and was combined with RNAseq data to verify predicted gene structure. Comparison of this genome with the other V. riparia genome and available cultivated grapevine genomes demonstrate a high degree of quality in this assembly. Mapping of RNAseq reads and genotyping-by-sequencing data and comparisons to gene databases indicate several changes in key plant transcription factor gene families in this wild species. This assembly provides a good reference sequenced and gene models for understanding V. riparia's contributions in grape breeding and research.

Technical Abstract: 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., (VR37/PI588259) with the size of ~495 Mb for 69,616 scaffolds and a N50 length of 518,740 bp. Using RNA-seq data 40,019 coding sequences were predicted and annotated. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models found 95.6% 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 with latest V. vinifera (PN40024 12X.2) reference genome showed 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 and V. vinfera PN40024 has identified genetic relationships to phenotypic variation between species. This assembly provides reference sequences and gene models for understanding V. riparia's genetic contributions in grape breeding and research.