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

Abstract

<i>Vitis riparia</i>, 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 <i>V. riparia</i> 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 <i>V. riparia</i> ESTs, BACs, and three de novo transcriptome assemblies of three different <i>V. riparia</i> genotypes resulting in >98% of respective sequences/transcripts mapping with this assembly. Alignment of the <i>V. riparia</i> assembly and predicted CDS with the latest <i>V. vinifera</i> '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 <i>V. vinifera</i> transcription factors. QTL mapping to <i>V. riparia</i> 'Manitoba 37' and <i>V. vinifera</i> PN40024 has identified genetic relationships to phenotypic variation between species. This assembly provides reference sequences, gene models for marker development and understanding <i>V. riparia</i>'s genetic contributions in grape breeding and research.