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. ‘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.
Highlights
Grapes (Vitis spp.), used for wine, juice, table grapes, raisins, and rootstocks are the most valuable fruit crop in the world
The final assembly and gene models were compared with the reference genome V. vinifera PN40024 12X.2 and V3 annotation and other recent Vitis cultivar assemblies and gene conservation was analyzed
The SNP markers were aligned to the V. riparia ‘Manitoba 37’ and V. vinifera genomes and quantitative trait loci regions over genic locations were mapped to the genomes using V. riparia phenotypes
Summary
Grapes (Vitis spp.), used for wine, juice, table grapes, raisins, and rootstocks are the most valuable fruit crop in the world. While the cultivated species Vitis vinifera is the predominant species used in the industry, other wild grape species are important contributors to commercial production. Several North American species have been used by breeders to develop scion and rootstock cultivars that are disease, insect, and abiotic stress tolerant[1]. Evidence from ongoing genome sequencing projects in grapevine demonstrates high variability between cultivars and that the wild grapevine. Recent nuclear DNA analyses suggest that the most recent common Vitis ancestor for the existing global grape species originated in North America, diversifying from the rest of Vitaceae ~28 Mya (CI 41.2, 16.2 Mya), with Vitis and Muscadinia diverging ~18 Mya[8]. The Vitis genus, containing about 60 interfertile living species, is suggested to have diversified at
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
