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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, Diaz Roberto, Swaminathan Padmapriya
Horticulture research 2020 v.7 no.92 pp. -
Vitis riparia, Vitis vinifera, chromosome mapping, genetic relationships, genome assembly, grapes, heterozygosity, indigenous species, nucleotide sequences, phenotypic variation, quantitative trait loci, rootstocks, scions, sequence homology, stress tolerance, transcription factors, transcriptome, transcriptomics, winter hardiness, North America
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.