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

Horticulture Research
Sagar PatelPadmapriya Swaminathan

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 plan...Continue Reading

References

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Citations

Dec 11, 2020·The Plant Journal : for Cell and Molecular Biology·Yi WangZhenchang Liang
Apr 11, 2021·Proceedings of the National Academy of Sciences of the United States of America·Cheng ZouJason P Londo

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Datasets Mentioned

BETA
PRJNA550997

Methods Mentioned

BETA
amplicon sequencing
RNASeq

Software Mentioned

show
PLATANUS
GenomeScope
nucmer
ClustalW
GapCloser
BLASTX
rmdup
VCFtools
ggtree

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