grapegenomics.com - News

08.30.2022 - New resources available

VitisNet Grapevine Molecular Networks

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VitisNet annotations and molecular networks data are now available for download at grapegenomics.com

09.02.2022 - New Preprint

HiFi chromosome-scale diploid assemblies of the grape rootstocks 110R, Kober 5BB, and 101-14 Mgt

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The three North American Vitis species, V. riparia, V. rupestris, and V. berlandieri, are the main species used for breeding grape rootstocks. Here, we report the diploid chromosome-scale assembly of three widely used rootstocks derived from these species: Richter 110 (110R), Kober 5BB, and 101-14 Millardet et de Grasset (Mgt).
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07.20.2022 - New dataset available

Vitis vinifera cv. Pinot Noir cl. ENTAV115

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Vitis vinifera cv. Pinot Noir cl. ENTAV115 genome assembly and annotation from 2007 are now hosted on www.grapegenomics.com. Genome browser, blast service, and download are now publicly available.

07.15.2022 - Updated Genome

Vitis vinifera PN40024 v4

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Vitis vinifera PN40024 genome has been updated to v4 thanks to COST Action INTEGRAPE and Grapedia Team. Genome browser and blast services are now available www.grapegenomics.com.

07.13.2022 - New genome available

Vitis 101-14 Mgt

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Vitis Interspecific Crossing 101-14 Mgt (Millardet et de Grasset; V. riparia x V. rupestris) diploid chromosome scale genome assembly is now available www.grapegenomics.com.

07.13.2022 - New genome available

Vitis 110R

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Vitis Interspecific Crossing 110R (Richter 110; V. berlandieri x V. rupestris) diploid chromosome scale genome assembly is now available www.grapegenomics.com.

07.13.2022- New genome available

Vitis Kober 5BB

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Vitis Interspecific Crossing Kober 5BB (V. berlandieri x V. riparia) diploid chromosome scale genome assembly is now available www.grapegenomics.com.

06.10.2022 - New Article

Assembly of complete diploid phased chromosomes from draft genome sequences

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HaploSync uses a genetic map and/or the genome of a closely related species to guide the scaffolding of a diploid assembly into phased pseudomolecules for each chromosome. It compares alternative haplotypes to identify and correct misassemblies independent of a reference, fills assembly gaps with unplaced sequences, and resolves collapsed homozygous regions.
[... see more]

06.13.2022 - New Article

Haplotype-resolved powdery mildew resistance loci reveal the impact of heterozygous structural variation on NLR genes in Muscadinia rotundifolia

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Muscadinia rotundifolia cv. Trayshed is a valuable source of resistance to grape powdery mildew. It carries two powdery mildew resistance-associated genetic loci, Run1.2 on chromosome 12 and Run2.2 on chromosome 18. The purpose of this study was to identify candidate resistance genes associated with each haplotype of the two loci.
[... see more]

04.26.2022 - New genome available

Vitis acerifolia

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Vitis acerifolia diploid chromosome scale genome assembly is now available www.grapegenomics.com.

04.26.2022 - New genome available

Vitis aestivalis

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Vitis aestivalis diploid chromosome scale genome assembly is now available www.grapegenomics.com.

04.26.2022 - New genome available

Vitis berlanderi

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Vitis berlanderi diploid chromosome scale genome assembly is now available www.grapegenomics.com.

04.26.2022 - New genome available

Vitis girdiana

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Vitis girdiana diploid chromosome scale genome assembly is now available www.grapegenomics.com.

04.26.2022 - New genome available

Vitis monticola

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Vitis monticola diploid chromosome scale genome assembly is now available www.grapegenomics.com.

04.26.2022 - New genome available

Vitis mustangensis

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Vitis mustangensis diploid chromosome scale genome assembly is now available www.grapegenomics.com.

04.26.2022 - New genome available

Vitis riparia

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Vitis riparia diploid chromosome scale genome assembly is now available www.grapegenomics.com.

04.26.2022 - New genome available

Vitis rupestris

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Vitis rupestris diploid chromosome scale genome assembly is now available www.grapegenomics.com.

03.07.2022 - New Paper

‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.).

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We employed a multiple platform approach to produce long-range genomic data for two different ‘Nebbiolo’ clones, namely: optical mapping, long-reads and linked-reads. We performed a haplotype-resolved de novo assembly for cultivar ‘Nebbiolo’ (clone CVT 71) and used an ab-initio strategy to annotate it.. [... see more]

03.07.2022 - New genome available

Vitis vinifera cv Nebbiolo cl. CVT 71

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Vitis vinifera cv Nebbiolo cl. CVT 71 diploid genome assembly and annotation are now publicly available on www.grapegenomics.com.

03.03.2022 - New genome available

Vitis vinifera cv. Pinot Noir cl. FPS123

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Vitis vinifera cv. Pinot Noir cl. FPS123 pseudochromosome scale diploid genome assembly and annotation are now publicly available on www.grapegenomics.com.

11.24.2021 - New Preprint

Characterization of the grape powdery mildew genetic resistance loci in Muscadinia rotundifolia Trayshed

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Muscadinia rotundifolia cv. Trayshed is a valuable source of resistance to grape powdery mildew (PM). It carries two PM resistance (R) loci, Run1.2 on chromosome 12 and Run2.2 on chromosome 18. This study identified the nucleotide-binding leucine-rich repeat (NLR) genes composing each R locus and their associated defense mechanisms.
[... see more]

11.15.2021 - New Preprint

Assembly of complete diploid phased chromosomes from draft genome sequences

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HaploSync uses a genetic map and/or the genome of a closely related species to guide the scaffolding of a diploid assembly into phased pseudomolecules for each chromosome. It compares alternative haplotypes to identify and correct misassemblies independent of a reference, fills assembly gaps with unplaced sequences, and resolves collapsed homozygous regions.
[... see more]

06.02.2021 - New Paper

Rootstock influences the effect of grapevine leafroll-associated viruses on berry development and metabolism via abscisic acid signalling

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Using a dedicated experimental vineyard, we studied the responses to Grapevine leafroll-associated virus (GLRaV) in ripening berries from Cabernet Franc grapevines grafted to different rootstocks and with zero, one, or pairs of leafroll infection(s). [... see more]

04.12.2021 - New genome available

Vitis vinifera cv. Riesling cl. FPS 24

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Vitis vinifera cv. Riesling cl. FPS 24 is now publicly available on the website. Used in Zou et al. 2021, the genome was assembled in diploid-aware fashion from SMRT sequencing long reads. Follow this link to dedicated page with dwonloads and online resources.

04.12.2021 - New Paper

Multiple independent recombinations led to hermaphroditism in grapevine

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We studied the grape sex-determining region (SDR) in 12 Vitis genomes and demonstrated its conservation across 556 genotypes including 193 accessions from 47 world-wide wild grapevine species and 363 accessions of cultivated grapevine. Although the grape SDR is recombination free in all wild species, we found two distinct hermaphrodite (H) haplotypes [... see more]

02.17.2021 - New genome available

Vitis vinifera cv. Cabernet Franc clone FPS04

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Vitis vinifera cv. Cabernet Franc clone FPS04 - Genome browser and blast resources have been released for the draft assembly and annotation of Cabernet Franc genome

02.10.2021 - New genome available

Muscadinia rotundifolia cv. Trayshed genome v2.0: diploid chromosome-scale assembly

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Muscadinia rotundifolia cv. Trayshed v2.0 is now publicly available on the website. Used in Cochetel et al. 2021, the new assembly reports the sequences in a diploid chromosome-scale genome. Follow this link to dedicated page with dwonloads and online resources.

02.10.2021 - New Paper

Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence

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Muscadinia rotundifolia, has been cultivated for centuries in the southeastern United States and is resistant to pathogens that detrimentally affect Vitis vinifera. Single molecule real-time reads were combined with optical maps to reconstruct the two haplotypes of each of the 20 M. rotundifolia chromosomes [... see more]

06.09.2020 - New Paper

The genetic basis of sex determination in grapes

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It remains a major challenge to identify the genes and mutations that lead to plant sexual differentiation. Here, we study the structure and evolution of the sex-determining region (SDR) in Vitis species. We report an improved, chromosome-scale Cabernet Sauvignon genome sequence and the phased assembly of nine wild and cultivated grape genomes [... see more]

12.12.2019 - New BiorXiv

The genetic basis of sex determination in grapevines (Vitis ssp.)

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Sex determination in grapevine evolved through a complex succession of switches in sexual systems. Phased genomes built with single molecule real-time sequencing reads were assembled for eleven accessions of cultivated hermaphrodite grapevines and dioecious males and females [... see more]

12.12.2019 - New Paper

The genomic diversification of grapevine clones

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Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better appreciate clone diversity and involved defining the nature of somatic mutations throughout the genome. Fifteen Zinfandel winegrape clone genomes were sequenced and compared to one another using a highly contiguous genome reference produced from one of the clones [... see more]

11.13.2019 - New Book

The Grape Genome

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This book describes the current state of international grape genomics, with a focus on the latest findings, tools and strategies employed in genome sequencing and analysis, and genetic mapping of important agronomic traits. It also discusses how these are having a direct impact on outcomes for grape breeders and the international grape research community. While V. vinifera is a model species, it is not always appreciated that its cultivation usually requires the use of other Vitis species as rootstocks. [... see more]

09.03.2019 - New Paper

The population genetics of structural variants in grapevine domestication

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Structural variants (SVs) are a largely unexplored feature of plant genomes. Little is known about the type and size of SVs, their distribution among individuals and, especially, their population dynamics. Understanding these dynamics is critical for understanding both the contributions of SVs to phenotypes and the likelihood of identifying them as causal genetic variants in genome-wide associations. [... see more]

05.01.2019 - New Paper

Diploid Genome Assembly of the Wine Grape Carménère

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In this genome report, we describe the sequencing and annotation of the genome of the wine grape Carménère (clone 02, VCR-702). Long considered extinct, this old French wine grape variety is now cultivated mostly in Chile where it was imported in the 1850s just before the European phylloxera epidemic. [... see more]

03.01.2019 - New Paper

Iso-seq allows genome-independent transcriptome profiling of grape berry development

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Though whole genome assembly and annotation can reveal the relatively unique or “private” gene space of any particular cultivar, transcriptome reconstruction is a more rapid, less costly, and less computationally intensive strategy to accomplish the same goal. In this study, we used single molecule-real time sequencing (SMRT) to sequence full-length cDNA (Iso-Seq) and reconstruct the transcriptome of Cabernet Sauvignon berries during berry ripening [... see more]