ArticleBMC genomics2019
The genomic diversification of grapevine clones.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed, 135 citations in OpenAlex.
- A dual genome-methylome map of clonal evolution in grapevine.Genome biology · 2026Article
- Layer-specific genetic variation unlocks secondary metabolite diversity in long-lived clonal peppermint.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- A complex reciprocal translocation is linked to reduced gamete viability in a loose-bunch grapevine somatic variant.BMC plant biology · 2026Article
- Genome resequencing and custom genotyping elucidates the origin and dissemination history of an emblematic grapevine cultivar, 'Tempranillo Tinto'.Horticulture research · 2025Article
- Exploring intra-varietal variation for complex traits in grapevine (Vitis vinifera L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Clonal strains of the fresh-market potato cultivar Russet Norkotah changed the domestication gene CDF1.Plant physiology · 2025Article
- Harnessing clonal diversity in grapevine: from genomic insights to modern breeding applications.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Impacts of reproductive systems on grapevine genome and breeding.Nature communications · 2025Article
- The genomic and epigenomic landscapes of hemizygous genes across crops with contrasting reproductive systems.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genome Scan Analysis for Advancing Knowledge and Conservation Strategies of Primitivo Clones (Plants (Basel, Switzerland) · 2025Article
- Exploration of chaos game representation and integrative deep learning approaches for whole-genome sequencing-based grapevine genetic testing.Bioinformatics advances · 2025Article
- Grapevine pangenome facilitates trait genetics and genomic breeding.Nature genetics · 2024Article
- Epigenetic differences between wild and cultivated grapevines highlight the contribution of DNA methylation during crop domestication.BMC plant biology · 2024Article
- Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation.Horticulture research · 2024Article
- From buds to shoots: insights into grapevine development from the Witch's Broom bud sport.BMC plant biology · 2024Article
- Distinct structural variants and repeat landscape shape the genomes of the ancient grapes Aglianico and Falanghina.BMC plant biology · 2024Article
- A super-pangenome of the North American wild grape species.Genome biology · 2023Article
- Identification of grapevine clones via high-throughput amplicon sequencing: a proof-of-concept study.G3 (Bethesda, Md.) · 2023Article
- A Molecular Toolbox to Identify and Quantify Grape Varieties: On the Trace of "Glera".Foods (Basel, Switzerland) · 2023Article
Corrections and comments
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Authors and funding
14 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundVegetatively 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, Zinfandel 03.
resultsThough most heterozygous variants were shared, somatic mutations accumulated in individual and subsets of clones. Overall, heterozygous mutations were most frequent in intergenic space and more frequent in introns than exons. A significantly larger percentage of CpG, CHG, and CHH sites in repetitive intergenic space experienced transition mutations than in genic and non-repetitive intergenic spaces, likely because of higher levels of methylation in the region and because methylated cytosines often spontaneously deaminate. Of the minority of mutations that occurred in exons, larger proportions of these were putatively deleterious when they occurred in relatively few clones.
conclusionsThese data support three major conclusions. First, repetitive intergenic space is a major driver of clone genome diversification. Second, clones accumulate putatively deleterious mutations. Third, the data suggest selection against deleterious variants in coding regions or some mechanism by which mutations are less frequent in coding than noncoding regions of the genome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.