ArticleBMC genomics2022
'Nebbiolo' genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.).
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 18 citations in OpenAlex.
- A complex reciprocal translocation is linked to reduced gamete viability in a loose-bunch grapevine somatic variant.BMC plant biology · 2026Article
- Rpv2 is part of a cluster of NLRs specific to Vitis rotundifolia and confers total resistance to grapevine downy mildew.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Phased T2T genome assemblies facilitate the mining of disease-resistance genes inHorticulture research · 2025Article
- Navigating triplet repeats sequencing: concepts, methodological challenges and perspective for Huntington's disease.Nucleic acids research · 2025Review
- Grapevine pangenome facilitates trait genetics and genomic breeding.Nature genetics · 2024Article
- Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation.Horticulture research · 2024Article
- Chimeras in Merlot grapevine revealed by phased assembly.BMC genomics · 2023Article
- The complete reference genome for grapevine (Horticulture research · 2023Article
- Review
- CRISPR/Cas9-Mediated Enrichment Coupled to Nanopore Sequencing Provides a Valuable Tool for the Precise Reconstruction of Large Genomic Target Regions.International journal of molecular sciences · 2023Article
- Boosting grapevine breeding for climate-smart viticulture: from genetic resources to predictive genomics.Frontiers in plant science · 2023Review
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Authors and funding
14 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
background'Nebbiolo' is a grapevine cultivar typical of north-western Italy, appreciated for producing high-quality red wines. Grapevine cultivars are characterized by possessing highly heterozygous genomes, including a great incidence of genomic rearrangements larger than 50 bp, so called structural variations (SVs). Even though abundant, SVs are an under-explored source of genetic variation mainly due to methodological limitations at their detection.
resultsWe 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. The annotated assembly enhanced our ability to detect SVs, enabling the study of genomic regions not present in the grapevines' reference genome and accounting for their functional implications. We performed variant calling analyses at three different organizational levels: i) between haplotypes of clone CVT 71 (primary assembly vs haplotigs), ii) between 'Nebbiolo' and 'Cabernet Sauvignon' assemblies and iii) between clones CVT 71 and CVT 185, representing different 'Nebbiolo' biotypes. The cumulative size of non-redundant merged SVs indicated a total of 79.6 Mbp for the first comparison and 136.1 Mbp for the second one, while no SVs were detected for the third comparison. Interestingly, SVs differentiating cultivars and haplotypes affected similar numbers of coding genes.
conclusionsOur results suggest that SVs accumulation rate and their functional implications in 'Nebbiolo' genome are highly-dependent on the organizational level under study. SVs are abundant when comparing 'Nebbiolo' to a different cultivar or the two haplotypes of the same individual, while they turned absent between the two analysed clones.
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