ArticleBMC genomics2011
Analysis of high-identity segmental duplications in the grapevine genome.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Article
- Distinct structural variants and repeat landscape shape the genomes of the ancient grapes Aglianico and Falanghina.BMC plant biology · 2024Article
- Comparative Genomic Analysis of Asian Cultivated Rice and Its Wild Progenitor (International journal of molecular sciences · 2023Article
- Article
- Article
- Genome-wide analysis of theFrontiers in plant science · 2022Article
- Seeing the Forest through the (Phylogenetic) Trees: Functional Characterisation of Grapevine Terpene Synthase (Plants (Basel, Switzerland) · 2021Article
- Article
- Segmental duplications are hot spots of copy number variants affecting barley gene content.The Plant journal : for cell and molecular biology · 2020Article
- The Soybean Laccase Gene Family: Evolution and Possible Roles in Plant Defense and Stem Strength Selection.Genes · 2019Article
- Transcriptomic and genomic structural variation analyses on grape cultivars reveal new insights into the genotype-dependent responses to water stress.Scientific reports · 2019Article
- Revised Phylogeny of thePlant physiology · 2018Article
- Analysis of Copy Number Variation in the Abp Gene Regions of Two House Mouse Subspecies Suggests Divergence during the Gene Family Expansions.Genome biology and evolution · 2017Article
- Sequence Polymorphisms and Structural Variations among Four Grapevine (Frontiers in plant science · 2017Article
- How Single Molecule Real-Time Sequencing and Haplotype Phasing Have Enabled Reference-Grade Diploid Genome Assembly of Wine Grapes.Frontiers in plant science · 2017Article
- Genome-wide characterisation and expression profile of the grapevine ATL ubiquitin ligase family reveal biotic and abiotic stress-responsive and development-related members.Scientific reports · 2016Article
- Odintifier--A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing.BMC bioinformatics · 2015Article
- A UDP-Glucose:Monoterpenol Glucosyltransferase Adds to the Chemical Diversity of the Grapevine Metabolome.Plant physiology · 2014Article
- The role of retrotransposons in gene family expansions: insights from the mouse Abp gene family.BMC evolutionary biology · 2013Article
- Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice.PloS one · 2013Article
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Authors and funding
7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundSegmental duplications (SDs) are blocks of genomic sequence of 1-200 kb that map to different loci in a genome and share a sequence identity > 90%. SDs show at the sequence level the same characteristics as other regions of the human genome: they contain both high-copy repeats and gene sequences. SDs play an important role in genome plasticity by creating new genes and modeling genome structure. Although data is plentiful for mammals, not much was known about the representation of SDs in plant genomes. In this regard, we performed a genome-wide analysis of high-identity SDs on the sequenced grapevine (Vitis vinifera) genome (PN40024).
resultsWe demonstrate that recent SDs (> 94% identity and >= 10 kb in size) are a relevant component of the grapevine genome (85 Mb, 17% of the genome sequence). We detected mitochondrial and plastid DNA and genes (10% of gene annotation) in segmentally duplicated regions of the nuclear genome. In particular, the nine highest copy number genes have a copy in either or both organelle genomes. Further we showed that several duplicated genes take part in the biosynthesis of compounds involved in plant response to environmental stress.
conclusionsThese data show the great influence of SDs and organelle DNA transfers in modeling the Vitis vinifera nuclear DNA structure as well as the impact of SDs in contributing to the adaptive capacity of grapevine and the nutritional content of grape products through genome variation. This study represents a step forward in the full characterization of duplicated genes important for grapevine cultural needs and human health.
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