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Open Access Research article

Analysis of high-identity segmental duplications in the grapevine genome

Giuliana Giannuzzi1, Pietro D'Addabbo1, Marica Gasparro2, Maurizio Martinelli34, Francesco N Carelli1, Donato Antonacci2* and Mario Ventura15*

Author Affiliations

1 Department of Biology, University of Bari, Bari 70126, Italy

2 Agricultural Research Council, Research Unit for Table Grapes and Wine Growing in Mediterranean Environment (CRA-UTV), Turi (BA) 70010, Italy

3 National Institute of Nuclear Physics (INFN), Bari 70126, Italy

4 Department of Physics, University of Bari, Bari 70126, Italy

5 Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA

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BMC Genomics 2011, 12:436  doi:10.1186/1471-2164-12-436

Published: 26 August 2011

Abstract

Background

Segmental 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).

Results

We 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.

Conclusions

These 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.