Analysis of high-identity segmental duplications in the grapevine genome

BMC Genomics

Research Article

Donato Antonacci¹  Marica Gasparro¹  Francesco N Carelli²  Giuliana Giannuzzi²  Pietro D'Addabbo²  Mario Ventura³  Maurizio Martinelli⁴ 

[1] Agricultural Research Council, Research Unit for Table Grapes and Wine Growing in Mediterranean Environment (CRA-UTV), 70010, Turi (BA), Italy;Department of Biology, University of Bari, 70126, Bari, Italy;Department of Biology, University of Bari, 70126, Bari, Italy;Department of Genome Sciences, University of Washington School of Medicine, 98195, Seattle, Washington, USA;National Institute of Nuclear Physics (INFN), 70126, Bari, Italy;Department of Physics, University of Bari, 70126, Bari, Italy;

关键词: Duplicate Gene;    Segmental Duplication;    Vitis Vinifera;    Read Depth;    Duplicate Region;   

DOI  :  10.1186/1471-2164-12-436

 received in 2011-05-11, accepted in 2011-08-26,  发布年份 2011

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Giannuzzi et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.