title: Deconstruction of the (paleo)polyploid grapevine genome based on the analysis of transposition events involving NBS resistance genes.
abstract: Plants have followed a reticulate type of evolution and taxa have frequently merged via allopolyploidization. A polyploid structure of sequenced genomes has often been proposed, but the chromosomes belonging to putative component genomes are difficult to identify. The 19 grapevine chromosomes are evolutionary stable structures: their homologous triplets have strongly conserved gene order, interrupted by rare translocations. The aim of this study is to examine how the grapevine nucleotide-binding site (NBS)-encoding resistance (NBS-R) genes have evolved in the genomic context and to understand mechanisms for the genome evolution. We show that, in grapevine, i) helitrons have significantly contributed to transposition of NBS-R genes, and ii) NBS-R gene cluster similarity indicates the existence of two groups of chromosomes (named as Va and Vc) that may have evolved independently. Chromosome triplets consist of two Va and one Vc chromosomes, as expected from the tetraploid and diploid conditions of the two component genomes. The hexaploid state could have been derived from either allopolyploidy or the separation of the Va and Vc component genomes in the same nucleus before fusion, as known for Rosaceae species. Time estimation indicates that grapevine component genomes may have fused about 60 mya, having had at least 40-60 mya to evolve independently. Chromosome number variation in the Vitaceae and related families, and the gap between the time of eudicot radiation and the age of Vitaceae fossils, are accounted for by our hypothesis.
authors.affiliation: IASMA Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Trento, Italy.
authors.forename: Giulia
authors.initials: G
authors.lastname: Malacarne
authors.forename: Michele
authors.initials: M
authors.lastname: Perazzolli
authors.forename: Alessandro
authors.initials: A
authors.lastname: Cestaro
authors.forename: Lieven
authors.initials: L
authors.lastname: Sterck
authors.forename: Paolo
authors.initials: P
authors.lastname: Fontana
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.forename: Roberto
authors.initials: R
authors.lastname: Viola
authors.forename: Riccardo
authors.initials: R
authors.lastname: Velasco
authors.forename: Francesco
authors.initials: F
authors.lastname: Salamini
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D032461:Chromosomes, Plant / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics*; D060467:Disease Resistance / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D005810:Multigene Family; D009711:Nucleotides / Q000378:metabolism; D010163:Paleontology; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics* / Q000276:immunology; D011123:Polyploidy; D013997:Time Factors; D027843:Vitis / Q000235:genetics* / Q000276:immunology
chemical_list: D004251:DNA Transposable Elements; D009711:Nucleotides