title: Characterization of resistance gene analogues (RGAs) in apple (Malus × domestica Borkh.) and their evolutionary history of the Rosaceae family.
abstract: The family of resistance gene analogues (RGAs) with a nucleotide-binding site (NBS) domain accounts for the largest number of disease resistance genes and is one of the largest gene families in plants. We have identified 868 RGAs in the genome of the apple (Malus × domestica Borkh.) cultivar 'Golden Delicious'. This represents 1.51% of the total number of predicted genes for this cultivar. Several evolutionary features are pronounced in M. domestica, including a high fraction (80%) of RGAs occurring in clusters. This suggests frequent tandem duplication and ectopic translocation events. Of the identified RGAs, 56% are located preferentially on six chromosomes (Chr 2, 7, 8, 10, 11, and 15), and 25% are located on Chr 2. TIR-NBS and non-TIR-NBS classes of RGAs are primarily exclusive of different chromosomes, and 99% of non-TIR-NBS RGAs are located on Chr 11. A phylogenetic reconstruction was conducted to study the evolution of RGAs in the Rosaceae family. More than 1400 RGAs were identified in six species based on their NBS domain, and a neighbor-joining analysis was used to reconstruct the phylogenetic relationships among the protein sequences. Specific phylogenetic clades were found for RGAs of Malus, Fragaria, and Rosa, indicating genus-specific evolution of resistance genes. However, strikingly similar RGAs were shared in Malus, Pyrus, and Prunus, indicating high conservation of specific RGAs and suggesting a monophyletic origin of these three genera.
authors: Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.
authors: Michele
authors: M
authors: Perazzolli
authors: Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.
authors: Giulia
authors: G
authors: Malacarne
authors: United States Department of Agriculture-Agricultural Research Service Plant Genetic Resources Unit, Geneva, New York, United States of America.
authors: Angela
authors: A
authors: Baldo
authors: Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.
authors: Laura
authors: L
authors: Righetti
authors: United States Department of Agriculture-Agricultural Research Service Plant Genetic Resources Unit, Geneva, New York, United States of America.
authors: Aubrey
authors: A
authors: Bailey
authors: Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.
authors: Paolo
authors: P
authors: Fontana
authors: Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.
authors: Riccardo
authors: R
authors: Velasco
authors: Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.
authors: Mickael
authors: M
authors: Malnoy
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics*; D019143:Evolution, Molecular; D018745:Genome, Plant; D027845:Malus / Q000235:genetics*; D010802:Phylogeny