Location: Plant Genetic Resources ResearchTitle: Characterization of resistance gene analogues (RGAs) in Apple (Malus 6domestica Borkh.) and their evolutionary history of the Rosaceae family) Author
Submitted to: PLoS One
Publication Type: Peer reviewed journal
Publication Acceptance Date: 11/17/2013
Publication Date: 2/5/2014
Citation: Perazzolli, M., Malacarne, G., Baldo, A.M., Righetti, L., Bailey, A., Fontana, P., Velasco, R., Malnoy, M. 2014. Characterization of resistance gene analogues (RGAs) in apple (Malus 6domestica Borkh.) and their evolutionary history of the Rosaceae family. PLoS One. 9(2):e83844. Interpretive Summary: How are disease resistance genes related among Rosaceae? Plants in the Rosaceae family share disease-resistance genes found in many other plants. These genes are active in pathogen recognition, cellular signaling, and protein interaction. We surveyed a specific class of these genes which contain a nucleotide-binding site (NBS) domain in wild and domesticated apples, cherries, and raspberries, in combination with these genes already found in strawberries, pears, and stonefruit. More than 1400 resistance gene sequences were identified and classified according to sequence similarity. We learned that some subclasses of the genes are found only in specific genera, shedding light on the evolution and distribution of this important class of genes.
Technical 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 RGAsare 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 ofMalus, Fragaria, and Rosa, indicating genus-specific evolution of resistance genes. However, strikingly similar RGAs were shared in Malus, Pyrus, andPrunus, indicating high conservation of specific RGAs and suggesting a monophyletic origin of these three genera.