Abstract
BackgroundNucleotide binding site leucine-rich repeats (NBS-LRR) genes encode a large class of disease resistance (R) proteins in plants. Extensive studies have been carried out to identify and investigate NBS-encoding gene families in many important plant species. However, no comprehensive research into NBS-encoding genes in the Rosaceae has been performed.ResultsIn this study, five whole-genome sequenced Rosaceae species, including apple, pear, peach, mei, and strawberry, were analyzed to investigate the evolutionary pattern of NBS-encoding genes and to compare them to those of three Cucurbitaceae species, cucumber, melon, and watermelon. Considerable differences in the copy number of NBS-encoding genes were observed between Cucurbitaceae and Rosaceae species. In Rosaceae species, a large number and a high proportion of NBS-encoding genes were observed in peach (437, 1.52%), mei (475, 1.51%), strawberry (346, 1.05%) and pear (617, 1.44%), and apple contained a whopping 1303 (2.05%) NBS-encoding genes, which might be the highest number of R-genes in all of these reported diploid plant. However, no more than 100 NBS-encoding genes were identified in Cucurbitaceae. Many more species-specific gene families were classified and detected with the signature of positive selection in Rosaceae species, especially in the apple genome.ConclusionsTaken together, our findings indicate that NBS-encoding genes in Rosaceae, especially in apple, have undergone extreme expansion and rapid adaptive evolution. Useful information was provided for further research on the evolutionary mode of disease resistance genes in Rosaceae crops.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0208-x) contains supplementary material, which is available to authorized users.
Highlights
Nucleotide binding site leucine-rich repeats (NBS-LRR) genes encode a large class of disease resistance (R) proteins in plants
Three of the eight species were from the Cucurbitaceae: cucumber (Cucumis sativus), melon (Cucumis melo) and watermelon (Citrullus lanatus), while the other five were from the Rosaceae, peach (Prunus persica), mei (Prunus mume), strawberry (Fragaria vesca), pear (Pyrus bretschneideri) and apple (Malus domestica)
Different patterns in NBS-encoding gene numbers were observed between Cucurbitaceae and Rosaceae
Summary
Nucleotide binding site leucine-rich repeats (NBS-LRR) genes encode a large class of disease resistance (R) proteins in plants. The battle between plants and pathogens has gone on since they first emerged in the Earth’s ecosystem This ongoing battle against pathogens has led to two types of immune responses in plants: a basal response to pathogen-associated molecular patterns (PAMPs) and a gene-for-gene response specific to a pathogen [1,2,3,4]. The former is present constitutively and the latter is induced upon exposure to pathogens. This defense mechanism has aroused people’s great interest, because it is possible to exploit the natural inducible defenses to engineer
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