title: A genome-wide comparison of NB-LRR type of resistance gene analogs (RGA) in the plant kingdom.
abstract: Plants express resistance (R) genes to recognize invaders and prevent the spread of pathogens. To analyze nucleotide binding site, leucine-rich repeat (NB-LRR) genes, we constructed a fast pipeline to predict and classify the R gene analogs (RGAs) by applying in-house matrices. With predicted ~37,000 RGAs, we can directly compare RGA contents across entire plant lineages, from green algae to flowering plants. We focused on the highly divergent NBLRRs in land plants following the emergence of mosses. We identified entire loss of Toll/Interleukin-1 receptor, NBLRR (TNL) in Poaceae family of monocots and interestingly from Mimulus guttatus (a dicot), which leads to the possibility of species-specific TNL loss in other sequenced flowering plants. Using RGA maps, we have elucidated a positive correlation between the cluster sizes of NB-LRRs and their numbers. The cluster members were observed to consist of the same class of NB-LRRs or their variants, which were probably generated from a single locus for an R gene. Our website ( http://sol.kribb.re.kr/PRGA/ ), called plant resistance gene analog (PRGA), provides useful information, such as RGA annotations, tools for predicting RGAs, and analyzing domain profiles. Therefore, PRGA provides new insights into R-gene evolution and is useful in applying RGA as markers in breeding and or systematic studies.
authors.affiliation: Green Bio Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.
authors.forename: Jungeun
authors.initials: J
authors.lastname: Kim
authors.forename: Chan Ju
authors.initials: CJ
authors.lastname: Lim
authors.forename: Bong-Woo
authors.initials: BW
authors.lastname: Lee
authors.forename: Jae-Pil
authors.initials: JP
authors.lastname: Choi
authors.forename: Sang-Keun
authors.initials: SK
authors.lastname: Oh
authors.forename: Raza
authors.initials: R
authors.lastname: Ahmad
authors.forename: Suk-Yoon
authors.initials: SY
authors.lastname: Kwon
authors.forename: Jisook
authors.initials: J
authors.lastname: Ahn
authors.forename: Cheol-Goo
authors.initials: CG
authors.lastname: Hur
mesh_terms: D001665:Binding Sites; D019295:Computational Biology; D014644:Genetic Variation; D018745:Genome, Plant; D007930:Leucine / Q000235:genetics*; D010802:Phylogeny; D057865:Plant Immunity / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*; D010944:Plants / Q000235:genetics*; D020449:Repetitive Sequences, Amino Acid; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D010940:Plant Proteins; D007930:Leucine