title: Dynamic nucleotide-binding site and leucine-rich repeat-encoding genes in the grass family.
abstract: The proper use of resistance genes (R genes) requires a comprehensive understanding of their genomics and evolution. We analyzed genes encoding nucleotide-binding sites and leucine-rich repeats in the genomes of rice (Oryza sativa), maize (Zea mays), sorghum (Sorghum bicolor), and Brachypodium distachyon. Frequent deletions and translocations of R genes generated prevalent presence/absence polymorphism between different accessions/species. The deletions were caused by unequal crossover, homologous repair, nonhomologous repair, or other unknown mechanisms. R gene loci identified from different genomes were mapped onto the chromosomes of rice cv Nipponbare using comparative genomics, resulting in an integrated map of 495 R loci. Sequence analysis of R genes from the partially sequenced genomes of an African rice cultivar and 10 wild accessions suggested that there are many additional R gene lineages in the AA genome of Oryza. The R genes with chimeric structures (termed type I R genes) are diverse in different rice accessions but only account for 5.8% of all R genes in the Nipponbare genome. In contrast, the vast majority of R genes in the rice genome are type II R genes, which are highly conserved in different accessions. Surprisingly, pseudogene-causing mutations in some type II lineages are often conserved, indicating that their conservations were not due to their functions. Functional R genes cloned from rice so far have more type II R genes than type I R genes, but type I R genes are predicted to contribute considerable diversity in wild species. Type I R genes tend to reduce the microsynteny of their flanking regions significantly more than type II R genes, and their flanking regions have slightly but significantly lower G/C content than those of type II R genes.
authors.affiliation: Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, People's Republic of China, 430070.
authors.forename: Sha
authors.initials: S
authors.lastname: Luo
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.forename: Qun
authors.initials: Q
authors.lastname: Hu
authors.forename: Jiongjiong
authors.initials: J
authors.lastname: Chen
authors.forename: Kunpeng
authors.initials: K
authors.lastname: Li
authors.forename: Chen
authors.initials: C
authors.lastname: Lu
authors.forename: Hui
authors.initials: H
authors.lastname: Liu
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
authors.forename: Hanhui
authors.initials: H
authors.lastname: Kuang
mesh_terms: D000483:Alleles; D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics / Q000378:metabolism; D017124:Conserved Sequence; D017343:Genes, Plant; D056426:Genetic Loci; D007930:Leucine / Q000378:metabolism*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D005810:Multigene Family; D009711:Nucleotides / Q000235:genetics / Q000378:metabolism*; D006109:Poaceae / Q000235:genetics* / Q000378:metabolism; D017354:Point Mutation; D011110:Polymorphism, Genetic; D011544:Pseudogenes; D017384:Sequence Deletion; D026801:Synteny; D014178:Translocation, Genetic
chemical_list: D009711:Nucleotides; D007930:Leucine