title: Evolution of a complex disease resistance gene cluster in diploid Phaseolus and tetraploid Glycine.
abstract: We used a comparative genomics approach to investigate the evolution of a complex nucleotide-binding (NB)-leucine-rich repeat (LRR) gene cluster found in soybean (Glycine max) and common bean (Phaseolus vulgaris) that is associated with several disease resistance (R) genes of known function, including Rpg1b (for Resistance to Pseudomonas glycinea1b), an R gene effective against specific races of bacterial blight. Analysis of domains revealed that the amino-terminal coiled-coil (CC) domain, central nucleotide-binding domain (NB-ARC [for APAF1, Resistance genes, and CED4]), and carboxyl-terminal LRR domain have undergone distinct evolutionary paths. Sequence exchanges within the NB-ARC domain were rare. In contrast, interparalogue exchanges involving the CC and LRR domains were common, consistent with both of these regions coevolving with pathogens. Residues under positive selection were overrepresented within the predicted solvent-exposed face of the LRR domain, although several also were detected within the CC and NB-ARC domains. Superimposition of these latter residues onto predicted tertiary structures revealed that the majority are located on the surface, suggestive of a role in interactions with other domains or proteins. Following polyploidy in the Glycine lineage, NB-LRR genes have been preferentially lost from one of the duplicated chromosomes (homeologues found in soybean), and there has been partitioning of NB-LRR clades between the two homeologues. The single orthologous region in common bean contains approximately the same number of paralogues as found in the two soybean homeologues combined. We conclude that while polyploidization in Glycine has not driven a stable increase in family size for NB-LRR genes, it has generated two recombinationally isolated clusters, one of which appears to be in the process of decay.
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
authors.forename: Tom
authors.initials: T
authors.lastname: Ashfield
authors.forename: Ashley N
authors.initials: AN
authors.lastname: Egan
authors.forename: Bernard E
authors.initials: BE
authors.lastname: Pfeil
authors.forename: Nicolas W G
authors.initials: NW
authors.lastname: Chen
authors.forename: Ram
authors.initials: R
authors.lastname: Podicheti
authors.forename: Milind B
authors.initials: MB
authors.lastname: Ratnaparkhe
authors.forename: Carine
authors.initials: C
authors.lastname: Ameline-Torregrosa
authors.forename: Roxanne
authors.initials: R
authors.lastname: Denny
authors.forename: Steven
authors.initials: S
authors.lastname: Cannon
authors.forename: Jeff J
authors.initials: JJ
authors.lastname: Doyle
authors.forename: Valérie
authors.initials: V
authors.lastname: Geffroy
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Roe
authors.forename: M A
authors.initials: MA
authors.lastname: Saghai Maroof
authors.forename: Nevin D
authors.initials: ND
authors.lastname: Young
authors.forename: Roger W
authors.initials: RW
authors.lastname: Innes
mesh_terms: D000595:Amino Acid Sequence; D001499:Bayes Theorem; D004171:Diploidy; D060467:Disease Resistance; D019143:Evolution, Molecular; D017343:Genes, Plant; D005810:Multigene Family; D027805:Phaseolus / Q000737:chemistry / Q000235:genetics* / Q000276:immunology / Q000382:microbiology; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics; D054730:Protein Interaction Domains and Motifs; D011549:Pseudomonas / Q000276:immunology / Q000472:pathogenicity; D011995:Recombination, Genetic; D012641:Selection, Genetic; D016415:Sequence Alignment; D013025:Glycine max / Q000737:chemistry / Q000235:genetics* / Q000276:immunology / Q000382:microbiology; D057891:Tetraploidy
chemical_list: D010940:Plant Proteins