title: Comparative analysis of peanut NBS-LRR gene clusters suggests evolutionary innovation among duplicated domains and erosion of gene microsynteny.
abstract: • Plant genomes contain numerous disease resistance genes (R genes) that play roles in defense against pathogens. Scarcity of genetic polymorphism makes peanut (Arachis hypogaea) especially vulnerable to a wide variety of pathogens. • Here, we isolated and characterized peanut bacterial artificial chromosomes (BACs) containing a high density of R genes. Analysis of two genomic regions identified several TIR-NBS-LRR (Toll-interleukin-1 receptor, nucleotide-binding site, leucine-rich repeat) resistance gene analogs or gene fragments. We reconstructed their evolutionary history characterized by tandem duplications, possibly facilitated by transposon activities. We found evidence of both intergenic and intragenic gene conversions and unequal crossing-over, which may be driving forces underlying the functional evolution of resistance. • Analysis of the sequence mutations, protein secondary structure and three-dimensional structures, all suggest that LRR domains are the primary contributor to the evolution of resistance genes. The central part of LRR regions, assumed to serve as the active core, may play a key role in the resistance function by having higher rates of duplication and DNA conversion than neighboring regions. The assumed active core is characterized by significantly enriched leucine residue composition, accumulation of positively selected sites, and shorter beta sheets. • Homologous resistance gene analog (RGA)-containing regions in peanut, soybean, Medicago, Arabidopsis and grape have only limited gene synteny and microcollinearity.
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
authors.forename: Milind B
authors.initials: MB
authors.lastname: Ratnaparkhe
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.|Center for Genomics and Computational Biology, School of Life Sciences, School of Sciences, Hebei United University, Tangshan, Hebei 063000, China.
authors.forename: Xiyin
authors.initials: X
authors.lastname: Wang
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
authors.forename: Jingping
authors.initials: J
authors.lastname: Li
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
authors.forename: Rosana O
authors.initials: RO
authors.lastname: Compton
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
authors.forename: Lisa K
authors.initials: LK
authors.lastname: Rainville
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
authors.forename: Cornelia
authors.initials: C
authors.lastname: Lemke
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
authors.forename: Changsoo
authors.initials: C
authors.lastname: Kim
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
authors.forename: Haibao
authors.initials: H
authors.lastname: Tang
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
mesh_terms: D020816:Amino Acid Motifs / Q000235:genetics; D000596:Amino Acids; D010367:Arachis / Q000235:genetics*; D001483:Base Sequence; D001665:Binding Sites; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D060467:Disease Resistance / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000235:genetics*; D017343:Genes, Plant; D000090263:Leucine-Rich Repeat Proteins; D029902:Medicago / Q000235:genetics; D008958:Models, Molecular; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D009711:Nucleotides / Q000378:metabolism*; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D012641:Selection, Genetic; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D026801:Synteny / Q000235:genetics*
chemical_list: D000596:Amino Acids; D004251:DNA Transposable Elements; D000090263:Leucine-Rich Repeat Proteins; D009711:Nucleotides; D011506:Proteins