title: The repetitive component of the A genome of peanut (Arachis hypogaea) and its role in remodelling intergenic sequence space since its evolutionary divergence from the B genome.
abstract: OBJECTIVE
  Peanut (Arachis hypogaea) is an allotetraploid (AABB-type genome) of recent origin, with a genome of about 2·8 Gb and a high repetitive content. This study reports an analysis of the repetitive component of the peanut A genome using bacterial artificial chromosome (BAC) clones from A. duranensis, the most probable A genome donor, and the probable consequences of the activity of these elements since the divergence of the peanut A and B genomes.
  
  
  METHODS
  The repetitive content of the A genome was analysed by using A. duranensis BAC clones as probes for fluorescence in situ hybridization (BAC-FISH), and by sequencing and characterization of 12 genomic regions. For the analysis of the evolutionary dynamics, two A genome regions are compared with their B genome homeologues.
  
  
  RESULTS
  BAC-FISH using 27 A. duranensis BAC clones as probes gave dispersed and repetitive DNA characteristic signals, predominantly in interstitial regions of the peanut A chromosomes. The sequences of 14 BAC clones showed complete and truncated copies of ten abundant long terminal repeat (LTR) retrotransposons, characterized here. Almost all dateable transposition events occurred <3·5 million years ago, the estimated date of the divergence of A and B genomes. The most abundant retrotransposon is Feral, apparently parasitic on the retrotransposon FIDEL, followed by Pipa, also non-autonomous and probably parasitic on a retrotransposon we named Pipoka. The comparison of the A and B genome homeologous regions showed conserved segments of high sequence identity, punctuated by predominantly indel regions without significant similarity.
  
  
  CONCLUSIONS
  A substantial proportion of the highly repetitive component of the peanut A genome appears to be accounted for by relatively few LTR retrotransposons and their truncated copies or solo LTRs. The most abundant of the retrotransposons are non-autonomous. The activity of these retrotransposons has been a very significant driver of genome evolution since the evolutionary divergence of the A and B genomes.
authors.affiliation: University of Brasilia, Department of Genetics, Campus Universitário, Brasília DF, Brazil.
authors.forename: David J
authors.initials: DJ
authors.lastname: Bertioli
authors.forename: Bruna
authors.initials: B
authors.lastname: Vidigal
authors.forename: Stephan
authors.initials: S
authors.lastname: Nielen
authors.forename: Milind B
authors.initials: MB
authors.lastname: Ratnaparkhe
authors.forename: Tae-Ho
authors.initials: TH
authors.lastname: Lee
authors.forename: Soraya C M
authors.initials: SC
authors.lastname: Leal-Bertioli
authors.forename: Changsoo
authors.initials: C
authors.lastname: Kim
authors.forename: Patricia M
authors.initials: PM
authors.lastname: Guimarães
authors.forename: Guillermo
authors.initials: G
authors.lastname: Seijo
authors.forename: Trude
authors.initials: T
authors.lastname: Schwarzacher
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
authors.forename: Pat
authors.initials: P
authors.lastname: Heslop-Harrison
authors.forename: Ana C G
authors.initials: AC
authors.lastname: Araujo
mesh_terms: D010367:Arachis / Q000235:genetics*; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D021901:DNA, Intergenic; D019143:Evolution, Molecular; D018745:Genome, Plant; D017404:In Situ Hybridization, Fluorescence; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid; D018626:Retroelements / Q000502:physiology
chemical_list: D021901:DNA, Intergenic; D018626:Retroelements
keywords: A. duranensis; Arachis hypogaea; BAC sequencing; BAC-FISH; genome evolution; groundnut; homeology; peanut; phylogeny; retrotransposons