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

• Published in: Annals of botany Vol. 112; no. 3; pp. 545 - 559
• Main Authors: Bertioli, David J, Vidigal, Bruna, Nielen, Stephan, Ratnaparkhe, Milind B, Lee, Tae-Ho, Leal-Bertioli, Soraya C. M, Kim, Changsoo, Guimarães, Patricia M, Seijo, Guillermo, Schwarzacher, Trude, Paterson, Andrew H, Heslop-Harrison, Pat, Araujo, Ana C. G
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.08.2013
• Subjects: Arachis - genetics; Arachis hypogaea; bacterial artificial chromosomes; Chromosomes; Chromosomes, Artificial, Bacterial - genetics; clones; divergent evolution; DNA; DNA, Intergenic; Evolution, Molecular; fluorescence in situ hybridization; Genes; genome; Genome, Plant; Genomes; Genomics; In Situ Hybridization, Fluorescence; intergenic DNA; Open reading frames; Original; Peanuts; Phylogeny; Pipas; Repetitive Sequences, Nucleic Acid; Retroelements - physiology; Retrotransposons; sequence analysis; Signals; terminal repeat sequences; groundnut; A. duranensis; BAC sequencing; BAC-FISH; Arachis hypogaea; genome evolution; phylogeny; homeology; peanut; retrotransposons
• ISSN: 0305-7364; 1095-8290
• DOI: 10.1093/aob/mct128

Background and AimsPeanut (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.MethodsThe 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.Key ResultsBAC-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.ConclusionsA 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.