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

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 fro...

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Bibliographic Details
Published in:Annals of botany 2013-08, Vol.112 (3), p.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: Article
Language:English
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
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Summary: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
ISSN:0305-7364
1095-8290
DOI:10.1093/aob/mct128