302. Bertioli DJ, Vidigal B, Nielen S, Ratnaparkhe MB, Lee T-JH, Leal-Bertioli SCM, Kim C, Guimaraes PM, Seijo G, Schwarzacher T, Paterson AH, Heslop-Harrison P, Araujo ACG. 2013. 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. Annals of Botany 112 (3): 545-559. doi: dx.doi.org/10.1093/aob/mct128

Background and Aims 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.

Key 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.

Key words: Arachis hypogaea, A. duranensis, peanut, groundnut, BAC-FISH, BAC sequencing, retrotransposons,
genome evolution, phylogeny, homeology, botany, crops, evolution, chromosomes, genomes, retrotransposons, plants, oilseed, legumes, evolution, genomics

Journal paper: PDF http://aob.oxfordjournals.org/cgi/reprint/mct128?
ijkey=U1wI9U4pRGFP2Tr&keytype=ref

Author preprint linked here:Bertioli_Repetitive_DNA_in_Peanut_Arachis_AuthorMS.

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