SEIJO Jose Guillermo
The repetitive component of the A genome of peanut (Arachis hypogaea L.) and its role in the erosion of genome sequence similarity over evolutionary time.
BERTIOLI, D.J; VIGIDAL B; SEIJO JG; ET AL
ANNALS OF BOTANY
OXFORD UNIV PRESS
Lugar: Oxford; Año: 2013 vol. 112 p. 545 - 545
Background Cultivated peanut (A. hypogaea L. is a very important tropical crop, valued both for subsistence and as a cash crop. It is an allotetraploid of recent origin with an AABB-type genome. Its most probable diploid ancestors are A. duranensis (Krapov. & W.C. Greg.) and A. ipaënsis (Krapov. & W.C. Greg.). Peanut has a large genome of about 2.8 Gb with a high repetitive content. This manuscript reports an analysis of the repetitive component of the peanut genome using BAC clones for fluorescent in situ hybridization (BAC-FISH), and sequence analysis of 12 genomic regions totalling 1.26 Mb from A. duranensis, the most probable A genome donor. In addition, two of these regions are compared to their homeologous counterparts in the B genome. Results In situ hybridization with peanut, using as probes 27 BAC clones containing about 100,000 pb of A. duranensis genomic DNA, gave signals predominantly from the interstitial regions of the A genome chromosomes. All signals were disperse and characteristic of repetitive DNA. To investigate further, the sequences of 14 A. duranensis BAC clones were analysed. These clones harboured complete and remnant fragments of ten abundant long terminal repeat (LTR) retrotransposons, all of which were completely characterized. Almost all dateable transposition events occurred less than 3.5 million years ago corresponding to the estimated divergence of the A and B genomes. These retrotransposons accounted for more than one third of the analysed genomic regions. The most abundant, named Feral was non-autonomous and apparently parasitic on the transposon FIDEL, this pair of transposons accounted for one sixth of the analysed sequence. The next most abundant retrotransposon Pipa, was also non-autonomous. It carries an enigmatic ORF that has no obvious similarities to any known protein, but is under purifying evolutionary selection. Also, to study the evolutionary dynamics of the genome sequences, two of the A genome regions were compared to their B genome homeologous regions. This showed conserved segments of high sequence identity, punctuated by predominantly indel regions without significant similarity. There was a marked tendency for the variable regions to be repetitive. Conclusions A substantial proportion of the highly repetitive component of peanut A genome appears to be accounted for by relatively few LTR retrotransposons, and their remnants or solo LTRs. The most abundant of the retrotransposons are non-autonomous. The activity of these transposons since the evolutionary divergence of the A and B genomes has been a very significant driver of the erosion of genome sequence similarity, and explains much of the divergence in sequence similarity of the two genome components.