Intraspecific variability of the repeatome in Arachis duranensis (Leguminosae)

SAMOLUK SS; CHALUP, LAURA M. I.; AGOSTINI F; ROBLEDO G.; SEIJO JG

Congreso; 8vo Congreso Argentino de Bioinformática y Biología Computacional; 2017

BackgroundPlant genomes are composed by a wide variety of repetitive sequences. These sequences have the potential to lead the genome evolution through the various actions they promote. Molecular markers and in situ hybridization experiments suggested that changes in the repetitive fractions may have been a main force leading to genomic differentiation among species of section Arachis (homonymous genus). However, a wide characterization of the repetitive fraction is still lacking for a better understanding of the organization, structure and evolution among this group of species, and nothing is known about the variation of the repeatome within species. In this context, we characterized the repeatome of four different accessions of the wild diploid A. duranensis (A genome) to provide insights into the intraspecific variability of the repeatome in Arachis. For this purpose, low-depth whole genome sequencing was carried out using MiSeq technology (Illumina) and a graph-based read clustering algorithm was applied for de novo identification, quantification and annotation of repeats.ResultsThe bioinformatic analysis resulted in the identification and quantification of repeats making up 70.1?73.9% of the investigated genomes. The four accessions showed a similar profile of repetitive sequences, however, differences in the genome representation of the different kind of repeats were observed. Like in most studied eukaryotic genomes, the genomes were dominated by LTR- retroelements, mainly those belonging to the Ty3-gypsy superfamily. The major component of this superfamily was the family Fidel/Feral, whose genome representation ranged from 28% to 31% among the different accessions. By contrast, the fraction of non-LTR retrotransposons showed similar proportions in all the accessions analyzed (10%). Compared with retrotransposons, DNA transposons were found at relatively low frequencies but with an intraspecific variation of 2.6-3.8%. The ribosomal genes represented less than 1% of the repetitive fraction with the exception of accession Se2848, with abundance near to 3%. Finally, the abundance of satDNA sequences varied between 5% and 6%. ConclusionIn spite of the four A. duranensis accessions have common profiles of repetitive sequences, changes in the genome representation of particular families may have partially driven the genome evolution at intraspecific level.