Characterization of long interspersed non- LTR elements in section Arachis

SAMOLUK S.; CARÍSIMO D.; ROBLEDO, G.; SEIJO G.

Oro Verde

Congreso; 3er Congreso Argentino de Bioinformática y Biología Computacional; 2012

Asociación Argentina de Bioinformática y Biología Computacional

Section Arachis (genus Arachis, Leguminosae) is composed of 29 wild diploid species belonging to five different genomes (A, B, D, F y K) and two allotetraploid species (AABB). Experiments based on molecular mapping and genome in situ hybridization suggested that changes in the repetitive fractions may have been a main force leading to genomic differentiation in Arachis. To test this hypothesis, degenerate primers were designed to isolate and characterize a conserved region of the reverse transcriptase gene from long interspersed non-LTR elements (LINEs) from eight species representing five different genomes of Arachis. The 37 isolated clones showed the conserved amino acid motifs characteristic of the reverse transcriptase of LINEs. These sequences were compared by the pairwaise method and a Neighbour- Joining tree was constructed using the program MEGA, version 5 [1]. Even though the alignment of nucleotides showed a high interspecific nucleotide divergence, the deduced amino acid sequences evidenced high percentages of similarity. Nineteen sequences had stop codons and the introduction of frameshifts in the reading frame of some sequences was necessary to optimize the alignment. Amino acid sequences from other angiosperms and gymnosperms with homology to the reverse transcriptase of the LINEs isolated from Arachis were recovered from public databases using BLASTx tool [2] and incorporated to the tree. The topology of the tree showed that the sequences isolated from Arachis were grouped into a unique cluster without species-specific subclusters. On the other hand, all the recovered sequences from public databases (which included some from legume species) grouped into another well separated cluster. The sequences grouped in the latter cluster had much deeper branches than those observed in the cluster of Arachis sequences.