Analysis of the rDNAs loci variability by next generation sequencing in a wild diploid Arachis species

CHALUP L.; SAMOLUK SS.; AGOSTINI F.; ROBLEDO G.; SEIJO G.

Congreso; VIII Argentinian Bioinformatics and Computational Biology Congress; 2017

Analysis of the rDNAs loci variability by next generation sequencing in a wild diploid Arachis speciesThe ribosomal DNA repeats are an extensively studied repetitive gene family. 45 rDNA repeat unit contains the sequence for the 26S, 5.8S and 18S rRNA gene, as well as two transcribed spacers (the ITS1 and ITS2) and a large intergenic spacer (IGS). By contrast the 5S rDNA unit has only one gene and a short intergenic spacer (NTS). Both rDNA repeats are organized in arrays at one or more loci. Each array contains hundreds to thousands of identical to near-identical repeats. These repeats are homogenized by evolutionary forces as unequal crossing-over and gene conversion, which are collectively referred to as concerted evolution. Although concerted evolutionary forces have long been known to homogenize repeats within individual loci, there are few robust demonstrations of concerted evolution among repeats from different loci. Moreover, it is thought that the loci located near the centromere are less exposed to the evolutionary forces leading to concerted evolution than those distally located.In this sense,Arachis glandulifera is a good model for the study of evolutionary processes in ribosomal genes because it has five 45S rDNA loci but only one 5S rDNA. Moreover, and, and inclusive the 45S rDNA loci are variable in size and position. In this work we applied low-depth whole genome sequencing was carried out using MiSeq technology (Illumina) and a graph-based read clustering algorithm approaches to compare the whole genomic variation between the two families of rDNA. The levels of sequence heterogeneity across both coding and non-coding regions of the 5S rDNA and 45S rDNA loci were also investigated.