Finding wheat chromosome 4D miRNA production sites and target genes across the whole genome through a computational approach

CRESCENTE JM; VANZETTI L; GONZÁLEZ S; GUIDOBALDI F; RIVAROLA M; VALARIK M; SIMKOVA H; DOLEZEL J; TRANQUILLI G; PANIEGO N; VIVIANA ECHENIQUE; HELGUERA M

Foz de Iguazú

Congreso; XI International Plant Molecular Biology Congress; 2015

IPMB

Plant microRNAs (miRNAs) play important roles in post-transcriptional generegulation by targeting mRNAs for cleavage or repressing translation emergingas important players in biotic and abiotic stress responses for crops. We developeda bioinformatic pipeline capable to detect 21bp miRNA putative production sitesfrom the wheat chromosome -4D and putative target genes located across the whole wheat genome. As result, 2732 miRNAs were detectedfrom a 29058821bp-miRNA library, which, were likely originated from 1740 shortDNA regions (200-300bp) located within 1472 4D scaffolds. Also 709 of 1740short DNA regions were defined as hotspots (including ≥4 different miRNA). The70% of detected hotspots showed homology with transposable-elements (TE),mostly MITEs-ClassII, Mariner. The remaining 30% would be putative not-describedTEs or low repetitive DNA regions including genes. On the other hand,1031 short DNA regions originating 3 or less different miRNA each, weredetected, including 53% with high homology with TEs (mostly ClassI, Gypsy). Asbefore, the remaining 47% were either not, described TEs or low repetitive DNAregion including genes. In a second analysis step, the pipeline challenged theIWGSC gene/transcript annotation against the 2732 miRNAs from chromosome-4D, and we observed that 1595 miRNAs as candidates for regulation of 560 genesacross the 21 wheat chromosomes. The chromosome 2D showed the highest number oftargetgenes-(50) and the 3B showed the lowest value on target genes-(6). Asconclusion the developed pipeline was an efficient tool to detect miRNAproducing regions and explore putative target genes across the whole wheatgenome.