Una novedosa pipeline bioinformática para el análisis de transcriptomas de novo: aplicación en Nothofagus pumilio

ESTRAVIS-BARCALÁ, M; ARANA, MV; MARCHELLI, P; HEER, K; ZIEGENHAGEN, B; BELLORA, N

Simposio; Simposio de Genómica Funcional de Plantas; 2017

Nothofagus pumilio (common name: Lenga) is the most abundant treespecies of the template Patagonian forest, the southernmost woody ecosystem onEarth. Despite its ecological and economical importance, physiological andmolecular studies in N. pumilio are scarce, and the genomic resourcesfor the whole genus are very limited (only a partial draft transcriptome for N.nervosa, a related species). Given our interest in the overall effect ofhigh temperatures in N. pumilio?s physiology in a context of climatechange, we performed NGS on leaf poly-A-selected RNA from plants exposed tocontrasting temperatures (20° and 34°C) in a growth chamber controlledenvironment. Two biological replicates from independent experiments weresequenced for each temperature. The non-model nature of this species implied a denovo assembly and all downstream analysis with no reference genome. In thistalk we present some problems of great interest to the non-model plant speciescommunity and how we managed to overcome them with a hands-on programmingapproach. We will show an original bioinformatic pipeline that integrates denovo transcriptome assembly and transcriptome mapping, with both standardand new tools developed in our lab aimed to solve basic problems faced byworking without a reference genome, such as mis-assembled contigs, sequenceredundancy and strand specificity. Besides, this pipeline allows the annotationagainst a custom database (in our case, 12 broad-leaf tree transcriptomes froman open-access website, http://www.hardwoodgenomics.org/). Finally, we will showdifferential expression and transcriptome-based phylogeny results using ourcorrected transcriptome.