RNA-Seq: Yellow Nutsedge (Cyperus esculentus) transcriptome analysis of lipid-accumulating tubers from early to late developmental stages

Abstract: Thanks to high amounts of starch and oil amassed in the parenchyma of its tubers, yellow nutsedge (Cyperus esculentus) stands as a unique plant species with regards to nutrient biosynthesis and accumulation in underground organs. In the last decades, understanding of enzymatic processes in lipid, starch and sugar pathways underwent great improvements. Nevertheless, the underlying mechanisms of carbon allocation in sink tissues are still obscure, and insights may be rendered through the study of yellow nutsedge. Furthermore, in the global context of a still rising need for vegetable oils, Cyperus esculentus appears as a promising candidate for the introduction of novel high-yield oil species. Here is presented the first in-depth analysis of the yellow nutsedge tuber transcriptome, which was conducted using Roche 454 sequencing and targeted two developmental stages, coinciding with (i) the beginning of oil accumulation, but also (ii) an important increase of starch content, and finally (iii) a substantial drop in sugar amount. Denovo assembly led to a reference transcriptome of 37k transcripts, which underwent extensive functional and biological pathway annotation, leaving only 7 % of completely unknown sequences. A set of 186 differentially expressed genes (DEGs) was cross-confirmed by three different R packages. To cover the most important changes, top-30 rankings of up and down-regulated genes were investigated. Except a pronounced up-regulation of the WRI1 transcription factor (27-fold), no enzyme related to lipid, starch or sugar was found. Instead, massive changes in growth activity and stress response were observed. Analysis of expression at individual stages showed that several lipid, sugar and starch genes are actually abundant but would undergo changes of lower intensities, hence not visible in the top-30s. A private and user-friendly web-interface has been developed and compiles all the data and results generated through this study, providing with a convenient access for additional investigations, along with directives for further work.