Analysis and annotation of metabolic pathways and nutrient transporters in two non model plants

To grow properly, plants require inorganic nutrient that are taken up from the soil and become incorporated into a variety of important compounds with structural and physiological roles. Crop production is often limited by low phyto-availability of essential mineral elements and excessive concentrations of potentially toxic mineral elements. Nutrient uptake in the soil is achieved by cation exchange, where root hairs pump hydrogen ions (H+) into the soil through proton pumps. These hydrogen ions displace cations attached to negatively charged soil particles so that the cations are available for uptake by the root. Cross-talk at molecular level between plant nutrients, metabolic pathways and biological processes are not fully understood and transcriptomic analysis could be an effective tool to explain these links in plants whose genome is not already sequenced. In this work, 454 sequencing of Kalanchoe x houghtonii and Arundo donax transcriptomes allow identification of genes putative involved in nutrient uptake and metabolic pathways. Total RNA was isolated from K. x houghtonii leaves (K_L) and A. donax culms (A_C) and roots (A_R) by RNeasy Plant Mini kit (QIAGEN); about 25 ?g of RNA of each group were then prepared for cDNA normalization and library construction by Eurofins MWG Operon. Sequencing, performed on a Genome Sequencer GS FLX Titanium Instrument, generated a total of 593,130, 825,369 and 776,467 raw reads for K_L, A_C and A_R respectively. After trimming of adaptor and low quality base, 454 reads were independently assembled with MIRA for K. x houghtoni and with CLC genomics workbench for A. donax obtaining 138,816, 164,248 and 146,278 unigenes for K_L, A_C and A_R respectively. Annotation of unigenes with Blast2GO assigned GO term to 48,788, 72,170 and 62,157 unigenes and Enzyme Commission number (EC number) to 10,027, 23,032 and 20,211 for K_L, C_L and R_L respectively. This annotation permitted to relate gene function to Kyoto Encyclopedia of Gene and Genome (KEGG) pathways database. In detail, for nitrogen metabolism (map00910) putative orthologous were identified for 13, 16 and 13 different enzyme, while for sulfur metabolism (map00920) 13, 16 and 17 different enzyme for K_L, A_C and A_R respectively. Moreover some unigenes (2 in K_L, 5 in A_C and 16 in A_R) were annotated as orthologs of silicon transporters.