The development of inexpensive and highly productive biomass sources of biofuel is a priority in global climate change biology. Arundo donax, also known as the giant reed, is recognized as one of the most promising nonfood bioenergy crops in Europe. Despite its relevance, to date no genomic resources are available to support the characterization of the developmental, adaptive and metabolic traits underlying the high productivity of this nonmodel species. We hereby present the first report on the de novo assembly of bud, culm, leaf and root transcriptomes of A. donax, which can be accessed through a customized BLAST server (http://ecogenomics.fmach.it/arundo/) for mining and exploring the genetic potential of this species. Based on functional annotation and homology comparison to 19 prospective biofuel Poaceae species, we provide the first genomic view of this so far unexplored crop and indicate the model species with highest potential for comparative genomics approaches. The analysis of the transcriptome reveals strong differences in the enrichment of the Gene Ontology categories and the relative expression among different organs, which can guide future efforts for functional genomics or genetic improvement of A. donax. A set of homologs to key genes involved in lignin, cellulose, starch, lipid metabolism and in the domestication of other crops is discussed to provide a platform for possible enhancement of productivity and saccharification efficiency in A. donax.

In order to understand plant/pathogen interaction, the transcriptome of uninfected (1S) and infected (2I) plant was sequenced at 3’end by the GS FLX 454 platform. De novo assembly of high-quality reads generated 27,231 contigs leaving 37,191 singletons in the 1S and 38,393 in the 2I libraries. ESTcalc tool suggested that 71% of the transcriptome had been captured, with 99% of the genes present being represented by at least one read. Unigene annotation showed that 50.5% of the predicted translation products shared significant homology with protein sequences in GenBank. In all 253 differential transcript abundance (DTAs) were in higher abundance and 52 in lower abundance in the 2I library. 128 higher abundance DTA genes were of fungal origin and 49 were clearly plant sequences. A tBLASTn-based search of the sequences using as query the full length predicted polypeptide product of 50 R genes identified 16 R gene products. Only one R gene (PGIP) was up-regulated. The response of the plant to fungal invasion included the up-regulation of several pathogenesis related protein (PR) genes involved in JA signaling and other genes associated with defense response and down regulation of cell wall associated genes, non-race-specific disease resistance1 (NDR1) and other genes like myb, presqualene diphosphate phosphatase (PSDPase), a UDP-glycosyltransferase 74E2-like (UGT). The DTA genes identified here should provide a basis for understanding the A. coronaria/T. discolor interaction and leads for biotechnology-based disease resistance breeding.

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