Transcriptomics of Arundo donax: a promising biomass and bioenergy species.
Arundo donax reference transcriptome: Global warming, high energy demands and dwindling fossil energy reserves are presenting the urgent need to improve sustainable sources of renewable energy. Lignocellulosic biomass derived from non-food bioenergy crops is an attractive source of renewable energy because it can be efficiently converted into ethanol and stored. This, in turn, allows a steady supply of energy which can stabilize energy grids with increasingly large shares of renewable energy from intrinsically discontinuous aeolic and photovoltaic sources. Perennial rhizomatous grasses have been widely indicated as the most promising non-food bioenergy crops, as they have high yields, extended growth seasons, low input requirements, and good resistance to both biotic and abiotic stresses. In addition, they can be grown in marginal soils, thus reducing the land competition with food-crops. Arundo donax L., also known as the giant reed, is recognized as one of the most promising non-food bioenergy crops in regions with Mediterranean climates, where, however, if not autochthonous, it can become invasive. To further our understanding of the mechanisms underlying the extreme adaptability and robustness of this poorly studied non-model species, we carried out the RNA-Seq characterization of A. donax bud, culm, leaf and root transcriptomes to provide the first reference transcriptome for this species (Sablok et al. 2014) . We additionally carried the analysis of whole root and shoot transcriptomes of young A. donax plants subjected to two different leveals of water stress and compared them to the transcriptome of unstressed plants (Fu et al. 2016).
We provide to the scientific community a web-server to search for homologs of known genes in:
(1) A. donax first reference transcriptome assembly (bud, culm, leaf and root)
(2) A. donax first water-stressed transcriptome assembly (leaf and root)
The web-server is available at: Arundo Web BLAST server
References: If you use this server for academic use, please cite
Sablok, G., Fu, Y., Bobbio, V., Laura, M., Rotino, G.L., Bagnaresi, P., Allavena, A., Velikova, V., Viola, R., Loreto, F., Li, M. and Varotto, C. (2014) Fuelling genetic and metabolic exploration of C3 bioenergy crops through the first reference transcriptome of Arundo donax L. Plant Biotechnol. J., 12(5):554–567. doi: 10.1111/pbi.12159
Fu, Y., Poli, M., Sablok, G., Wang, B., Liang, Y., La Porta, N., Velikova, V., Loreto, F., Li, M., Varotto, C. (2016) Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-Seq. 9: 54. Biotechnol Biofuels, 9:54. doi: 10.1186/s13068-016-0471-8
Priyam, A., Woodcroft, B.J., Rai, V., Munagala, A., Moghul, I., Ter, F., Gibbins, M.A., Moon, H., Leonard, G., Rumpf, W. and Wurm, Y. (2015) Sequenceserver: a modern graphical user interface for custom BLAST databases. biorxiv doi: 10.1101/033142.
Contact: If you are facing problems in using the server, please contact: Claudio Varotto, firstname.lastname@example.org
Important Note for Server Access: In case of problems to access the server, first please ask your system administrator or firewall manager to open the 4567 port and after that re-access the BLAST server. Thanks!