EST-database search of plant defensins - an example using sugarcane, a large and complex genome.

EST (Expressed Sequence Tags) databases are increasing in number and size, especially regarding cultivated plants. Sugarcane is one of the most important tropical and subtropical crops, presenting a complex polyploid genome of hybrid origin, bearing a challenge for the understanding of genetic processes in higher plants. In the present work a general search was carried out on the largest Sugarcane EST Database (SUCEST) that includes 237,954 ESTs aiming to identify defensin antimicrobial peptides - a class of small, basic, cysteine-rich peptides distributed throughout the kingdoms. Using a computational approach 17 new defensin isoforms could be identified. Main steps for the search, characterization and evaluation of the defensin expression profile are presented. Prevalent expression tissues were leaf roll, lateral bark, root apex, base of inflorescence, developing seed, and calli. Bioinformatics and phylogenetic analysis of the primary structure of the sugarcane defensin candidates as well as the 3D structures obtained by comparative modeling support their role as antimicrobials.

Abundance and diversity of resistance genes in the sugarcane transcriptome revealed by in silico analysis.

Resistance genes (R-genes) are responsible for the first interaction of the plant with pathogens being responsible for the activation (or not) of the defense response. Despite their importance and abundance, no tools for their automatic annotation are available yet. The present study analyzed R-genes in the sugarcane expressed sequence tags database which includes 26 libraries of different tissues and development stages comprising 237,954 expressed sequence tags. A new annotation routine was used in order to avoid redundancies and overestimation of R-gene number, common mistakes in previous evaluations. After in silico screening, 280 R-genes were identified, with 196 bearing the complete domains expected. Regarding the alignments, most of the sugarcane's clusters yielded best matches with proteins from Oryza sativa, probably due to the prevalence of sequences of this monocot in data banks. All R-gene classes were found except the subclass LRR-NBS-TIR (leucine-rich repeats, nucleotide-binding site, including Toll interleukin-1 receptors), with prevalence of the kinase (Pto-like) class. R-genes were expressed in all libraries, but flowers, transition root to shoot, and roots were the most representative, suggesting that in sugarcane the expression of R-genes in non-induced conditions prevails in these tissues. In leaves, only low level of expression was found for some gene classes, while others were completely absent. A high allelic diversity was found in all classes of R-genes, sometimes showing best alignments with dicotyledons, despite the great number of genes from rice, maize and other grasses deposited in data banks. The results and future possibilities regarding R-genes in sugarcane research and breeding are further discussed.

Abundance and diversity of resistance genes in the sugarcane transcriptome revealed by in silico analysis

Resistance genes (R-genes) are responsible for the first interaction of the plant with pathogens being responsible for the activation (or not) of the defense response. Despite their importance and abundance, no tools for their automatic annotation are available yet. The present study analyzed R-genes in the sugarcane expressed sequence tags database which includes 26 libraries of different tissues and development stages comprising 237,954 expressed sequence tags. A new annotation routine was used in order to avoid redundancies and overestimation of R-gene number, common mistakes in previous evaluations. After in silico screening, 280 R-genes were identified, with 196 bearing the complete domains expected. Regarding the alignments, most of the sugarcane’s clusters yielded best matches with proteins from Oryza sativa, probably due to the prevalence of sequences of this monocot in data banks. All R-gene classes were found except the subclass LRR-NBS-TIR (leucine-rich repeats, nucleotide-binding site, including Toll interleukin-1 receptors), with prevalence of the kinase (Pto-like) class. R-genes were expressed in all libraries, but flowers, transition root to shoot, and roots were the most representative, suggesting that in sugarcane the expression of R-genes in non-induced conditions prevails in these tissues. In leaves, only low level of expression was found for some gene classes, while others were completely absent. A high allelic diversity was found in all classes of R-genes, sometimes showing best alignments with dicotyledons, despite the great number of genes from rice, maize and other grasses deposited in data banks. The results and future possibilities regarding R-genes in sugarcane research and breeding are further discussed.