Building The Sugarcane Genome For Biotechnology And Identifying Evolutionary Trends

Background: Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.Results: Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. 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Characterization of the superoxide dismutase gene family in seeds of two Ricinus communis L. genotypes submitted to germination under water restriction conditions

Abiotic stresses are the most important environmental factors that negatively affects crop production worldwide, whereas germination is the most critical phase in the plants life cycle. Water availability is essential for proper seed imbibition and vigorous germination and often scarce for Ricinus communis (castor bean) cultivated in semiarid regions of Brazil. Water restriction generally leads to the generation of reactive oxygen species (ROS) and one of the major families of enzymes that counteract ROS are superoxide dismutases (SODs). The objective of this study was to identify and characterize the SOD gene family of R. communis by phylogenetic, biochemical and gene expression analysis and link it to the effect of osmoconditioning on seed vigor. We characterized the effect of osmotic conditioning treatments of seeds of two contrasting R. communis cultivars, EBDA MPA34 and PARAGUAÇU, on germination performance. We also searched the R. communis genome for SOD genes and analyzed them phylogenetically and evaluated their activity and expression in embryos of seeds imbibed under different PEG concentrations (water restriction stress). We could show that some of these treatments improved germinability and vigor of seeds and seedlings in a cultivar-dependent manner. Additionally, R. communis seeds turned out to be very sensitive to the inhibition of germination by osmotic stress even at relative low concentrations. Eight SOD genes were found in the R. communis genome and classified based on phylogenetic analysis, protein domains and prediction of subcellular localization. SOD gene expression was mostly induced during seed imbibition, although their expression was generally inhibited in osmotic potentials below −0.6 MPa and showed partly different gene expression profiles between contrasting cultivars. Cv. PARAGUAÇU showed increased seed vigor after osmoconditioning as compared to cv. EBDA MPA34 which could be related to higher responses of some cv. PARAGUAÇU SOD genes to stress. Our results indicate that SOD genes might be of special interest for R. communis genetic engineering aimed at the increase of production in semiarid regions.</p