Sugarcane smut caused by Sporisorium scitamineum is a critical fungal disease in the sugarcane industry. However, molecular mechanistic studies of pathological response of sugarcane to S. scitamineum are scarce and preliminary. Here, transcriptome analysis of sugarcane disease induced by S. scitamineum at 24, 48 and 120 h was conducted, using an S. scitamineum-resistant and -susceptible genotype (Yacheng05-179 and “ROC”22). The reliability of Illumina data was confirmed by real-time quantitative PCR. In total, transcriptome sequencing of eight samples revealed gene annotations of 65,852 unigenes. Correlation analysis of differentially expressed genes indicated that after S. scitamineum infection, most differentially expressed genes and related metabolic pathways in both sugarcane genotypes were common, covering most biological activities. However, expression of resistance-associated genes in Yacheng05-179 (24–48 h) occurred earlier than those in “ROC”22 (48–120 h), and more transcript expressions were observed in the former, suggesting resistance specificity and early timing of these genes in non-affinity sugarcane and S. scitamineum interactions. Obtained unigenes were related to cellular components, molecular functions and biological processes. From these data, functional annotations associated with resistance were obtained, including signal transduction mechanisms, energy production and conversion, inorganic ion transport and metabolism, and defense mechanisms. Pathway enrichment analysis revealed that differentially expressed genes are involved in plant hormone signal transduction, flavonoid biosynthesis, plant-pathogen interaction, cell wall fortification pathway and other resistance-associated metabolic pathways. Disease inoculation experiments and the validation of in vitro antibacterial activity of the chitinase gene ScChi show that this sugarcane chitinase gene identified through RNA-Seq analysis is relevant to plant-pathogen interactions. In conclusion, expression data here represent the most comprehensive dataset available for sugarcane smut induced by S. scitamineum and will serve as a resource for finally unraveling the molecular mechanisms of sugarcane responses to S. scitamineum.

Heavy metals have been increasingly released into our environment. We present here, for the first time, the global industrial age production of Cd, Cu, Cr, Hg, Ni, Pb, and Zn, and their potential accumulation and environmental effects in the pedosphere. World soils have been seriously polluted by Pb and Cd and slightly by Zn. The potential industrial age anthropogenic Pb, Hg, and Cd inputs in the pedosphere are 9.6, 6.1, and 5.2 times those in the lithosphere, respectively. The potential anthropogenic heavy metal inputs in the pedosphere increased tremendously after the 1950s, especially for Cr and Ni. In 2000, the cumulative industrial age anthropogenic global production of Cd, Cr, Cu, Hg, Ni, Pb, and Zn was 1.1, 105, 451, 0.64, 36, 235, and 354 million tonnes, respectively. The global industrial age metal burdens per capita (in 2000) were 0.18, 17.3, 74.2, 0.10, 5.9, 38.6, and 58.2 kg for Cd, Cr, Cu, Hg, Ni, Pb, and Zn, respectively. Acidification may increase the bioavailability and toxicity of heavy metals in the pedosphere. The improvement of industrial processing technology reducing the metal dispersion rate, the recycling of metal-containing outdated products, by-products and wastes, and the development of new substitute materials for heavy metals are possible strategies to minimize the effects of heavy metals on our environment.

BackgroundSugarcane smut can cause losses in cane yield and sugar content that range from 30% to total crop failure. Losses tend to increase with the passage of years. Sporisorium scitamineum is the fungus that causes sugarcane smut. This fungus has the potential to infect all sugarcane species unless a species is resistant to biotrophic fungal pathogens. However, it remains unclear how the fungus breaks through the cell walls of sugarcane and causes the formation of black or gray whip-like structures on the sugarcane plants.ResultsHere, we report the first high-quality genome sequence of S. scitamineum assembled de novo with a contig N50 of 41 kb, a scaffold N50 of 884 kb and genome size 19.8 Mb, containing an estimated 6,636 genes. This phytopathogen can utilize a wide range of carbon and nitrogen sources. A reduced set of genes encoding plant cell wall hydrolytic enzymes leads to its biotrophic lifestyle, in which damage to the host should be minimized. As a bipolar mating fungus, a and b loci are linked and the mating-type locus segregates as a single locus. The S. scitamineum genome has only 6 G protein-coupled receptors (GPCRs) grouped into five classes, which are responsible for transducing extracellular signals into intracellular responses, however, the genome is without any PTH11-like GPCR. There are 192 virulence associated genes in the genome of S. scitamineum, among which 31 expressed in all the stages, which mainly encode for energy metabolism and redox of short-chain compound related enzymes. Sixty-eight candidates for secreted effector proteins (CSEPs) were found in the genome of S. scitamineum, and 32 of them expressed in the different stages of sugarcane infection, which are probably involved in infection and/or triggering defense responses. There are two non-ribosomal peptide synthetase (NRPS) gene clusters that are involved in the generation of ferrichrome and ferrichrome A, while the terpenes gene cluster is composed of three unknown function genes and seven biosynthesis related genes.ConclusionsAs a destructive pathogen to sugar industry, the S. scitamineum genome will facilitate future research on the genomic basis and the pathogenic mechanisms of sugarcane smut.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-996) contains supplementary material, which is available to authorized users.

Catalase is an iron porphyrin enzyme, which serves as an efficient scavenger of reactive oxygen species (ROS) to avoid oxidative damage. In sugarcane, the enzymatic activity of catalase in a variety (Yacheng05–179) resistant to the smut pathogen Sporisorium scitamineum was always higher than that of the susceptible variety (Liucheng03–182), suggesting that catalase activity may have a positive correlation with smut resistance in sugarcane. To understand the function of catalase at the molecular level, a cDNA sequence of ScCAT1 (GenBank Accession No. KF664183), was isolated from sugarcane infected by S. scitamineum. ScCAT1 was predicted to encode 492 amino acid residues, and its deduced amino acid sequence shared a high degree of homology with other plant catalases. Enhanced growth of ScCAT1 in recombinant Escherichia coli Rosetta cells under the stresses of CuCl2, CdCl2 and NaCl indicated its high tolerance. Q-PCR results showed that ScCAT1 was expressed at relatively high levels in the bud, whereas expression was moderate in stem epidermis and stem pith. Different kinds of stresses, including S. scitamineum challenge, plant hormones (SA, MeJA and ABA) treatments, oxidative (H2O2) stress, heavy metal (CuCl2) and hyper-osmotic (PEG and NaCl) stresses, triggered a significant induction of ScCAT1. The ScCAT1 protein appeared to localize in plasma membrane and cytoplasm. Furthermore, histochemical assays using DAB and trypan blue staining, as well as conductivity measurement, indicated that ScCAT1 may confer the sugarcane immunity. In conclusion, the positive response of ScCAT1 to biotic and abiotic stresses suggests that ScCAT1 is involved in protection of sugarcane against reactive oxidant-related environmental stimuli.

Summary• Brassica juncea is a potential candidate plant for phytoremediation of a number of heavy metals, but little is known about the phytotoxicity of chromium (Cr) for this plant in Cr(III)-and Cr(VI)-contaminated soils.• Chromium distribution and phytotoxicity at the whole plant and cellular levels were studied using chemical, light microscopy, scanning electron microscopy and transmission electron microscopy analyses.• Bioavailability of Cr in soils was low, but the uptake significantly increased at phytotoxic levels. Chromium from Cr(VI)-contaminated soils was more phytotoxic than from Cr(III)-contaminated soils. Chromium causes growth retardation, reduces the number of palisade and spongy parenchyma cells in leaves, results in clotted depositions in the vascular bundles of stems and roots, and increases the number of vacuoles and electron dense materials along the walls of xylem and phloem vessels.• Our results suggest that B. juncea is not a good candidate for phytoremediation of soils with lower Cr. However, it is able to accumulate significant amounts of Cr in both shoots and roots at higher soil-Cr concentrations despite severe phytotoxic symptoms.