Project description:Following a request from the European Commission, the EFSA Panel on Plant Health performed a pest categorisation of Coniferiporia sulphurascens and Coniferiporia weirii, two well-defined and distinguishable fungal species of the family Hymenochaetaceae. The pathogens are regulated in Council Directive 2000/29/EC (Annex IAI, under the previous name Inonotus weirii for both species) as a harmful organism whose introduction into the EU is banned. The two pathogens are native to North America, where C. sulphurascens causes laminated root rot primarily in Douglas fir (Pseudotsuga menziesii) and grand fir (Abies grandis), while C. weirii causes cedar laminated root and butt rot mainly in cedars (Thuja plicata and Cupressus nootkatensis). C. weirii has been reported from Japan and China, and C. sulphurascens from China, Russia and Turkey. Neither species has been reported from the EU. C. sulphurascens may infect all conifers, while C. weirii is reported to mainly cause disease in tree species of Thuja spp. and Cupressus spp. The two pathogens could enter the EU mainly via wood with bark, isolated bark and plants for planting (including artificially dwarfed plants) of Pinaceae and Cupressaceae. Both fungi could establish in the EU, as hosts are present and climatic conditions are favourable. The two pathogens would be able to spread following establishment by the pathways mentioned for entry and also by dissemination of basidiospores and root contact with infected root/wood. Should the pathogen be introduced in the EU, impacts can be expected on coniferous woodlands, plantations and ornamental trees, thus leading to reduced tree growth and ecosystem service provision. The key uncertainties concern (i) the distribution of the two pathogens in Asia, (ii) the level of susceptibility of conifers native to Europe and (iii) the role of plants for planting as a pathway of entry and spread. For both pathogens, the criteria assessed by the Panel for consideration as a potential quarantine pest are met. As the two pests are not present in the EU, not all the criteria for consideration as regulated non-quarantine pests are met.

Project description:Alfalfa, [Medicago sativa (L.) sativa], a widely-grown perennial forage has potential for development as a cellulosic ethanol feedstock. The application of genomic approaches would advance development of alfalfa as a cellulosic feedstock. However, the genomics of alfalfa, a non-model species, is still in its infancy. The recent advent of RNA-Seq, a massively parallel sequencing method for transcriptome analysis, provides an opportunity to expand the identification of alfalfa genes and polymorphisms, and conduct in-depth transcript profiling. Cell walls in stems of alfalfa genotype 708 have higher cellulose and lower lignin concentrations compared to cell walls in stems of genotype 773. Using the Illumina GA-II platform, a total of 198,861,304 expression sequence tags (ESTs, 76 bp in length) were generated from cDNA libraries derived from elongating stem (ES) and post-elongation stem (PES) internodes of 708 and 773. These ESTs were de novo assembled into 132,153 unique sequences. By combining the de novo assembled ESTs (132,153 sequences) with our previously identified EST sequences (341,984 sequences, unpublished data), and the ESTs available from GenBank (12,371 sequences), we built the first Alfalfa Gene Index (MSGI 1.0). MSGI 1.0 contains 124,025 unique sequences including 22,729 tentative consensus sequences (TCs), 22,315 singletons and 78,981 pseudo-singletons. We identified a total of 1, 294 simple sequence repeats (SSR) among the sequences in MSGI 1.0. In addition, a total of 10,826 single nucleotide polymorphisms (SNPs) were predicted between the two genotypes. Transcript profiling of stem internodes of genotypes 708 and 773 was conducted by quantifying the number of Illumina EST reads that were mapped to sequences in MSGI 1.0. We identified numerous candidate genes that may play a role in stem development as well as candidate genes that may contribute to the differences in cell wall composition in stems of the two genotypes. Our results demonstrate that RNA-Seq can be successfully used for gene identification, polymorphism detection and transcript profiling in alfalfa, a non-model, allogamous, autotetraploid species. The alfalfa gene index (MSGI 1.0) assembled in this study, and the SNPs, SSRs and candidate genes identified can be used to improve alfalfa as a cellulosic feedstock.

Project description:Alfalfa, [Medicago sativa (L.) sativa], a widely-grown perennial forage has potential for development as a cellulosic ethanol feedstock. The application of genomic approaches would advance development of alfalfa as a cellulosic feedstock. However, the genomics of alfalfa, a non-model species, is still in its infancy. The recent advent of RNA-Seq, a massively parallel sequencing method for transcriptome analysis, provides an opportunity to expand the identification of alfalfa genes and polymorphisms, and conduct in-depth transcript profiling. Cell walls in stems of alfalfa genotype 708 have higher cellulose and lower lignin concentrations compared to cell walls in stems of genotype 773. Using the Illumina GA-II platform, a total of 198,861,304 expression sequence tags (ESTs, 76 bp in length) were generated from cDNA libraries derived from elongating stem (ES) and post-elongation stem (PES) internodes of 708 and 773. These ESTs were de novo assembled into 132,153 unique sequences. By combining the de novo assembled ESTs (132,153 sequences) with our previously identified EST sequences (341,984 sequences, unpublished data), and the ESTs available from GenBank (12,371 sequences), we built the first Alfalfa Gene Index (MSGI 1.0). MSGI 1.0 contains 124,025 unique sequences including 22,729 tentative consensus sequences (TCs), 22,315 singletons and 78,981 pseudo-singletons. We identified a total of 1, 294 simple sequence repeats (SSR) among the sequences in MSGI 1.0. In addition, a total of 10,826 single nucleotide polymorphisms (SNPs) were predicted between the two genotypes. Transcript profiling of stem internodes of genotypes 708 and 773 was conducted by quantifying the number of Illumina EST reads that were mapped to sequences in MSGI 1.0. We identified numerous candidate genes that may play a role in stem development as well as candidate genes that may contribute to the differences in cell wall composition in stems of the two genotypes. Our results demonstrate that RNA-Seq can be successfully used for gene identification, polymorphism detection and transcript profiling in alfalfa, a non-model, allogamous, autotetraploid species. The alfalfa gene index (MSGI 1.0) assembled in this study, and the SNPs, SSRs and candidate genes identified can be used to improve alfalfa as a cellulosic feedstock. Examination of 2 different tissue types at different developmental stages (Elongating vs. post-elongation stem internodes) in two alfalfa genotypes (708 and 773) with divergent cell wall composition in stems.

Project description:The aim of this experiment was to compare the transciptome of the fall armyworm (Spodoptera frugiperda) strain SUS (a laboratory insecticide-susceptible standard) with organophosphate (OP) and pyrethroid (PYR) resistant strains were collected in cornfields located in Minas Gerais and Mato Grosso States, Brazil, in 2008 and maintained in the laboratory under selection with chlorpyrifos (at increasing discriminating doses from 100 up to 400 M-BM-5g of insecticide/g of insect in a topical bioassay) or lambda-cyhalothrin (from 8.4 up to 27 M-BM-5g of insecticide/g of insect) respectively The custom microarray used in this study was designed using the Agilent eArray platform (Agilent Technologies). A SurePrint HD (8M-CM-^W15k) expression array was designed using the base composition and the best probe methodologies to design sense orientation 60-mer probes with a 3M-bM-^@M-2 bias. The FAW EST database (SPODOBASE) was used as the reference transcriptome (Negre, Hotelier et al. 2006). These sequences are derived from 8 cDNA libraries as follows: Sf1F: Fat body, Sf1H: Hemocyte, Sf1M: Midgut, Sf1P: Pool of various tissues, Sf2H: Immune Challenged hemocytes, Sf2L: Sf21 Cell lines sequences, Sf2M: Xenobiotic Induced Midgut and Sf9L: Sf9 cell lines sequences. All assembled contigs and singlets were kindly sent by the website maintainers. The BLAST2GO software v.2.3.1 (http://www.blast2go.org) was used to annotate the EST database. 60-mer probes were designed for all 7,552 assembled contigs and 5,519 annotated singlets (BlastX), totaling 13,071 sequences. For contigs encoding detoxification enzymes (P450s, GSTs and CEs) three probes were designed. Additional probe groups for 15 control genes were also included. For reference all sequences are included in the zip file with array data. References: Negre, V., T. Hotelier, et al. (2006). "SPODOBASE : an EST database for the lepidopteran crop pest Spodoptera." BMC Bioinformatics 7: 322. Two-condition experiment. Slide 1: SUS vs. OP S. fugiperda strains. Slide 2: SUS vs. PYR S. fugiperda strains. Biological replicates: 4 pools of RNA extracted from four pools of 5 second instar larvae. Technical Replicates: None, the biological replicates incorporated a dye swap. Total replication: four replicates for each strain.

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Coniferiporia sulphurascens

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