Coupled transcriptomics and metabolomics to generate pathway predictions.

<p>The top panels (A–D) represent the algorithm schema and the bottom panels (E–H) represent the corresponding steps with data for an example pathway, C8 production. Cyan, green, and purple are used to denote different experimental conditions (1, 2, and 3 and CB, PD4, and PD14 for the schematic and the C8 pathway data, respectively). GC/MS total ion chromatograms (orange box, A & E) are used to generate compound co-occurrence profiles (red box, B & F). These compound co-occurrence profiles are used to group and order the compounds based on patterns of correlation and anti-correlation to build a possible biosynthetic pathway (brown box C & G). Genes for which the expression profile matches the compound profile are considered correlated and therefore likely candidates for the biosynthetic pathway of interest (gray box D & H). Retrosynthesis is then used to match correlated genes with a reaction in the pathway, represented by roman numerals denoted on pathway arrows (brown box, C&G).</p

Analysis of cellulose-related expression.

<p><i>A. sarcoides</i> transcription was profiled when grown on potato-dextrose media for 4 days (PD4), cellulose (CELL) and cellobiose (CB). (A) The total number of genes with quantile normalized log₂(RPKM) greater than 2 was computed for each condition. The venn diagram shows the overlap of these genes across the three conditions. (B) Genes were partitioned according to their homology to the four main CAZY families: Glycoside Hydrolase (GH), Glucosyl Transferase (GT), Carbohydrate Esterase (CE), Carbohydrate Binding Modules (CBM). The homologs were then filtered to include only those genes which showed a standard deviation across the three conditions greater than 0.5. Each family was separately clustered (hierarchical, Euclidean distance, single linkage). The colorbar represents the quantile normalized log₂ (RPKM) value from white (low expression) to dark blue (high expression). Note: CBM can co-occur with all families. Only those genes that had exclusively a CBM domain were clustered in the CBM matrix to avoid duplication. (C) A table of the most highly expressed genes includes genes not directly involved in degradation, such as swollenin and chitin synthase (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002558#s2" target="_blank">Results</a> for more details).</p

Compound gene co-expression profiles.

<p>Each plot shows the quantile-normalized log₂ (RPKM) for each set of genes of co-expressed with a particular compound profile (green 001, red 010, blue 100, cyan 101, purple 110, and black 111) across all 6 conditions (CB, PD4, PD14, AMM, CELL, and OAC). The first three conditions (CB, PD4, and PD14) represent the conditions where the compounds analyzed in this study were detected. The remaining conditions serve as the nulls (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002558#pgen.1002558.s030" target="_blank">Text S1f</a>or details). Within the plots, each line corresponds to a single gene.</p

Genomic Analysis of the Necrotrophic Fungal Pathogens <i>Sclerotinia sclerotiorum</i> and <i>Botrytis cinerea</i>

<div><p><i>Sclerotinia sclerotiorum</i> and <i>Botrytis cinerea</i> are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of <i>S. sclerotiorum</i> and two strains of <i>B. cinerea</i>. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the <i>S. sclerotiorum</i> assembly to 16 chromosomes and found large-scale co-linearity with the <i>B. cinerea</i> genomes. Seven percent of the <i>S. sclerotiorum</i> genome comprises transposable elements compared to <1% of <i>B. cinerea</i>. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of <i>B. cinerea</i>–specific secondary metabolites relative to <i>S. sclerotiorum</i>. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between <i>S. sclerotiorum</i> and <i>B. cinerea</i>. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.</p></div