Bradford Condon

University of Tennessee | UTK

Adaptive radiations fuel speciation and are characterized by rapid genetic diversification and expansion into new ecological niches. Historically, these processes were believed to be driven by selection on novel mutations but genomic analyses now indicate that standing variation and gene flow often have prominent roles. How “old” variation is combi...

Online biological databases housing genomics, genetic and breeding data can be constructed using the Tripal toolkit. Tripal is an open-source, internationally developed framework that implements FAIR data principles and is meant to ease the burden of constructing such websites for research communities. Use of a common, open framework improves the s...

Despite tremendous advancements in high throughput sequencing, the vast majority of tree genomes, and in particular, forest trees, remain elusive. Although primary databases store genetic resources for just over 2,000 forest tree species, these are largely focused on sequence storage, basic genome assemblies, and functional assignment through exist...

The scientists that study and work to improve forest health need information on where pests and diseases are spreading, as well as where healthy, resilient trees remain. TreeSnap is a citizen science project and mobile app created to meet this need by enabling citizens to easily submit global positioning system (GPS) locations, photos, and observat...

Community biological databases provide an important online resource for both public and private data, analysis tools and community engagement. These sites house genomic, transcriptomic, genetic, breeding and ancillary data for specific species, families or clades. Due to the complexity and increasing quantities of these data, construction of online...

Tripal is an open-source, resource-efficient toolkit for construction of genomic, genetic and breeding databases. It facilitates development of biological websites by providing tools to integrate and display biological data using the generic database schema, Chado, together with Drupal, a popular website creation and content management system. Trip...

Tripal community database construction toolkit utilizing the content management system Drupal. Tripal is used to make biological, genetic and genomic data more discoverable, shareable, searchable and standardized. As funding for community-level genomics databases declines, Tripal’s open-source codebase provides a means for sites to be built and mai...

The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require datamanagement plans for publicly funded research. Furthermore, the value of data increases exponentially when they are pr...

Tripal is an open-source biological community database construction toolkit utilizing the content management system Drupal. Tripal is used to make biological, genetic and genomic data more discoverable, shareable, searchable, and standardized. As funding for community level genomics databases declines, Tripal's open source codebase provides a means...

The Southern Corn Leaf Blight epidemic of 1970 devastated fields of T-cytoplasm corn planted in monoculture throughout the eastern US. The epidemic was driven by race T, a previously unseen race of Cochliobolus heterostrophus. A second fungus, Phyllosticta zeae-maydis, with the same biological specificity, appeared coincidentally. Race T produces T...

Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multihost pathogen that infects multiple grasses and cereals, is responsible for the...

Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity, and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multi-host pathogen that infects multiple grasses and cereals, is responsible for t...

The sfp-type 4'-phosphopantetheinyl transferase Ppt1 is required for activation of nonribosomal peptide synthetases, including α-aminoadipate reductase (AAR)for lysine biosynthesis, and polyketide synthases, enzymes that biosynthesize peptide and polyketide secondary metabolites, respectively. Deletion of the PPT1 gene, from the maize pathogen, Coc...

Cochliobolus is a young genus, in the class Dothideomycetes, which includes closely related plant pathogenic and saprophytic fungal species. In this review, genome similarities and differences among sequenced Cochliobolus pathogens that cause different diseases on different hosts are detailed. Gene content and genome organization are highly similar...

Background Cochliobolus heterostrophus is a dothideomycete that causes Southern Corn Leaf Blight disease. There are two races, race O and race T that differ by the absence (race O) and presence (race T) of ~ 1.2-Mb of DNA encoding genes responsible for the production of T-toxin, which makes race T much more virulent than race O. The presence of rep...

Iron is an essential nutrient and prudent iron acquisition and management are key traits of a successful pathogen. Fungi use nonribosomally synthesized secreted iron chelators (siderophores) or Reductive Iron Assimilation (RIA) mechanisms to acquire iron in a high affinity manner. Previous studies with the maize pathogen, Cochliobolus heterostrophu...

The gene SRE1, encoding the GATA transcription factor, Sre1 (siderophore biosynthesis repressor) was identified in the genome of the maize pathogen, Cochliobolus heterostrophus, and deleted. Mutants were altered in sensitivity to iron, oxidative stress, and virulence to the host. To gain insight into mechanisms of this combined regulation, genetic...

Cochliobolus heterostrophus is a foliar pathogen of maize, causing Southern Corn Leaf Blight. It is a necrotrophic pathogen that causes lesions on leaves and other aboveground organs of the plant. If the host is sensitive to the polyketide T-toxin produced by the pathogen, symptoms are severe, as manifested in major crop loss in the early 1970s. Th...

[This corrects the article DOI: 10.1371/journal.ppat.1003037.].

Setosphaeria turcica, a hemibiotrophic pathogenic dothideomycete, is the causal agent of Northern Leaf Blight of maize which periodically causes significant yield losses worldwide. To explore molecular mechanisms of fungal pathogenicity and virulence to the host, an efficient targeted gene knockout transformation system using Agrobacterium tumefaci...

Author Summary The filamentous ascomycete genus Cochliobolus includes highly aggressive necrotrophic and hemibiotrophic pathogens with particular specificity to their host plants, often associated with production of host selective toxins (HST) that allow necrotrophs to trigger host cell death. Hemibiotrophs must keep their hosts alive during initia...

A C. heterostrophus dispensable chromosome is present in some but not all C. heterostrophus strains. Mauve alignment [44] of the genome of strains Hm540 and C5. Colored blocks [Locally Collinear Blocks (LCB)] indicate matches between genomes. Note there are only a few matches (colored blocks) in Hm540 to scaffold S16/chromosome B1 in C5. The C5 S16...

Analysis of the mating type region in Cochliobolus spp. and S. turcica. S. turcica 28A, C. sativus ND90Pr, C. carbonum 26-R-13, C. heterostrophus Hm540, and C. heterostrophus PR1x412, and the reference C. heterostrophus C5 strains are MAT1-1, while the others are MAT1-2. 10 kb regions flanking the MAT idiomorphs were aligned for each mating type. I...

Maximum likelihood tree of PKS ketosynthase (KS) domains identified using Augustus (A) and Genewise (B). RAxML using the WAGF model with a gamma distribution was used to infer the maximum likelihood tree and bootstrap support was determined using the fast-bootstrap method with 1000 bootstrap replicates. See Materials and Methods. Plain branches at...

Summary of repetitive elements identified in the unique region of isolate ND90Pr. (DOC)

Comparison of estimates for C. heterostrophus strain C5 chromosome sizes based on CHEF gel analysis and assembly size. (DOC)

RFLP map coordinates on the C5 assembly. (XLS)

Master NRPS AMP domain inventories. (XLS)

C. sativus SSR sequences anchor sequenced scaffolds to the genetic map. Genetic map of C. sativus based on 68 SSR markers, 102 amplified fragment length polymorphism (AFLP) markers, 34 RFLP markers, two polymerase chain reaction–amplified markers, the mating type locus (CsMAT), and the barley cultivar-specific virulence locus (VHv1). Of the 37 link...

Maximum likelihood tree of NRPS AMP-binding (AMP) domains identified using Augustus (A) and Genewise (B). RAxML using the RTREVF model with a gamma distribution was used to infer the maximum likelihood tree and bootstrap support was determined using the fast-bootstrap method with 1000 bootstrap replicates. See Materials and Methods. AMP domains are...

Quantification of spot blotch disease induced by the C. sativus wild type and mutant (Δ115356) on barley cv. Bowman. Disease rating was taken at 7 days after inoculation and is based on a 1 to 9 scale [118]. Four replicates were used. Error bar indicates the standard deviation. (PDF)

Quantitative real-time PCR analysis of S. turcica PKS gene (protein ID 161586) during infection of maize cultivar W64A-N. Gene expression was normalized based on the expression of the β-actin gene. Values are relative expression levels compared to that in mycelia grown on LCA medium. Samples were collected at 3, 5, 6, 7, and 8 days after inoculatio...

SNPs across species detected with Mummer. (XLS)

Genetic distance correlates with physical distance on the C. heterostrophus map. RFLP markers located on the same scaffold were used to plot genetic distance against physical distance. Genetic distances between RFLPs determined by Tzeng et al. [8]. (PDF)

MUMMER MAT alignments. (DOC)

Regions of low coverage of C5, by other sequences. (DOC)

Forty three predicted genes in the unique region of isolate ND90Pr associated with the virulence locus VHv1. (DOC)

Supplementary Methods. Mapping scaffolds onto the C. heterostrophus genetic map. Mapping scaffolds to the C. sativus genetic map. Mating type region comparisons. (DOCX)

Primers used in quantitative real time-PCR of C. sativus and S. turcica genes. (DOC)

Master SSP inventories and associated SNPs. (XLS)

Master PKS KS domain inventories. (XLS)

Gene counts of classes that have been implicated in plant pathogenesis. Gene counts in extant species (indicated right of the tree) and estimated gene counts in inferred last common ancestors (indicated on the tree nodes) are given. A. Genes encoding small secreted proteins. B. Genes encoding proteins involved in secondary metabolite production. C....

Principal component analysis and hierarchical clustering of lipase family assignments of 18 Dothideomycetes and outgroups. Colored squares represent the centroid of each cluster of species, indicated with the same color. Taxonomy: Ag., Agaricales; Cap., Capnodiales; Dia., Diaporthales; Hel., Helotiales; Hyp., Hypocreales; Hys., Hysteriales; Mag., M...

Annotations of the genes in the two syntenic blocks from Table S4. Each syntenic block contains 5 multi-gene families. (XLS)

Functional annotation terms that are over- or under-represented in genes that are part of an orthologous pair that is co-regulated in Mycosphaerella graminicola and Leptosphaeria maculans. See also Table S6. (XLS)

Functional annotation terms that are over- or under-represented in genes of which the product is not part of the core proteome. (XLS)

Multi-gene families that are expanded or depleted in the various comparisons in Table 3. In each comparison the organisms are marked as part of either the in-group or the out-group. Note that each comparison has its own tab. (XLS)

Predicted kinases in the genomes of the 18 Dothideomycetes and in those of the outgroups. For each kinase type in each genome, the absolute number is indicated, as well as the percentage of total kinases in that genome. CAMK (calmodulin-regulated kinases); CMGC family (cyclin-dependent kinases, mitogen-activated protein kinases, CDK-like kinases, a...

Statistics of predicted small secreted proteins (SSPs) in the genomes of the 18 Dothideomycetes and in those of the outgroups. (XLS)

Distribution of polyketide synthases across the 18 Dothideomycetes relative to the highly curated set in Cochliobolus heterostrophus set [40] . (XLS)

Predicted genes involved in secondary metabolism. Genomes of organisms belonging to the Pleosporales and Hysteriales generally contain more genes involved in this process than the Capnodiales, especially in the case of Polyketide synthase Type I. (TIFF)

Assembly and annotation statistics of the genomes of 18 Dothideomycetes described in this report. (XLS)

Two syntenic blocks of genes are identified in the genomes of the Dothideomycetes. Genes are located sequentially on the scaffolds. Each protein ID represents one predicted gene. The cluster ID represents the ID of the multi-gene family to which each gene belongs. Each gene that is part of a syntenic block has a syntenic ID. (XLS)

Syntenic blocks of genes are identified in the genomes of six Mycosphaerellaceae. Genes are located sequentially on the scaffolds. Each protein ID represents one predicted gene. The cluster ID represents the ID of the multi-gene family to which each gene belongs. Each gene that is part of a syntenic block has a syntenic ID. (XLS)

Functional annotation terms that are over- or under-represented in genes that are located in at least one syntenic block (described in Table S9). For each species the over-represented terms are indicated. (XLS)

Distribution of nonribosomal peptide synthetases across the 18 Dothideomycetes relative to the highly curated set in Cochliobolus heterostrophus set [39] . (XLS)

Presence of components of the repeat induced point mutations (RIP) and silencing machineries in the genomes of Dothideomycetes. All Dothideomycetes contain the same complement of components. For each component in each genome the protein ID of the best blastp hit and the corresponding E-value are indicated. In some cases the gene was missed during g...

Additional considerations concerning Dothideomycetes phylogeny and divergence time estimates. (DOC)

Ratio of predicted core and non-core proteins in the 18 genomes of Dothideomycetes . (TIFF)

Phylogeny and gene count of predicted casein kinase 1 (CK1) genes in the genomes of 18 Dothideomycetes . (TIFF)

Presence of aflatoxin-like genes in Dothideomycetes and other fungi. Aflatoxin-like genes were found using BLASTP (e-value of 10−5) of predicted amino acid sequences of Dothistroma septosporum dothistromin genes (main block of 14 Ds genes) or Aspergillus flavus sterigmatocystin (verA [aflN] and omtB [aflO]) or aflatoxin genes (omtA [aflP], ordA [af...

Distribution of peptidase families in Dothideomycetes and other fungal classes. Putative peptidases were classified based on the MEROPS database. A. Non-secreted and secreted peptidases. B. Secreted peptidases. Letters above columns indicate significant differences between peptidase content means as determined by a Tukey's HSD test after significan...

Orthologous pairs of genes between Mycosphaerella graminicola and Leptosphaeria maculans that are up- or down-regulated in both organisms when expression during relatively early infection is compared to expression relatively late in infection. Each row represents an orthologous pair of genes. The protein IDs, expression ratio, GO annotation and PFA...

Syntenic blocks of genes are identified in the genomes of eight Pleosporales. Genes are located sequentially on the scaffolds. Each protein ID represents one predicted gene. The cluster ID represents the ID of the multi-gene family to which each gene belongs. Each gene that is part of a syntenic block has a syntenic ID. (XLS)

Functional annotation terms that are over- or under-represented in genes that are located in at least one syntenic block (described in Table S8). For each species the over-represented terms are indicated. (XLS)

PFAM domains that are expanded or depleted in the various comparisons in Table 3. In each comparison the organisms are marked as part of either the in-group or the out-group. Note that each comparison has its own tab. (XLS)

Predicted genes involved in secondary metabolism. (XLS)

Individual carbohydrate-active enzyme (CAZyme) family counts in the genomes of 18 Dothideomycetes and the outgroups. (XLS)

Predicted peptidases in the genomes of 18 Dothideomycetes and in those of the outgroups used. Both the full set of peptidases and the subset of secreted peptidases are indicated. (XLS)

Repetitive content and transposable element (TE) annotation for the 18 Dothideomycetes . (XLS)

Predicted kinases in the genomes of 18 Dothideomycetes and in those of the outgroups used. (DOC)

Dothistromin and aflatoxin biosynthetic pathways in Dothideomycetes . (DOC)

Principal component analysis and hierarchical clustering of protease family assignments of 18 Dothideomycetes and outgroups. A matrix was constructed containing the number of proteases assigned to each MEROPS family in each fungal species. Analyses were performed with the Rcmdr package of R, and the results graphed along the first two components. C...

Number of genes encoding peptidases in the genomes of Capnodiales , Pleosporales and Hysteriales fungi. (TIFF)

Classification of synteny type in comparisons of 18 Dothideomycetes. The genome of Aspergillus nidulans was used as an outgroup. (XLS)

Simple repeats are over-represented near the inversion breakpoints in relatively closely related mesosyntenic scaffold pairs. The number of breakpoints that has at least one simple repeat within 500 bp distance is significantly higher than can be explained by chance. (XLS)

Additional statistics on the putatively dispensable chromosomes. (XLS)

Distribution of terpene synthases across the 18 Dothideomycetes relative to the Cochliobolus heterostrophus JGI set. Cutoff is greater than 70% identity at the amino acid level. (XLS)

Predicted lipases in the genomes of Dothideomycetes. Both the full set of lipases and the subset of secreted lipases are indicated. (XLS)

Statistics on members of expanded orphan multi-gene families. An expanded orphan multi-gene family is defined here as a gene family with at least 2 members that is present in only one Dothideomycete and in none of the outgroups. Family members frequently include small secreted proteins, but relatively few PFAM domains (XLS)

Accession numbers of sequences that were used to estimate the phylogenetic relationships between the 67 organisms in Figure 1 . (XLS)

Comparative transcriptomics during pathogenesis. (DOC)

Functional annotation terms that are over- or under-represented in genes that are located in regions up to 2 kbp from Transposable Elements. (XLS)