OmniMapFree: A unified tool to visualise and explore sequenced genomes

<p>Abstract</p> <p>• Background</p> <p>Acquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif search results, and GO annotations are displayed. However, for many species, a growing volume of additional experimental information is available but this is rarely searchable within the landscape of the entire genome.</p> <p>• Results</p> <p>We have developed a generic software which permits users to view a single genome in entirety either within its chromosome or supercontig context within a single window. This software permits the genome to be displayed at any scales and with any features. Different data types and data sets are displayed onto the genome, which have been acquired from other types of studies including classical genetics, forward and reverse genetics, transcriptomics, proteomics and improved annotation from alternative sources. In each display, different types of information can be overlapped, then retrieved in the desired combinations and scales and used in follow up analyses. The displays generated are of publication quality.</p> <p>• Conclusions</p> <p>OmniMapFree provides a unified, versatile and easy-to-use software tool for studying a single genome in association with all the other datasets and data types available for the organism.</p

The Predicted Secretome of the Plant Pathogenic Fungus Fusarium graminearum: A Refined Comparative Analysis

The fungus Fusarium graminearum forms an intimate association with the host species wheat whilst infecting the floral tissues at anthesis. During the prolonged latent period of infection, extracellular communication between live pathogen and host cells must occur, implying a role for secreted fungal proteins. The wheat cells in contact with fungal hyphae subsequently die and intracellular hyphal colonisation results in the development of visible disease symptoms. Since the original genome annotation analysis was done in 2007, which predicted the secretome using TargetP, the F. graminearum gene call has changed considerably through the combined efforts of the BROAD and MIPS institutes. As a result of the modifications to the genome and the recent findings that suggested a role for secreted proteins in virulence, the F. graminearum secretome was revisited. In the current study, a refined F. graminearum secretome was predicted by combining several bioinformatic approaches. This strategy increased the probability of identifying truly secreted proteins. A secretome of 574 proteins was predicted of which 99% was supported by transcriptional evidence. The function of the annotated and unannotated secreted proteins was explored. The potential role(s) of the annotated proteins including, putative enzymes, phytotoxins and antifungals are discussed. Characterisation of the unannotated proteins included the analysis of Pfam domains and features associated with known fungal effectors, for example, small size, cysteine-rich and containing internal amino acid repeats. A comprehensive comparative genomic analysis involving 57 fungal and oomycete genomes revealed that only a small number of the predicted F. graminearum secreted proteins can be considered to be either species or sequenced strain specific

Proteome analysis of the Albugo candida–Brassica juncea pathosystem reveals that the timing of the expression of defence-related genes is a crucial determinant of pathogenesis

White rust, caused by Albugo candida, is a serious pathogen of Brassica juncea (Indian mustard) and poses a potential hazard to the presently developing canola-quality B. juncea industry worldwide. A comparative proteomic study was undertaken to explore the molecular mechanisms that underlie the defence responses of Brassica juncea to white rust disease caused by the biotrophic oomycete Albugo candida. Nineteen proteins showed reproducible differences in abundance between a susceptible (RH 819) and a resistant variety (CBJ 001) of B. juncea following inoculation with A. candida. The identities of all 19 proteins were successfully established through Q-TOF MS/MS. Five of these proteins were only detected in the resistant variety and showed significant differences in their abundance at various times following pathogen inoculation in comparison to mock-inoculated plants. Among these was a thaumatin-like protein (PR-5), a protein not previously associated with the resistance of B. juncea towards A. candida. One protein, peptidyl-prolyl cis/trans isomerase (PPIase) isoform CYP20-3, was only detected in the susceptible variety and increased in abundance in response to the pathogen. PPIases have recently been discovered to play an important role in pathogenesis by suppressing the host cell's immune response. For a subset of seven proteins examined in more detail, an increase in transcript abundance always preceded their induction at the proteome level. These findings are discussed within the context of the A. candida–Brassica juncea pathosystem, especially in relation to host resistance to this pathogen

Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis.

The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicolawas sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed “mesosynteny” is very different from synteny seen between other organisms. A surprising feature of the M. graminicolagenome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and may have evolved from endophytic ancestors

Analysis of <i>F.graminearum</i> secretome proteins and genes with no predicted function for cysteine content, the presence of internal amino acid repeats, Pfam domains, gene family size and presence in other Fusaria species and <i>Mycosphaerella graminicola</i>.

*<p>Abbreviations used in this table MPL = Mature peptide length, NC = Number of cysteine residues, Percentage cysteine residues in mature peptide, RR = Number of radar repeats, Pfam = Pfam domains, <i>Fv</i> = <i>F. verticillioides</i>, <i>Fol = Fusarium oxysporum</i> f. sp. <i>lycopersici</i>, <i>Fs</i> = <i>F. solani</i>, <i>Mg</i> = <i>Mycosphaerella graminicola</i>.</p>**<p>Pfams: 05792/10528.</p><p>M = FGSG_10435 Pfams: 01034, 01822, 03154, 03935, 03999, 04415, 04484, 04683, 05109, 05110, 05539, 05642, 05792, 05955, 06075, 06933, 07010, 07218, 07263, 08550, 08580, 08601, 08639, 08702, 08729, 09319, 09595, 09726, 09786 and 10033.</p

Weak expression of the pathogenesis related PR-b₁ gene and localization of related protein during symbiotic endomycorrhizal interactions in tobacco roots

The production of pathogenesis related PR-b₁ protein has been compared in tobacco roots infected by the pathogenic fungus Chalara elegans and during symbiotic interactions with the vesicular arbuscular endomycorrhizal fungus Glomus mosseae. PR-b₁ protein could be detected by Western blotting of soluble protein extracts from pathogen-infected roots but not of endomycorrhizal tobacco roots. However, Northern analysis of total RNA extracts from endomycorrhizal roots revealed a single hybridization signal which was extremely weak when compared to that of C. elegans-infected tobacco roots. Indirect immunogold labelling showed that PR-b₁ antigen was very localized in endomycorrhizal roots and limited to host material in the interfacial matrix surrounding living intracellular fungal haustoria (arbuscules) in parenchyma cortical cells. Results are discussed in relation to PR-b₁ protein synthesis in pathogen interactions and host control in the endomycorrhizal symbiosis

The bioinformatics pipelines used to predict the <i>F. graminearum</i> secretome.

<p>(<b>A</b>) The total secretome and (<b>B</b>) the refine secretome.</p