A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao

Additional file 1:

Genome statistical validations. A) Estimation of genome length using dog genome survey protocol, B) Estimate of distribution of gap sizes in M. perniciosa genome assembly, C) Estimate of misassembly sequences due to repetitive regions.

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Additional file 2:

MCL analysis of M. perniciosa gene models. All predicted proteins were compared all-against-all using WU-TBLASTX. A score (-log (E-value)) for each pair of proteins (u, v) with significant BLAST hits (Evalue ≤ 1e-5) was assigned. The MCL algorithm (inflation parameter 2.0) was applied to find clusters in this graph. This method is fully automatic and protein clusters reported were not subjected to manual curation. ID: number of the MCL family; #members: number of gene models present in each family; Norm factor: factor used to normalize the number of gene models present in each family (see methods); Norm#members: normalized number of gene models present in each family. Annotation: words associated to each family after correlation of gene models with AutoFACT annotation. In parenthesis are the occurrence numbers of each word. Each worksheet shows the ranking of families using normalization factor (Rank_Norm) or not using this factor (Rank_Non_Norm).

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Additional file 3:

Functional annotation of M. perniciosa gene models discussed in this paper. ID: gene model; First Hit (BLASTX-NR): Most similar sequence in GenBank; E-value: E-value of most similar sequence; AutoFACT annotation: automatic annotation by AutoFACT; AutoFACT E-value: E-value of AutoFACT annotation; EST: presence (Y) or absence of an EST aligned in this gene model; MCL family: family annotated by MCL analysis. Worksheet P450: annotation of gene models similar to cytochrome P450 monooxygenases; Worksheet transposons: classification and annotation of gene models similar to transposable elements; Worksheet unknown gene families; annotation of top 20 MCL unknown gene families; Worksheet functional annotation: classification and annotation of gene models similar to efflux transporters, anti-oxidative enzymes, phytohormones biosynthesis related proteins, pheromone receptors, salicylate hydroxylases, effectors/elicitors/pathoghenicity associated proteins, cell wall degrading enzymes and intermediary metabolism enzymes (cytochrome pathway bypass, Glyoxylate pathway and oxalate formation, glycerol uptake and metabolism, extracellular sugar degrading enzymes and nitrogen regulation, uptake and metabolism enzymes), EC = enzyme classification http://expasy.org/enzyme/ webcite; Worksheet transporters; Relative percentage of transporters distribution in fungi genomes (see methods).

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Additional file 4:

Ranking of CDD-PFAM families annotated in M. perniciosa. Gene models were annotated based on CDD-PFAM-ID and ranked. This analysis was performed with other fungi genomes, which CDD-PFAM entries were classified according to M. perniciosa ranking. CDD-ID: CDD entry; PFAM Domain: PFAM entry; #Hits Domains: number of gene models containing each CDD-PFAM domain; %Hits Domains: percentage of gene models containing each CDD-PFAM domain in relation to total number of gene models containing a CDD-PFAM domain; %Hits PTN: Percentage of gene models containing each CDD-PFAM domain in relation to total number of M. perniciosa gene models; Rank: non-normalized M. perniciosa CDD-PFAM ranking; PTNS: proteins in each organism; Norm Factor: factor used to normalize the number of gene models containing each CDD-PFAM domain; # Hits Domains Norm: normalized number of gene models containing a CDD-PFAM domain; %Hits Domains Norm: percentage of gene models containing each CDD-PFAM domain in relation to total number of gene models containing each CDD-PFAM domain; %Hits PTN Norm: Normalized percentage of gene models containing each CDD-PFAM domain in relation to total number of M. perniciosa gene models; Rank Norm: normalized M. perniciosa CDD-PFAM ranking. Worksheets show the ranking of CDD-PFAM domains using normalization (Rank_Norm) or not using normalization (Rank_Non_Norm).

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Additional file 5:

BioCyc comparison between S. cerevisiae and M. perniciosa metabolic pathways. Worksheet Compounds: Comparison of number of reactions in each organism containing the compounds described in the table; Worksheet pathways: Comparison of number of pathways in each organism present in each pathway class. The two largest top-level classes, Biosynthesis and Degradation/Utilization/Assimilation, are broken down further to show the distribution of pathways among their next-level subclasses.

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Additional file 6:

Annotation of gene models with no similarity in BLASTX-NR encoding hypothetical small secreted proteins containing at least 2 cysteines. ID: gene model; # residues: number of amino acids of predicted protein encoded by the gene model; # cysteines: number of cysteines in predicted protein; Binomial RT; statistical analysis of cysteines presence in gene models (see methodological details in the file).

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Additional file 7:

Primers used in the amplification of no hits gene models encoding hypothetical small secreted proteins containing at least 2 cysteines. ID: gene model; Set of primers: Group of primers used for the amplication of a gene model. Primer sequence: sequence of primers (SPE – nested in sequence encoding the putative signal peptide; MAT – nested in sequence encoding the putative first amino acid of mature protein; END – nested in sequence containing the putative stop codon). Amplification: positive (Y) or negative (N); EST: presence (Y) or absence (N) of an EST aligned in this gene model; Length: length of amplicon in genomic and cDNA using two combinations of primers (SPE-END; MAT-END).

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Additional file 8:

Examples of amplifications of no hits gene models. PCR amplicons were run on 1% agarose gels. SPE: amplicons resulted from amplification with SPE and END primers; MAT: amplicons resulted from amplification with MAT and END primers; Ctl: water as template (control); Gen: genomic DNA as template; Glu: cDNA from saprotrophic mycelia grown in glucose as template; Cac: cDNA from saprotrophic mycelia grown in cacao extract as template; M: DNA molecular marker.

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Additional file 9:

Comparison of plant cell wall degrading enzymes in fungi that interact with plants. PFAM entries were correlated with the CAZy nomenclature http://www.cazy.org webcite of plant cell wall degrading enzymes.

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Additional file 10:

Genomic survey sequences and gene models nomenclature.

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