The evolutionary history of Cytochrome P450 genes in four filamentous Ascomycetes

Additional file 1:

All P450 genes, cds, cds length and locus name in A. nidulans, F. graminearum, M. grisea and N. crassa as annotated by the Broad Institute.. a. "Same" indicates the coding sequence (cds) used in the study exactly matches the locus predicted by the Broad Institute. "Include" indicates the cds in this study corresponds to a locus predicted by the Broad Institute where one or more exons were modified. "Not includ" indicates cds excluded from this study. b. Locus as defined by the Broad Institute

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Additional file 2:

NJ tree of 376 P450s from 4 filamentous Ascomycetes

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Additional file 3:

MP tree of 376 P450s from 4 filamentous Ascomycetes

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Additional file 4:

Collapsed NJ tree of 376 P450s from 4 filamentous Ascomycetes. Each collapsed branch is followed by a number representing the CYP family taxon name. The number in <> after the CYP family name represents the number of genes under this collapsed branch. Number after the ...represents the total number of branches containing other members of the same CYP family in this collapsed phylogeny.

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Additional file 5:

Collapsed MP tree of 376 P450s from 4 filamentous Ascomycetes. Each collapsed branch is followed by a number representing the CYP family taxon name. The number in <> after the CYP family name represents the number of genes under this collapsed branch. Number after the ...represents the total number of branches containing other members of the same CYP family in this collapsed phylogeny.

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Additional file 6:

Orthologous groups identified by COGs analyses. # indicates COGs containing genes from a different P450 family. * indicates CYP636A1 and CYP660A1 were assigned to clan550 while mgCYP611A1 was excluded. ** indicates bootstrap support <70% but >50%, see text for details.

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Additional file 7:

Complete linkage families formed at cutoff of 30% of sequence percentage identity. * refers to complete linkage families which were identical to standard families.

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Additional file 8:

Standard families not identical to complete linkage families are resolved to clans. # indicates standard family was split into different clans (see text). $ indicates family rejoined to a group exclusively consisting of this family members.

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Additional file 9:

The physical location of all P450 genes in AN, FG and NC genomes. Each horizontal line represents a chromosome. Those at the bottom followed by a number represent unanchored contigs. A vertical bar above (on 5-3' strand) or below (3'-5' strand) horizontal line marks the position and orientation of each CYP gene, the name of which is marked by omitting the leading "CYP". The number after each gene in parenthesis represents the clan to which this gene was assigned. For colour codes, see Figure 2.

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Additional file 10:

Distribution of the number of intron for each P450 gene among all 376 P450 genes

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Additional file 11:

Intron-exon organization pattern derived from two alignments. Clan alignment: alignment based on genes belonging to individual clans. All alignment: alignment of all 376 genes as described in text.

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Additional file 12:

Distribution of UIP values among multi-member P450 clans. UIP value of each clan was assigned to 10 intervals (0–0.1; 0.1–0.2; 0.2–0.3; ...0.9–1).

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Additional file 13:

Intron-exon organization of clan 58. Horizontal lines represent P450 amino acid sequences. A vertical bar on the horizontal line represents an intron. The number under the bar represents the intron phase.

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