Open Access Highly Accessed Research article

Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes

Venkatesh Moktali1, Jongsun Park2, Natalie D Fedorova-Abrams3, Bongsoo Park1, Jaeyoung Choi2, Yong-Hwan Lee24 and Seogchan Kang15*

Author Affiliations

1 Integrative Biosciences program in Bioinformatics & Genomics, The Pennsylvania State University, University Park, PA, USA

2 Fungal Bioinformatics Laboratory, Seoul National University, Seoul, Korea

3 Advanced Biomedical Computing Center, SAIC-Frederick, Frederick National Laboratory for Cancer Research, Frederick, MD, USA

4 Department of Agricultural Biotechnology and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea

5 Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA

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BMC Genomics 2012, 13:525  doi:10.1186/1471-2164-13-525

Published: 4 October 2012

Additional files

Additional file 1:

Pipeline employed in FCPD 1.2 version. The pipeline still consists of four steps employed in building the previous version of FCPD, but step 3 is now based on optimized parameters. Additionally, a new parameter, coverage, was added to the clustering procedure to further improve clustering results. (PDF 235 kb)

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Additional file 2:

Parameter optimization for clustering. (XLSX 10 kb)

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Additional file 3:

Distribution of CYP families into clans. (DOCX 26 kb)

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Additional file 4:

CYP family sizes follow a power law distribution. The graph shows the family size distribution across families. (PDF 167 kb)

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Additional file 5:

Characterized CYPs used for functional classification. (XLSX 12 kb)

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Additional file 6:

Top 10 CYP families in fungi. (XLSX 8 kb)

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Additional file 7:

The 30 largest clusters containing only fungal and oomycete CYPs. (XLSX 10 kb)

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Additional file 8:

Clans involved in the primary, secondary and xenobiotic metabolisms. (XLSX 9 kb)

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Additional file 9:

Blast hits to characterized CYPs. (XLSX 10 kb)

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Additional file 10:

Neighbor joining tree of CYP51. (PDF 703 kb)

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Additional file 11:

Neighbor joining tree of CYP61. (PDF 552 kb)

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Additional file 12:

Phylogenetic tree of CYP65 in Pezizomycotina. Basidiomycetes and Ascomycete yeast species lack family CYP65. In Pezizomycotina, there is large variation in the number of CYP65 family genes. Coccidioides and Neurospora spp. have only one and two members, respectively. On the other hand, Dothideomycetes fungi have 6–15 members. The tree was adapted from Medina et al. [70]. (TIFF 7901 kb)

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Additional file 13:

Neighbor joining tree of CYP65. (PDF 822 kb)

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Additional file 14:

Phylogenetic tree of CYP68. CYP68 family members are found in a number of secondary metabolism gene clusters. This family was lost in yeasts, and is absent in most Basidiomycetes except for some Homobasidiomycetes species. The tree was adapted from Medina et al. [70]. (TIFF 8118 kb)

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Additional file 15:

Neighbor joining tree of CYP505-CYP541. (PDF 507 kb)

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Additional file 16:

Maximum-likelihood tree of CYP52. (PDF 431 kb)

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Additional file 17:

Maximum-likelihood tree of CYP504. (PDF 395 kb)

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Additional file 18:

Phylogenetic tree of CYP540. (PDF 548 kb)

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Additional file 19:

Phylogenetic tree of CYP544. (PDF 443 kb)

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Additional file 20:

Phylogenetic of CYP5025. (PDF 437 kb)

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Additional file 21:

Phylogenetic of CYP645. (PDF 354 kb)

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