Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize
1 Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
2 Environmental Genetics and Molecular Toxicology Division, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, 45267-0056, USA
3 US Department of Energy Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, California, 94598, USA
4 Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, CNRS, UMR 6098, 163 Avenue de Luminy, 13288, Marseille, France
5 Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, l-l-l, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
6 Great Lakes Forestry Centre, 1219 Queen Street East, Sault Ste. Marie, Ontario, Canada, P6A 2E5
7 Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, Canada, M5S 3B3
8 CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
BMC Genomics 2012, 13:444 doi:10.1186/1471-2164-13-444Published: 2 September 2012
Additional file 1:
Table S1.P. carnosa sequencing summary. This describes the summary of libraries that were constructed for genome sequencing. Table S2.P. carnosa assembly summary. This describes the summary of the genome sequence assembly. Table S3. Gene model support by different lines of evidence. Statistics of predicted gene models. Table S4. Summary of P.carnosa annotations. This summarizes genome annotation according to various classifications. Table S5. Top 50 PFAM domains in Phanerochaete genomes. List of top 50 PFAM domains annotated in Phanerochaete genomes. Table S8. Comparison of the number of CAZymes in wood decaying basidiomycotina. General comparison of CAZyme gene members in various basidiomycotina [5,6,12,17,78,79]. Table S9. CAZymes that showed <60% identity to Phchr orthologs. List and gene expression data of CAZy members showing low sequence identity with orthologs in P. chrysosporium. Table S11. Comparison of the number of FOLymes in P. carnosa and selected Agaricomycotina. General comparison of FOLy members between several Agricomycotina . Table S12. Summary of oxidoreductases potentially involved in lignocellulose degradation by P. carnosa (Phaca) and P. chrysosporium (Phchr). Summary and comparison of specific oxidoreductase members between Phanerochaetes. Table S13. Tandem duplication of P450 genes in basidiomycete genomes. Summary table of P450 tandem duplication in known basidiomycete genomes [5,6,12,17,78-80]. Table S14. P450ome classification in P. carnosa and its membership comparison with P. hrysosporium. Summary table of P450 members in P. carnosa and P. chrysosporium. Table S15. P450s upregulated in wood degrading cultures. List of P450 members in P. carnosa that were upregulated during wood degrading cultivation . Table S16. UPLC peaks corresponding to wood-derived phenolic compounds that were transformed by P.carnosaor P. chrysosporium. Peak annotation and analysis of UPLC chromatograms. Table S17. Assignment of FT-IR peaks decomposed by P. carnosa and P. chrysosporium. Summary of the peaks detected in FT-IR analysis (Figure S7) [81-83]. Table S18. Gradient method of UPLC elution. Summarizing elution method used in UPCL analyses.
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Additional file 2:
Table S6. Genomic distribution of CAZymes and FOLymes on major scaffolds in P. carnosa. This table summarizes the distribution of CAZy and FOLy members located within the major scaffolds of the P. carnosa genome sequence.
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Additional file 3:
Figure S1. Pictures of P. carnosa and P. chrysosporium grown on various carbon sources. P. carnosa grew significantly slower than P. chrysosporium; as a result, pictures were taken after 13 and 3 days of cultivation for P. carnosa and P. chrysosporium, respectively. Cultivations were performed in duplicate and no significant differences in colony diameter or thickness were observed between the duplicates on any of the carbon sources. Monomeric and oligomeric carbon sources were used at a final concentration of 25 mM, while pure polymers were used at a final concentration of 1%. Crude plant biomass was used at a final concentration of 3%. Relative growth was determined by comparing the radius and density of the mycelia on a particular carbon source to that on D-glucose. The extent of growth relative to plates containing glucose are summarized as follows, from high to non-detectable: +++, ++, +, ±, -. This semi-quantitative, consistent assessment of both colony diameter and thickness allowed comparisons to include a broad range of substrates, including those that yield too little mycelia for accurate weight measurement, or that could interfere with protein measurements or ergosterol production [84,85]. Complete growth profiles of P. carnosa and P. chrysosporium, and other fungi can be found at . Figure S2. Phylogenetic tree of GH61 enzymes from P. carnosa and P. chrysosporium. Proteins are labeled with protein IDs from the JGI databases for Phanerochaete carnosa v1.0 (Phaca) and Phanerochaete chrysosporium v2.0 (Phchr). The sequences were aligned using MAFFT, and the tree was drawn by FigTree. In the heatmap bar, abbreviations are; Y, YMPG; F, balsam fir; P, lodgepole pine; S, white spruce; M, sugar maple . Heat map represents the number of sequence reads per million kb as shown in this figure and described in , 0 (black) to 50,000 (pink). Figure S3. Phylogenetic tree of GH5 enzymes in P. carnosa and P. chrysosporium. The tree was generated as described in Figure S2. Of the 34 upregulated wood-degrading CAZymes, that were at least four times more abundant in P. carnosa grown on at least one wood substrate compared to nutrient medium, 5 (15%) were GH5 enzymes . Figure S4. Phylogenetic tree of predicted sugar transporters and permeases from genomes of P. carnosa and P. chrysosporium. Proteins are labeled with protein IDs from the JGI database for P. carnosa v1.0 (Phaca) and P. chrysosporium v2.0 (Phchr). Protein sequences of transporters from other yeast and fungal species were used for pylogenetic comparison, including; An Aspergillus nidulans, Ao Aspergillus oryzae, Ca Candida albicans, Ci Candida intermedia, Gz Gibberella zeae, Hp Hansenula polymorpha, Kl Kluyveromyces lactis, Lb Laccaria bicolor, Nc Neurospora crassa, Pp Postia placenta, Ps Pichia stipitis, Sc Saccharomyces cerevisiae, Sp Schizosaccharomyces pombe, Tm Tuber melanosporum, and Tr Trichoderma reesei. The GenBank accession numbers of corresponding sequences are: AnHyp1 (XP_682442.1), AnHyp2 (XP_660070.1), AnMstA (CAC80843), Ao_BAE58341.1 (BAE58341.1), CaHgt1 (CAA76406), CaHgt4 (XP_723173), CaHgt11 (XP_719597), CiGxf1 (AJ937350), CiGxs1 (AJ875406), GzHyp1 (EAA74528), HpGcr1 (AAR88143), KlHgt1 (XP_451484), KlRag1 (XP_453656), KlRag4 (CAA75114), Lb_EDR07962 (EDR07962), NcHyp1 (XP_328858), NcHxt3 (CAD21508), NcNCU00801(EAA34565.1), NcNCU08114 (XP_963873.1), NcRco3 (CAE76420), Pp_115604 (EED81359), Ps_ABN65648.2 (ABN65648.2), PsSut1 (AAD00266), ScHxt1 (M82963), ScHxt7 (NP_010629), ScSnf3 (P10870), SpGht1 (Q9P3U6), Tm-CAZ81962.1 (CAZ81962.1), TrHxt1 (AAR23147), TrXlt1 (shown enlarged; AY818402), TrHxt2 (DQ852622; Ruohonen and Margolles-Clark, unpublished). The sequences were aligned using MAFFT, and the tree was drawn by FigTree. In the heatmap bar, abbreviations are: Y YMPG, F balsam fir, P lodge pole pine, S white spruce, M sugar maple . Group I contains a predicted monosaccharide transporter (ID 100265) and hypothetical proteins with high similarity to known sugar transporters. Group IV also contains known glucose transporters found in yeast species and cellulolytic fungi, including Trichoderma reesei and Neurospora crassa. Group V consists of high affinity glucose transporters in yeast and hexose transporters in fungal species, including the xylose transporter found in T. reesei. Group VI and VII contains predicted sugar transporters and putative sucrose transporters (ID 89844 and 254080). Group VIII consists of predicted cellobiose transporters found in yeasts and filamentous fungi, and biochemically characterized cellodextrin transporters from N. crassa (NcNCU00801 and 08114) . Figure S5. Phylogeny, genome position, and intron distribution of genes encoding manganese peroxidases and lignin peroxidases. Protein IDs of manganese peroxidases (A) and lignin peroxidases (B) of P. carnosa and P. chrysosporium are obtained from P. carnosa v1.0 and P. chrysosporium v2.0. Alternative names are from MacDonald et al.  for P. carnosa and from Vanden Wymelenberg et al.  for P. chrysosporium.Figure S6. Mycelial growth of P. carnosa and P. chrysosporium on heartwood and sapwood samples isolated from different hardwood and softwood species. Colony diameter was measured for P. carnosa grown on heartwood (A) and sapwood (B), and for P. chrysosporium grown on heartwood (C) and sapwood (D). Filled square (red), sugar maple; filled circle (green), yellow birch; filled triangle (blue), trembling aspen; filled diamond (pink), red spruce; open square (purple), white spruce; open circle (orange), balsam fir; open triangle (gray), red pine. Error bars show the standard deviation in biological triplicates. Since P. chrysosporium mycelia was no longer visible after day 8 of cultivation on heartwood of sugar maple, yellow birch, white spruce and balsam fir, those data were not obtained. Figure S7. Different modes of wood decay described by FT-IR analysis. (A) Grouping on Principal Components (PCs) 1 and 2 for normalized FT-IR data obtained from heartwood and sapwood samples of trembling aspen and red pine after cultivation of P. carnosa and P. chrysosporium. Circle; P. carnosa, triangle; P. chrysosporium, square; control (untreated wood samples). (B) PC loadings that distinguish wood samples treated with P. carnosa from corresponding control samples. For example, high positive loadings describe components in control samples that were lost in the decayed samples. Loadings for PC1 are shown for trembling aspen heartwood and red pine sapwood, while loadings for PC2 are shown for trembling aspen sapwood and red pine heartwood. (C) PC loadings that distinguish wood treated with P. carnosa from corresponding wood samples treated with P. chrysosporium. Horizontal dotted lines at magnitude |0.05| represent thresholds for loading significance. Corresponding wavenumbers (cm-1) are indicated for peaks with significant loadings; identities of significant wavenumbers are summarized in Additional file: Table. S17. Percent values given in y-axes denote the percent of total sample variance described by the PC.
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Additional file 4:
Table S7. List of CAZy members computationally annotated in P. carnosa. List of protein IDs computationally annotated as CAZy members in P. carnosa.
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Additional file 5:
Table S10. List of the genes involved in carbohydrate metabolism. List of P. carnosa and P. chrysosporium genes involved in carbohydrate metabolism accompanied with gene expression data of P. carnosa.
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