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Supporting Information Comparative genomic and transcriptomic analysis of Wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen Zehua Chen*, Diego A. Martinez*, Sharvari Gujja*, Sean M. Sykes*, Qiandong Zeng*, Paul J. Szaniszlo§, Zheng Wang†,1, Christina A. Cuomo*,1 *Broad Institute of MIT and Harvard, Cambridge, MA 02142. §The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712. †Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375. 1Corresponding authors: [email protected] and [email protected] Data availability: The assembly and annotation of Wangiella dermatitidis are available at the NCBI nucleotide database under the accession number AFPA01000000; RNA-Seq differential expression analysis of pH stress is available at the NCBI GEO database under record GSE51646. DOI: 10.1534/g3.113.009241 Figure S1 Independent expansion of MFS and APC transporter families in W. dermatitidis and selected aspergilli. (A) Average number of genes per genome for different category of MFS and APC families (Core families are the ortholog clusters shared by all four fungal groups; Shared, present in at least two out of the four fungal groups; Unique, unique to each group, including species-specific paralogous clusters and unclustered genes). (B) Enrichment of different category of MFS and APC transporters under different stress conditions (low pH or radiation). A positive normalized enrichment score (NES) indicates enrichment under stress conditions (pH 2.5 or with radiation), and a negative score indicates enrichment underChen normal et al, Figure conditions S1 (pH 6 or no radiation). Significant enrichments noted with **: q-value < 0.05; ***: q-value < 0.01. 2 SI Z. Chen et al. Z I J P C M G K A N F T H A. fumigatus Chr6 (Z) (C) T (C) (N) (sidI) (A) J K I M G F H P W. dermatitidis sc1.2 Transcription factor O-methyl transferase Long-chain fatty-acid-CoA ligase Amino cyclopropane carboxylate synthase Glutathione S-transferase Essential protein 5 Kb Dipeptidase MFS transporter Hypothetical protein Non-ribosomal peptide synthetase Methyltransferase Cytochrome P450 monooxygenase Thioredoxin reductase Figure S2 Gliotoxin biosynthetic gene cluster in A. fumigatus and conservation in W. dermatitidis. Gene symbols above each gene indicate the corresponding orthologs; symbols in parentheses were not identified as single copy orthologs of the corresponding A. fumigatus genes, but are part of the gene cluster and share sequence similarity. Gene identifiers for W. dermatitidis range from HMPREF1120_02977 (GliZ) to HMPREF1120_02933 (GliP). Chen et al, Figure S2 Z. Chen et al. 3 SI r H e d M M H W P Y M S H C R 0 P M P 8 E T B b m 6 R N P F H u C 4 m E r R 1 C i 5 2 0 g A Y E F 1 T i m U 2 C f 2 6 m o F 1 P 0 n u 9 0 0 F 0 p 1 8 2 u 1 L A 3 0 f 9 6 d 2 o r 2 6 1 i S 1 g 0 2 0 1 3 r A . r 0 A 0 n e 2 9 1 0 4 1 2 f c 8 4 e 8 1 c r f 1 t 5 0 u 0 0 3 6 0 7 F A 6 A 0 e 4 6 4 9 S T e 0 1 8 5 6 9 c C E 1 d n 0 5 4 . h . M 2 g N t 2 2 9 2 3 0 5 G S R 1 0 5 W 0 9 S G 8 W 3 3 0 8 6 c M t 7 g a W R p P 0 3 G 0 h 7 A g 9 c 9 r 9 3 r M 3 A o 7 3 0 E 5 6 a I g 8 1 c n 0 e e 5 6 d 7 M A W 0 7 5 0 8 f m N 5 1 3 1 0 5 r T N u e C N n 0 4 3 2 7 0 W H u 1 N A C T d m r f R 5 5 9 0 g 8 4 A . 2 m H C A d e P A 6 9 T 0 4 0 A 9 0 I U 5 f e r P E 9 2 m H T 4 u Y 1 2 2 i M 0 7 4 A r f T 7 1 b I E m S r I 0 C Y T 8 3 n H 1 u C E 1 2 0 A i o H U F 5 r 2 2 n g T 9 T H T 2 A T C E 5 M H 1 6 id C 0 1 7 n N Y R 3 1 P 2 1 8 N i P 0 3 R 3 1 0 c g M d m H E N 1 2 r M G 0 i u M F C 1 3 T a 0 n f P 1 2 t H M A A g R 11 U 2 e I G 0 i H E 2 0 6 T r C R 7 0 n M F 0 9 t E 4 4 A P 1 9 M e 9 0 0 ig R 1 0 0 r T 4 1 3 n E 2 0 6 th N g 3 A F 0 48 N e A 3 4 1 0 2 c u 0 20 M 12 3 W ra f g 0 Y 0 52 A 16 2 id C 0 5 de n 1 n TH 1 W r A 1g A um 2 18 0 5 Af T 3 6 de n 44 0 HI 02 W r A 2 2 ig TE 5 d 1 20 An 2 38 e AN 0 0 10 M r 8g 40 er N 87 th fu 09 Tt CU 82 e A 4g 00 0 T 0 63 42 te An 6 ra 23 r E Nc the N IT 68 M cra TH 52 67 er U0 992 Wd NC 22 115 Class VI TH 09 YC 120 Chitin Synthase M EF1 m PR Cim HM 62 068 IMG Trub AN C 657 4566 G07 An0 Anid TER Afum 7g055 2600 70An u1g1 Afu ig Af 2g018 6Anid 70Afu N104 T m A nig ERG02 5290A 562Tru An08g0 b 791Wder CIMG0 F112001 5598Cimm HMPRE HMPREF11200 23CScer Class II 6816Wder YBR0 Chitin Synthase AN0799Anid Afu8g05630Afum NCU04251Ncra An09g02290Anig er AN1555Anid THITE2108832Tt 3Mthe TERG08867T CTH230258 rub MY CI WScer MG0876 YNL192 6Cimm om HMP 2cSP REF112 3G6.1 00772 PAC1 ig NCU 1Wder S 60An 09324 4g006 M Ncra An1 fum YCT 80A H22 041 TH 9638 fu4g nid ITE 8Mth A 32A 211 e Class IV N70 b NC 3371 A Tru U04 Tte Chitin Synthase 49 T 350 r 056 m HIT Nc RG Cim E2 ra TE 55 r MY 115 086 de CT 879 G W H H Tt IM 981 er M 11 er C 07 Tt PR 291 20 75 C EF 6 11 76 he IM 11 Mth F 14 Mt G 20 e RE 2 4 a TE 05 0 P TE 76 cr R 02 87 HM HI 9 N A G 1 77 T 30 9 er N 04 Ci W 2 23 c 63 9 m de TH 5 S A 1 18 m r C U0 W m fu 7 T Y C 8 o A 2g An ru M N 03 Sp n 1 id b R 1 um 0 34 B 0 f H 2g 3 Y 9. A ig M 0 0 0 20 n N P 23 A 17 4 A id C R 4 fu C 4 0 n M U E 0 m B 1 1 0 F A P g 0 A m Y 4 1 n S 3 4 3 T C 3 1 ig Class I fu 0 2 im b H T 5 20 A 9g 5 C u C I H 2 0 2 r r I T N 0 n N 7 T e T M E 2 87 Chitin Synthase A A 4 3 d g E G 2 2 c 6 i A 9 ra 7 5 4 W n R 1 9 6 0 8 m A N G 0 1 4 W 3 9 A 6 5 5 0 G 0 7 fu g A f 0 8 d 4 0 i u 3 0 2 7 2 e M 8 A n d M n 2 1 4 M r I G 6 i r 2 7 0 3 0 A n A 0 g 8 9 C R 0 e Y 2 1 1 C T th E 0 6 0 A t e H n A 1 A C g 3 9 i t e T 2 7 6 T h a M 0 n m e g 7 t r N T 0 4 r 1 0 3 g T f 7 i T 2 i M u 4 m 8 c C 2 d 0 6 C C P H r 1 1 6 M m d H g n r i b 8 3 0 u g 3 0 N I Y R F 0 u I U 0 n m e b A n u M I g 6 5 4 4 5 f M 1 g T A E r 1 A 1 C E u 6 8 d 0 0 0 0 3 N A A m f 0 G E 1 f i G R 1 T u 0 8 T 9 2 F 7 0 A 0 1 A A W P 6 0 9 8 1 m 1 9 C H 3 1 n 0 2 1 1 0 n M 2 7 3 0 6 0 7 2 1 3 A 7 8 0 i 0 3 2 0 5 0 2 g H 2 5 0 2 A 0 5 5 M E 0 2 2 Protein domains: H 9 7 2 U 3 0 n 6 5 6 2 N A T g 7 T 0 3 t I N 0 i h C 2 0 4 7 0 g 7 2 g 8 c f C 7 u e H 1 A 0 5 5 0 r N 7 8 C m Y C a T n G 9 9 u 0 Glyco_hydro_12 7 7 f i M A R G i m 2 T m 3 5 A E 1 t M Class VII m m M e I W T 1 r C F t d Glycos_transf_2 h Chitin Synthase E e e r R Chitin_synth_1N P M Branch colors H Cellulose_synt W.
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