Supplementary Material Visual comparative omics of fungi for plant biomass deconstruction Shingo Miyauchi*, David Navarro, Igor V. Grigoriev, Anna Lipzen, Robert Riley, Didier Chevret, Sacha Grisel, Jean-Guy Berrin, Bernard Henrissat, Marie-Noëlle Rosso * Correspondence: Shingo Miyauchi, Marie-Noëlle Rosso:
[email protected],
[email protected] 1
Supplementary Data #
Data S1
Files Pycco310_Transcriptome&Secretome_per_node.xlsx Pycci137_Transcriptome&Secretome_per_node.xlsx Pycsa1264_Transcriptome&Secretome_per_node.xlsx
Descriptions The output files used for the estimation of Spearman’s rank correlation between transcriptome and secretome of the three Pycnoporus strains.
supplementaryTable_selectedGenes_pycco.aspen.xlsx supplementaryTable_selectedGenes_pycco.pine.xlsx supplementaryTable_selectedGenes_pycco.wheatstraw.xlsx Data S2
supplementaryTable_selectedGenes_pycci.aspen.xlsx supplementaryTable_selectedGenes_pycci.pine.xlsx supplementaryTable_selectedGenes_pycci.wheatstraw.xlsx
The lists of the genes selected for the potential involvement in the decomposition of plant substrates for the three Pycnoporus strains.
supplementaryTable_selectedGenes_pycsa.aspen.xlsx supplementaryTable_selectedGenes_pycsa.wheatstraw.xlsx
Pycco310_MBCluster_list_100.xlsx Data S3
Pycco310_MBCluster_list_320.xlsx Pycco310_MBCluster_Transcriptome&Secretome_100.xlsx Pycco310_MBCluster_Transcriptome&Secretome_320.xlsx
1) Results of 320 and 100 clusters generated with MBCluster.seq. The lists of genes with protein ID, log2 transformed read counts, log2 fold changes from the differential expression analysis. 2) The output files for the calculation of Spearman’s rank correlation between transcriptome and secretome for 320 and 100 clusters above.
Supplementary Material 2
Supplementary Figures
Figure S1: The integrated omics models of Pycci 137 and Pycsa 1264. Pycci 137: Pycnoporus cinnabarinus CIRM-BRFM 137. Pycsa 1264: Pycnoporus sanguineus CIRM-BRFM 1264. The node identification is labeled (i.e. 1 to 270). a: Mean transcription of biological replicates for the individual substrates. b: Clusters of highly transcribed genes (>12 log2 read count) were highlighted in circle. Grey: Common to all substrates. Light green: Maltose. Purple: Avicel. Pink: Apen, wheat straw, pine. NOTE: No RNA-seq data available for Pycsa1264 grown on pine. Pycci137
a Transcription (normalized log2 read count)
Maltose
Aspen
Avicel
15 253 235
254
236
217 199
237
201 183 165
145 127
146 128
109
147
92
37
38
19
39
20
41
22
2
157
103
105
48
49
106
161
52 34
15
145
108 89
53
146
91
54
93
37
94
39
20
41
22
2
3
97
43
24
8
253
254
255
236
217 199
237
201
163
164 145
165
109 91
110
166
93
57
37
38
60 41
22
117
43
64
44
46
66 47
28
8
10
49
123
32 13
161
124 106
51
52
33
34 15
163
109
53
102
46
157
103
48
108
35 16
93
54
57
37 19
38 20
18
1
112 94
113
76 58
39 22 3
41
62 43
24
64
27
7
119 101
91
8
46
121 103
b
66
68 49
30
31
11
50 32
12
51
14
19
112
58
59
39
23
43
24
4
8
67
29
30
10
31
11
12
32
125 108 89 72 53
34 15
90
71 52
33
126
107
51
14
162 144
88 70
50
13
124 106
69
49
161 143
87
68
48
216
179 180 160
123 105
234
197 198
142
86
270
252
215
178 159
122 104
85
66 47
28 9
121 103
269
233
196
141
18
251
214
177 158
140
84
268
232
195
54 36
17
250
213
176 157
120
65 46
175
102
267
231
194
139
83
64 45
27
7
119 101
212
53 35
16
249
90 72
52 34
266
193
156
138
82
63
26
6
118 100
81
44
25
5
117
211
174 155
137
51
230
108 89
71
15
248
192
173 154
99
62
42
172
265
126
107 88
33
162 144
125
70
50
229
210
106
14
247
191
136
80
61
41
22 3
116 98
79
60
40
21 2
115 97
264
228
161 143
87
32 13
246
209 190
153 135
263
227
160
124
69
49 31
12
245
208
171 152
134
78
262
105
216 197 198
142
86
234
179 180
159
68
48 30
215
196
123
104
270
252 233
214
178
141
85 67
11
226
189
170 151
114 96
77
207
103
47
244
158
122
269 251
232
195 177
140
84 66
29
261
225
157
102
10
243
188
133
113 95
76
260
206
169 150
132
46 28
224
187
168
45
213 194
176
121
268
250 231
212
139
83 65
9
242
205
149 131
94
57
20
167
75
38
1
18
111
259
101 82
27
156
120
267
249
230
193
175
138 119
64
8
223
186
100
44
241
204 185
148 130
93
56
54 36
17
110
37
203
166
258
222
155 137
81
26 7
240
184
147
74
55
53 35
16
165
129
92 73
72
52 34
15
109 91
90
257
202
43 25
6
221
99
63
211 192
174
154
266 248
229
210
191
118
265
247
228
173
136
80 62
42
239 220
183
146 128
126
71
164 145
108 89
70
33
13
125 107
88
201 182
127
256
153
117
98 79
24 5
238 219
200
162 144
255 237
181 163
161
124 106
87 69
199
216
143
254
218
97
209 190
172
264 246
227
208
135 116
61
41 23
4
152 134
78 60
40 22
3
236
217
179 180 160
142 123
235
197 198
178
105 86
67 48
29 10
122
85
215
39
151
263
245 226
189 171
115
96 77
59
207 188
133
262
244 225
170
150
95
206
187
114
261
243 224
205
169
132
76
21 2
253
270
234
94
242
186
149
58
38 20
204
113
260
223
168
131
75
241
185
148
93
259
222
203
112
57
1
240
167
130
74
37
252 233
196
159 141
104
84
47
28 9
177 158
269 251
214
195
140
120
102
213
176 157
268
232
92
19 18
147
258
221
184
111
56
54
202
166
129
73
36 17
250 231
194
139
83 65
212
175
267
249
230
193
156
138
82
45
26
6
118 100
63
174 155
137
81
211 192
173
266 248
229
210
154
117
44
25
5
172
265
247
228
191
136
99 80
61 42
23
116 98
79
209 190
153 135
264 246
227
208
171 152
115 97
78 60
4
170
263
245 226
189
134
114 96
59
207
151
262
244 225
188
133
77
40
21 2
169 150
132
261
243
206
187
168
95
75
205
186
149 131
260
224
146
110
55
239 220
183 165
128
90 72
53
34 15
201
145
257
238
182 164
109
256
219
200
127
89
52
33 14
162
126
71
51
32 13
107 88
237
218
181 163
144
255
236
199
161
125
70
50
31 12
216
143
87 69
49
30
160
254
217
197 198
124 106
86 68
235 234
179 180
142
105
85 67
11
159
253
252
215
196
123
270
233
214
178
141
122 104
84
29 10
158
251
232
195 177
140 121
66 47
28
213 194
176
269
250 231
212
139
83 65
9
242
223
204
167
259
241 222
185
148 130
74 56
203
166 147
258
240
221
184
111
92
55
36 17
165
73
5
202
129
110
91 90
257 239
220
183
146 128
126
72
35 16
164 145
108
71
201 182
127
256
238 219
200
162
89
255 237
218
181
10
125
88 70
14
199
144
107
87
50
31 12
216
143
254
236
217
179 180 160
69
253 235
15 234
197 198
178
105
68
215
142
86
67
30 11
122 104
270
252 233
196
159 141
85
48
29
9
121 103
84
214
177 158
140
269 251
232
195
176 157
120
102 83
65
45 27
7
119 101
82
213 194
139
268
250 231
212
175
267
249
230
193
156
138
118 100
63
26
6
174 155
137
81
211 192
173
266 248
229
210
154
99
62
25
5
172
265
247
228
191
136
80
61
24
4
116 98
79
42
23
3
115 97
209 190
153 135
264 246
227
208
171 152
263
245 226
189
170
78
59
207
134
262
244 225
188
151
114 96
40
21 2
169
133
77
58 39
20 1
113
76
206
187
150 132
95
75
56
19
112 94
74
168
261
243 224
205
186
149 131
260
242
223
204
167
259
241 222
185
148 130
111
92 73
55
184
147 129
258
240
221
203
183
146 128
220
202
182
127
257 239
219
200
181
256
238
218
101
249
268
Wheat straw
Pine 235
156
120
267
230
193
175
138
82
27
7
155
119
64 45
26
6
100 81
44
25
5
99
63
211 192
174
137
248 229
210
154
266
247
191
118
265
228
173
136
80 62
246
209
117
264
227
190 172
153
98 79
245
208
135 116
61 42
23 4
152 134
78 60
40
21
1
151
263
226
189 171
115
96 77
244
207 188
133
262
225
170
150
59
243
206
187
114
261
224
205
132
95 76
58
242
169
149
113
260
223
186
168
131
75
38
19 18
148
57
241
204 185
112
259
222
203
130
74 56
240
167
147
258
221
184
111
92 73
36 17
202
166
129
110
55
239 220
183 165
128
90 72
35 16
201
109
257
238
182 164
127
256
219
200
162
71
237
218
181
126
107 88
33 14
199
144
255
236
163
125
70 51
32 13
216
143
87
50
31 12
160
254
217
197 198
124
69
235 234
179 180
142
86
253
252
215
196
159
68
270
233
214
123
104
251
178
141
269
232
195
158
85
30 11
213
122
67
47 29
10
250
177
140
84
268
231
194 176
121
66
249
212
139
102
46
9
156
267
230
193
120
83 65
28
8
211
175
138
101 82
27
7
155
64 45
26
6
100
248
192
119
266
229
210
137
81
44
25
5
99
43
24
4
154
63
247
174
118
265
228
191
173
136
80 62
42
23
3
153
98 79
246
209 190
117
264
227
172
135 116
61
245
208
152 134
78 60
40
21
1
151
263
226
189 171
115 97
77 59
244
207 188
133
262
225
170
150
96
76 58
243
206
187
114
261
224
205
132
113 95
75 57
242
169
149 131
260
223
186
168
148
94
74 56
241
204 185
112
259
222
203
130
93
73 55
240
167
111
258
221
184
166
129
110
91
5
220
202
182 164
257 239
219
200
163
256
238
218
181
10
255
54
35
36
16
17
18
Pycsa1264 Transcription (normalized log2 read count)
a
Maltose 321
301
15
322
302
281
261
323
324 325
303 304
305
282
283 284
262 263
241
221
242
222
181 182 161
141
5
122
101 102 81
61
103
82
21
22
1
83
43
23
2
84
64
24
3
25
4
86
66
87
46
88
68
47
27
6
190
48
28
7
111 112
50
30
9
91
71
32
11
94
53
96
56
36
15
97
77
98
78
57
37
16
119
99
79
58
38
17
120
122
123
82
60
41
21
42
43
22
20
24
2
87
67
47
90
50
9
196
33
136
96
77
56
35
36
15
98
99
57
37
58
41
40
18
20
Wheat straw 321
301
322
302
281
261
323
324 325
303 304
305
282
283 284
262 263
241
221
242
222
201 202
181 182 161
141
122
81
103
82
41
22
1
83
43
23
2
84
64
24
3
25
4
86
66
5
87
46
88
68
47
27
6
190
48
28
7
111 112
50
30
9
91
71
32
11
53
54
35
14
137
96
56
16
119
98
78
57
37
120
99
79
58
38
17
139 140
59
39
18
161
19
20
103 82
41 22 1
185
83
84
43
126 106
85
44 24
25 4
26 5
108 109 87
67 46
88 68
47 27
6
190
48 28
7
49
193 172
91 71
50
32 11
94
53
54 35 14
177
137
96
56
179 180
37 16
98
120 99
79 58
38 17
160 139 140
119
78 57
220
199 200 178
138
97 77
260 240
218 219
117 118
36 15
280 259
239
157 158 159
76 55
279
197 198
136
95
339 340
299 300
258 238
217
176
156
75
34 13
196
175
115 116
74
33 12
216
134 135
93 73
52
195
155
114
277 278 257
20
319 320
297 298
237
60
40
19
337 338
256
236 215
174
133
92
51 31
10
194
154
113
72
276 255
214
173
152 153
111 112
30 9
192
275 254
39
18
317 318 296
100
l80
59
38
336
120
99
79
58
17
316
234 235 213
131 132
90
274 253
233 212
171 151
70
29 8
191
130
89 69
232
335
295
98
78
37
160
139 140
119
57
16
315
294
97
56
36
334
314
273
251 252
170
110
333
293
179 180
138
117 118
55
220
199 200
178
137
77
260
240
218 219
177
96
15
280
259
239
157 158 159
136
35
279
197 198
76
14
313
271 272
150
129
332
211
54
299 300
258
238
217
176
95
34
292
196
156
75
13
312
231 210
169
149
127 128
86
45
189 168
148
107
66
209
33
331
291
250 230
94
257
216
115 116
74
53
277 278
237
175
339 340
319 320
297 298
256
134 135
114
12
311
270
249 229
208
167 147
330
290
195
155
93
32
276
236
215
174
73
11
310
269
248
187 188 166
146
65
268
113
52
31
329
309
228
207
186
105
64
3
206
165 145
104
23 2
205
328
194
154
337 338
317 318
296
255
214
173
92
51
275
254
133
72
10
288 289
247 227
30
9
308
267
246
124 125
63 42
266
226
50
29
287
91
71
49
8
327
307 286
245
164
144
123
62
21
163
122
81
265
183 184
326
306
225
203 204
7
193
172
336
316
295
234 235
213
131 132
90
70
274
253
152 153
111 112
89
48
192
335
315
294
233
212
171
151
130
69
28
6
285
244 224
143
101 102
61
264
243
162
142
121
60
40
305
283 284
223
181 182
141
100
l80
324 325
27
5
191
110
88
68
47
26
323
242
87
67
211
170
129
108 109
46
303 304
262 263
222
25
190
150
273
232
334
314
293
251 252
231
210
169
149
127 128
86
45
189
333
313
292
271 272
250
230
209
332
312
291
270
249
168
148
331
311
290
229
208
167
66
4
201 202
179 180 160
24
282
241
220
199 200
178
138
97
77
36
15
177
261
221
85
3
322
302 281
260
240
218 219
117 118
76
55
280
259
239
157 158 159
136
95
279
197 198
301
299 300
258
238
217
176
156
75
34
13
196
175
94
257
216
115 116
74
33
12
195
319 320
277 278
237
321
339 340
297 298
256
134 135
93
73
52
276
155
114
317 318
236
215
174
133
92
51
31
10
194
337 338
296
255
214
154
113
72
316
275
254
173
152 153
336
295
234 235
193
172
315
274
213
131 132
90
49
192
171
151
70
29
8
191
335
294
253
233
212
334
314
293
273
232
211
130
89
69
313
251 252
170
110
333
292
271 272
150
129
312
231
210
169
149
108 109
67
26
189
332
291
250
230
209
127 128
311
270
249
168
148
331
290
229
208
167
107
330
310
269
248
187 188
106
45
268
207
126
85
309
228
147
329
288 289
247
166
146
65
44
267
186
105
308
227
206
165
145
328
287
246
124 125
63
42
266
185
104
307
226
205
164
144
123
62
21
163
327
286
245
225
183 184
101 102
61
265
244
224
143
306
285
203 204
162
142
121
264
243
223
326
23
2
207
107
330
310
269
248
187 188
106
44
268
126
65
43
22
1
b
●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●
84
309
228
147
329
288 289
247
166
146
105
64
42
21
19
83
63
267
186
124 125
308
227
206
165
328
287
246
145
104
82
62
266
185
123
307
226
205
164
144
103
81
60
39
17
122
61
59
38
16
100
163
327
286
245
225
183 184
143
306
265
244
224
326
285
203 204
162
101 102
l80
264
243
223
142
121
120
79
305
283 284
242
161
141
139 140
78
303 304
262 263
222
181 182
160
119
324 325
201 202
179 180
138
97
76
14
178
117 118
55
34
13
137
220
323
282
241
221
199 200
177
302
261
260
240
218 219
322
281
280
259
239
157 158 159
95
54
279
197 198
176
301
299 300
258
238
217
156
75
53
12
216
175
94
74
257
321
319 320
277 278
237
115 116
93
32
11
195
339 340
297 298
256
134 135
73
52
31
10
276
155
114
317 318
236
215
174
133
72
51
30
8
194
337 338
296
255
214
154
92
71
316
275
254
173
113
91
70
29
7
193
172
336
295
234 235
213
131 132
315
274
152 153
111 112
49
28
6
192
171
151
89
48
27
5
191
170
335
294
253
233
212
334
314
293
273
232
211
130
69
313
251 252
110
88
68
46
26
4
108 109
86
25
3
190
333
292
271 272
150
129
312
231
210
169
149
127 128
107
45
189
332
291
250
230
209
168
148
311
270
249
208
331
290
229
167
66
44
23
1
106
330
310
269
248
207
126
65
268
187 188
85
64
309
228
147
329
288 289
247
166
146
105
84
63
267
186
165
308
227
206
145
328
287
246
124 125
83
62
266
185
104
307
226
205
164
144
103
81
61
40
19
121
163
327
286
245
225
183 184
143
306
265
244
224
203 204
162
142
100
59
39
18
161
326
285
264
243
223
101 102
l80
305
283 284
201 202
141
139 140
303 304
242
222
181 182
160
324 325
262 263
241
220
323
282
261
179 180
138
117 118
76
35
14
137
302
221
199 200
178
322
281
260
240
218 219
177
301
280
259
239
157 158 159
136
55
279
197 198
321
299 300
258
238
217
176
95
54
34
13
196
156
75
257
216
175
319 320
277 278
237
115 116
74
33
12
195
339 340
297 298
256
134 135
93
73
52
276
155
114
317 318
236
215
174
133
92
51
31
10
194
337 338
296
255
214
154
113
72
316
275
254
173
152 153
336
295
234 235
193
172
315
274
213
131 132
90
49
192
171
151
70
29
8
191
335
294
253
233
212
334
314
293
273
232
211
130
89
69
313
251 252
170
110
333
292
271 272
150
129
312
231
210
169
149
108 109
67
26
5
189
332
291
250
230
209
127 128
311
270
249
168
148
331
290
229
208
167
107
330
310
269
248
187 188
106
45
268
207
126
85
309
228
147
329
288 289
247
166
146
65
44
267
186
105
308
227
206
165
145
328
287
246
124 125
63
42
266
185
104
307
226
205
164
144
123
62
41
0
163
327
286
245
225
183 184
143
306
265
244
224
326
285
203 204
162
142
121
264
243
223
201 202
10
Aspen
Avicel
●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●
39 18
100 l80
59
60 40
19
20
2
Figure S2: The integrated omics models of Pycci 137 and Pycsa 1264. Pycci 137: Pycnoporus cinnabarinus CIRM-BRFM 137. Pycsa 1264: Pycnoporus sanguineus CIRM-BRFM 1264. a: The genome-wide mean transcription of the genes from all conditions. b: The count of the total proteins secreted showing hotspots. c: The groups of substrate-specific highly transcribed genes (>12 log2 read count) were labeled and highlighted. C: Common to all substrates. M: Maltose. Av: Avicel. A: Aspen. P: Pine. W: Wheat straw. NOTE: No RNA-seq data available for Pycsa 1264 grown on pine.
Transcription (normalized log2 read count)
16
321 253
14 20
235 217
12 15 10
164 145
91
56
1
39
2
41
5
6
7
101
64 45
27 8
65 46
67 48
10
68 49
30
31
11
12
106
13
51
52 34
14
15
144
10
142
54 36
17
61 41
254
217
20
199
219 201
181 164
127
165
128 109
10 91
129
74 56
20 1
0
75
38
39
77
22 3
23 4
78
42 24
5
79
99
26 7
81
46
47 29
10
48 30
11
85 67
31 12
86 68
49
2
143 124
88
52 34
15
53 35
16
17
18
M253 254 Av Av 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 M 236 Av 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
M 199 Av 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 Av 182 183 184 185 186 187 188 189 M 190 191 M 192 193 194 195 196 197 198 181 AAv C W163 P 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 A 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 M 145 146 Av 131 132 133 134 135 136 137 138 139 140 141 142 143 144 MP M 130 127 128 Av 129 Av109M 110C 111 M 112 113 114 115 116 P 117 118 119 120 121 122 123 124 125 126 A91M Av92P A93 C94 95 96 97A 98 99 100 101 102 103 104 105 106 107 108 C P75 P76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 73 74 P AP AP A C AW 55 56 57 W 58 W 59 60 61 62 63 64 65 66 67 68 69 70 71 72 A P Av A39Av PW A44 45 46 47 48 49 50 51 52 53 54 C37 38C W 41 42 43 P 40 W A24P 25 AvW C19 C20 21C AW22P AW23Av 26 27 28 29 30 31 32 33 34 35 36 P W AAv A P AAv Av AvW C2 C3 W 1C 4P W 5 W6P 7W 8 9 10 11 12 13 14 15 16 17 18
0
103 82
22 1
9
51
12
13
239
137
55
179 180
138
15
98
2
43
126 106
85 65
44 24
45
4
46
5
47 27
6
7
110
48 29 8
59 39
17
172
91
51 31
10
11
133 114
52 33 12
54 35 14
137
178
56 37 16
119
120 99
79 58
38 17
160 139 140
98 78
57
220
179 180
138
97 77
260 240
199 200
117 118
36 15
239 218 219
177
96 76
55
280 259
157 158 159 136
95 75
34 13
176
156
339 340
279
238
217
20
299 300
258
197 198
115 116 94
74 53
237 216
175
155
257
19
319 320
297 298
277 278
196
134 135
93 73
215
174
337 338
256
236
195
154
113
32
214
173
92 72
276
60 40
18
317 318 296
255
234 235
152 153
71
275
194
336
316
295
254
213
131 132
50
274
193
111 112
30 9
171
90 70
49
212
335
315
294
253 233
192
151 130
89 69
28
170
129
88 68
211
191
150
108 109 87
67
210
169
149
273
232
334
314
293
251 252
231
190
168
148
107
26
209
127 128
86 66
25
167 147
230
333
313
292
271 272 250
189
332
312
291
270
229 208
331
311
290
249
228
207
166
330
310
269
248
187 188
146
105 84
64
3
206
165
268
227
329
309
100 l80
58 38
16
120 99
79
57 37
160 139 140
119
78
56 36
220
199 200 178
97 77
260 240
157 158 159
76
14
280 259
218 219
177
96
35
238
117 118
95
34
279
217
136
75
299 300
258
197 198 176
156
54
33
11
216 196
115 116
53
32
257 237
175
155
74
52
31
215
94
73
277 278
236
339 340
319 320
297 298
256
134 135 114
93
72
10
288 289
247
186
145
104 83
23
205
164
267
226
185
328
308 287
246
124 125
63 42
266
225
144
123
62
21
163
143
122
41
36
235
217
61
54
50
154
133 113
92
71
276
195
174
337 338
317 318 296
255
214 194
152 153
91
275
234 235
173
336
316
295
254
213
131 132
30
274
193 172
111 112
49
8
327
307 286
245
203 204
162
81
5
265
224
326
306 285
244
183 184
142
121
264
243 223
101 102
90 72
305
201 202
161
108 89
222
141
151
90
29
212
335
315
294
253 233
192 171
70
48
7
211
130
89
28
6
324 325
283 284
242
181 182
10
5
150
69
47
232
191 170
110
88
27
210
129
68
46
323
262 263
221
15
87
26
4
149
108 109
67
45
303 304 282
241
126
71
322
302
261
144
107
51
20
162
125
70
33 14
161
142
87
50
234
179 180
106
321
281
216
3
148
231
190 169
127 128
107 86
25
209
273
251 252
334
314
293
Pycsa1264 Frequency of secreted proteins
301
197 198
160
69
32 13
196
123 105
233
24
147
126
230
333
313
292
271 272 250
189 168
332
312
291
270
229 208
167
331
311
290
249
228
207
66
44
23
1
270
252
215
178
141
122 104
232
159
140 121
84 66
177 158
269 251
214
195
176
103
231 213
194
139
268
250
230
157
120
83 65
28 9
138
102
82
45
175
267
249
212
193
156
119 101
64
27 8
137
100
63 44
174
118
229 211
192
155
266 248
228
210
173
136
265
247
191
154
117
80
43 25
6
135
62
227
190 172
264 246
209
153
98
61
226
208
171
116
263
245
189
152 134
97
225
188
115
262
244
207
170
133
60 41
224
151
114 96
59 40
169
261
243
206
187
150 132
95 76
223 205
168
113
260
242
186
149 131
58
21 2
185
112 94
57
37 19
130 111
222 204
167
259
241
221
148
93
73 55
166
258
240
203 184
147
110 92
220
183
146
257 239
202
182
145
256
238
218
200
163
255 237
43
22
146
330
310
269
248
187 188 166
106
65
268
227
329
309 288 289
247
206
85
64
42
21
145
105 84
63
267
186 165
124 125 104
83
62
18
144
82
205
328
308 287
246 226
185 164
123 103
Pycci137 Frequency of secreted proteins 236
143
266
225
327
307 286
245
203 204
163
122
81
5
265
224
326
306 285
244
183 184 162
121
90
53
16
181 182 161
264
243 223
101 102
72
35
242 222
141
126
71
305
201 202
89
70
33
221
108
88
324 325
283 284
262 263
241
162
125 107
87
50 32
143
323
303 304 282
261
216
161
124
69
234
322
302 281
179 180 160
142
105 86
233
301
15
197 198
178
123
104
270
252
215
196
141
122
85
66
29
9
84
232
159
140
103
47
28
177
269 251
214
195
158
121
102
231 213
176
139 120
83
230
157
268
250
194
175
138
267
249
212
193
156
119
82
63
26
137
100
44
25
174
118
81
62 43
24
4
99
229 211
192
155
266 248
228
210
173
136
265
247
191
154
117
80
61 42
23
135
98
227
190 172
264 246
209
153
116
79
226
208
171 152
134
97
60
225
263
245
189
170
115
262
244
207 188
133
78
59
224
151
114
77
22 3
132
96
40
21
169
261
243
206
187
150
95 76
223 205
168
113
260
242
186
149 131
58
38 20
185
112 94
57
37 19
130
75
222 204
167
259
241
221
148
111
74
253
5
129
93
73 55
166
258
240
203 184
147
110 92
235
15
165
128 109
220
202 183
146
257 239
219 201
182
163
256
238
218
200
127
4
255 237
181
8 10 6 5
254
236
199
0
Count of secreted proteins
Pycsa1264 Global mean transcription
Pycci137 Frequency of secreted proteins Pycci137 Global mean transcription
b25
c
Pycsa1264
Pycci137
a 25
39 18
100 l80
59
60 40
19
20
Av A321 322 Av 323 Av 324 325 Av 326 327 328 329 330 331 M 332 333 334 335 336 337 338 339 340 W Av A301Av AvW W 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 Av AvW A281 Av Av W 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 C Av M 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 261 262 263 264 265 Av241M Av 242M 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 Av221MAv222M 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 Av201M 202 Av203W 204 205 206 W 207 208 209 210 211 212 213 214 215 216 217 218 219 220 C 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 181 Av 182M 183 184 Av A A 167 168 169 170 171 172 173 174 175 176 177 178 179 180 M Av 161 162M 163 164 165 166 W Av C 143C A144 M 156 157 158 159 160 141 142 W 145 146 147 148 149 150 151 152 153 154 155 Av A A C C M 133 134 135 136 137 138 139 140 C 127 128 129 130 131 132 121 122 123 124 W 125 126 Av 104C 105C Av C A103 Av Av M M M Av 101 102 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 W C81 82C 83C 84C Av85M AvA 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 C 63C 64C 65 66 Av67M A68M A69M 70 71 72 73 74 75 76 77 78 79 l80 61 62 C C42 43C C44 C45 46 C47 48 A49 50 51 52 53 54 55 56 57 58 59 60 41 C 22C 23C 24C 25C 26C 27C 28 29 A30 31A 32 33 34 35 36 37 38 39 40 21 Av AAv AAv C1 C2 C3 4 C5 AW 6 13 14 15 16 17 18 19 20 W7 8W 9 10A W11 W12 W
3
Supplementary Material
3
Supplementary Tables
Table S1: Spearman’s rank correlation of genome-wide transcriptome and secretome for the three Pycnoporus strains. Spearman’s rank correlation coefficients were calculated from the node-wise mean transcription and the total count of secreted proteins for the three Pycnoporus strains. The coefficients for the three strains were approximately 0.55 (p 12 log2 average read counts of the node on each biomass. Unique nodes/genes: The number of nodes containing genes highly transcribed on a single complex biomass (either aspen, pine, or wheat straw). Genes selected: The number of highly transcribed genes was determined by the further filtration based on the differential gene expression (log2 fold changes >1) with statistical significance (adjusted p < 0.05). Secretion detected: The secretion of proteins detected. The ratio of the detected proteins divided by the total genes is shown in the brackets. CAZyme: Carbohydrateactive enzymes. Unknown genes: genes with no functional annotations. Unknown secreted: Uncharacterized proteins identified in the secretomes. The detailed lists are available (Data S2). NOTE: No RNA-seq data available for Pycsa 1264 grown on pine. Pycnoporus cinnabarinus BRFM 137 (Pycci 137) Biomass
Biomassspecific nodes / genes
Unique nodes / genes
Genes selected
Secretion detected
Aspen
12 / 159
5 / 37
117
27 (23.0%)
Pine
11 / 194
3 / 65
124
24 (17.9%)
Wheat straw
8 / 129
-
78
21 (26.9%)
CAZymes AA1_1, EXPN, GH2, GH3, GH5_9, GH13_1, GH18, GH18CBM5, GH27, GH28, GH31, GH35, GH79, GH88, GH92, GH95, GH125 AA1_1, AA3_2, EXPN, GH2, GH3, GH5_9, GH13_1, GH18, GH27, GH28, GH31, GH35, GH37, GH88, GH92, GH95, GH92, GT4, GT32 AA1_1, EXPN, GH2, GH3, GH5_9, GH13_1, GH18, GH27, GH28, GH31, GH35, GH88, GH92, GH95, GH125
Unknown genes
Unknown secreted
31
2
31
2
19
1
Pycnoporus sanguineus BRFM 1264 (Pycsa 1264) Biomass
Biomass-specific nodes / genes
Unique nodes / genes
Genes selected
Secretion detected
Aspen
13 / 229
6 / 91
91
15 (16.5%)
Wheat straw
11 / 179
4 / 41
88
20 (22.7%)
Unknown genes
Unknown secreted
AA1_1, CE16, GH16, GH18, GH18CBM5, GH43, GH88, GH92, GH125
30
1
CE15, GH2, GH3, GH18, GH18-CBM5, GH28, GH43, GH76, GH88, GH92, GH95, GH125, PL8_4
21
1
CAZymes
8
4
Supplementary Texts
Text S1: Detailed descriptions of the profiles of Pycci 137 and Pycsa 1264 for the selection of genes regulated in substrate-specific manners and the selection of nodes enriched in secreted proteins. We focused on the genes from Pycci 137 and Pycsa 1264 that were differentially expressed and coregulated in response to the plant substrates (i.e. aspen, pine, and wheat straw) in contrast to the simple substrates (i.e. maltose and cellulose; data S2; table S3). In the case of Pycci 137, we identified eight, eleven and twelve nodes contained genes differentially regulated on wheat straw, pine, and aspen, respectively. Of these, seven nodes were commonly found in response to the three substrates. Those nodes were enriched in genes coding for CAZymes potentially active on the plant biomass. While the nodes selected from Pycco 310 contained several genes coding for family AA2 lignin-active enzymes, the nodes selected from Pycci 137 did not contain AA2 but did contain two genes coding for AA1_1 laccases (protein ID 8672; 3446). Laccases are thought to contribute to lignin depolymerization through the oxidation of lignin-derived phenolics (Munk et al., 2015). Consistent with the absence of AA2 peroxidases in the selected nodes, no gene coding for AA3_2 or AA5_1 auxiliary oxidoreductases was selected. The selected nodes contained genes coding for pectin-active enzymes GH28 (protein ID 8001; 3798), GH88 (8220), and hemicellulose such as a GH27 predicted arabinosidase (7245) and a GH95 predicted xyloglucanase (929). A gene coding for a predicted GH2 mannosidase (1092) was found in the nodes regulated on the three substrates despite only pine wood containing this saccharide, suggesting that this gene is not specifically regulated in response to mannan, but is rather coregulated with other biomass degrading enzymes. Among the co-regulated genes, some of them were predicted as cytochrome P450 genes, suggesting common mechanisms for metabolization of the degradation products by the fungus (protein IDs 2161; 8493; 1192). Some proteins that were predicted for secretion were notably co-regulated with biomass degrading CAZymes (e.g. protein IDs 1391; 2712; 4662). As observed for Pycco 310, some genes were specifically regulated on pine that could reflect a metabolic adaptation to this substrate, and to the detoxification of the molecules derived from its degradation (e.g. predicted cytochrome P450; protein ID 5741 and 5611). In the case of Pycsa 1264, we identified 11 and 13 nodes that contained genes differentially regulated on wheat straw and aspen respectively. The behavior of Pycsa 1264 was similar to Pycci 137 as Pycsa 1264 showed differential expression of an AA1_1 laccase (protein ID 1560767) on the plant substrates and the up-regulation of pectin (GH88; 1428239) and hemicellulose active enzymes including a predicted GH2 mannosidase (1664834) on the plant substrates. The three nodes containing the highest number of proteins detected in the secretome were selected from the secretomic topography of Pycci 137 and Pycsa 1264 (Table S2). The genes coding for the most frequently secreted proteins showed the similar tendencies to Pycco 310. The presence of Avicel might have triggered the intensive transcription of the genes that led to the production of cellulases and hemicellulases for all the strains. The selected nodes showed similar CAZyme contents as Pycco310, and contained a consistent number of CAZymes associated with a CBM1 module active on cellulose and glucan polymers. Notably, the genes coding for CBM1-associated CAZymes were systematically grouped in the same
9
Supplementary Material nodes (nodes 14 and 220 for Pycco 310, node 7 for Pycci 137, node 281 for Pycsa 1264), suggesting that those genes are co-regulated in response to the different substrates. As observed from the transcriptome analyses, we also detected AA1_1 predicted laccases and GH2 predicted mannosidase in the secretomes of Pycci 137. Furthermore, an AA8-AA3 predicted protein was found in the secretomes of the three strains and the corresponding genes belong to nodes that were enriched in secreted proteins. AA8-AA3 CAZymes, which are modular enzymes, correspond to cellobiose dehydrogenases. They act in synergy with AA9 Lytic Polysaccharide Monooxygenases for the oxidative cleavage of glycosidic bonds (Bennati-Granier et al., 2015). The association of AA8-AA3 and AA9 genes in a same node in Pycco 310 (node 14) and in Pycsa 1264 (node 281) shows that the genes are co-regulated therefore strengthening the hypothesis of synergetic activities in vivo. References 1. Bennati-Granier, C., Garajova, S., Champion, C., Grisel, S., Haon, M., Zhou, S., et al. (2015). Substrate specificity and regioselectivity of fungal AA9 lytic polysaccharide monooxygenases secreted by Podospora anserina. Biotechnol. Biofuels 8, 90. doi:10.1186/s13068-015-0274-3. 2. Munk, L., Sitarz, A. K., Kalyani, D. C., Mikkelsen, J. D., and Meyer, A. S. Can laccases catalyze bond cleavage in lignin? Biotechnol. Adv. 33, 13–24. doi:10.1016/j.biotechadv.2014.12.008.
10
