. 2016 Sep 12;113(39):10968–10973. doi: 10.1073/pnas.1608454113

Table S2.

Differential transcription of CAZy genes likely involved in lignocellulose saccharification during wood decay by P. placenta

Protein ID	Sequence description^*	FPKM			Ratio,^† log₂ (early/late)
Protein ID	Sequence description^*	0–5 mm	15–20 mm	30–35 mm	Ratio,^† log₂ (early/late)
Genes up-regulated during early decay
111730/43189	GH28, polygalacturonase^‡	1,770.99	215.86	22.67	3.89
126976/none	Expansin-like protein	261.02	57.76	38.47	2.44
128179/none	Expansin-like protein	150.22	41.98	15.31	2.39
52150^§	GH13, α-amylase	9.07	1.88	1.75	2.32
48716^§	GH92^‡	39.68	14.79	7.43	1.84
48548/44386	CE16	19.21	12.22	3.82	1.26
Genes up-regulated during late decay
121191/112658	GH12, endo-1,4-β-glucanase (Cel12A)^‡	414.97	10,658.18	40,000.00	−5.93
103675/117690	GH5, endo-1,4-β-glucanase (Cel5B)^‡	567.05	14,037.16	27,715.90	−5.20
113670/90657	GH10, endo-1,4-β-xylanase^‡ (Xyn10A-1)	145.72	3,401.12	2,565.03	−4.36
55907/none	Feruloyl esterase-like protein^‡	15.15	292.26	295.84	−4.28
112732/59600	GH53, arabinogalactan endo-β-galactosidase	67.14	1,161.40	845.39	−3.90
115648/108962	GH5, endo-1,4-β-glucanase (Cel5A)^‡	1,281.83	18,023.56	18,075.02	−3.82
105534/none	GH10, endo-1,4-β-xylanase^‡	191.33	2,595.68	2,490.97	−3.73
126692/111332	GH79, endo-β-glucuronidase^‡	280.47	3,693.17	3,375.15	−3.66
55267/62952	Feruloyl esterase-like protein	6.50	78.31	67.22	−3.48
95568/none	GH5, endo-1,4-β-mannosidase^‡	336.24	3,709.42	3,670.98	−3.46
57321/121831	GH5, endo-1,4-β-mannosidase^‡ (Man5A)	768.00	9,072.98	7,533.55	−3.43
108959/110682	CE16	680.29	7,037.75	5,530.26	−3.21
125801/none	CE16^‡	898.50	8,878.10	7,453.55	−3.18
127469/51213	GH3, exo-1,4-β-xylosidase^‡	179.48	1,862.10	1,345.82	−3.16
130413/none	GH115^‡	228.66	2,141.71	1,561.95	−3.02
57564/56576	GH2, β-mannosidase^‡	491.70	4,424.31	3,441.54	−3.00
128500/128225	GH3, β-glucosidase^‡	89.14	651.60	764.68	−2.99
128150/98662	GH27, α-galactosidase^‡	527.60	4,444.57	3,462.98	−2.91
110809/none	GH43, α-l-arabinofuranosidase^‡	271.14	2,325.25	1,300.73	−2.74
107557/none	GH3, β-glucosidase^‡	611.85	3,777.99	3,909.44	−2.65
46915/95677	GH3, β-glucosidase^‡	37.06	264.56	158.74	−2.51
100745/54928	CE8	68.00	470.28	193.50	−2.29
120395/none	GH27, α-galactosidase^‡	232.84	1,332.89	887.59	−2.25
62300/none	GH16, putative laminarinase	172.25	941.88	640.80	−2.20
112941/61089	GH16, putative laminarinase^‡	352.10	1,941.99	1,050.66	−2.09
127993/128101	GH35, β-galactosidase^‡	229.84	1,123.50	814.75	−2.08
128334^§	GH16, putative laminarinase	135.34	511.84	593.66	−2.03
128269^§	GH5, β-mannosidase	15.93	73.89	54.45	−2.01
116992^§	GH92, α-1,2-mannosidase^‡	23.10	108.61	70.45	−1.95
113112^§	GH15-CBM20, glucoamylase^‡	54.66	229.57	182.17	−1.91
52805/112669	GH12, endo-1,4-β-glucanase	176.46	852.44	258.96	−1.65
54936^§	CE8, Pectin esterase precursor	22.86	93.07	36.07	−1.50

Differentially expressed CAZy genes that have predicted secretion signal peptides are shown. Early expression (0–5 mm) is compared with late expression (15–20 mm or 30–35 mm). Criteria for inclusion are fold change in expression greater than fourfold (FDR < 0.05) and FPKM > 5. Data are mean values from three bioreplicates. CBM, cellulose-binding module; CE, carbohydrate esterase.

CAZy genes were assigned according to www.cazy.org (58). Genes were annotated with Blast2GO v3.2, and then were further verified by BlastP with the UnitProt database via the NCBI (www.ncbi.nlm.nih.gov/) and JGI (genome.jgi.doe.gov/Pospl1/Pospl1.home.html) databases.

^{^†}

Genes are ranked according to the ratios of early expression (0–5 mm) to late expression (average of the expression levels at 15–20 mm and 30–35 mm).

^{^‡}

The encoded protein has been observed and identified (9, 26, 29).

^{^§}

A second allele is present in these cases but is excluded because its fold change in expression was less than fourfold or its FPKM was <5.