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Table 1 Fungal carbohydrate metabolism and CAZy. EBSeq [42, 43] was used to estimate posterior probability of differential expression (PPDE) ≥ 0.95. A full DE transcript list including expression data, functional description (if available), gene ontology terms (if available) and secondary annotation (if available) is provided in Additional file 6

From: Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination

Monosaccharide transporters
Query id Cont mean tpm Treat mean tpm FC 1° annotation id Subject description
 c601571_g1_i1 0.33 275.43 830.24 gi|751683823|gb|KIM33975.1| Monosaccharide transporter (MST)
 c601571_g1_i3 0.00 25.71 High gi|751683823|gb|KIM33975.1| Monosaccharide transporter (MST)
 c601571_g1_i7 0.00 18.19 inf gi|749760949|gb|KII85851.1| Monosaccharide transporter (MST)
CAZy
 c601768_g1_i4 0.01 12.09 891.69 tr|A8N526|A8N526_COPC7 Exo-beta-1,3-glucanase (GH5)
 c601246_g1_i2 0.00 9.29 inf tr|S7QIL0|S7QIL0_GLOTA Glycoside hydrolase (GH13)
 c601246_g1_i3 0.00 8.75 inf tr|S7QIL0|S7QIL0_GLOTA Glycoside hydrolase (GH13)
 c601246_g1_i1 0.00 3.40 inf tr|S7QIL0|S7QIL0_GLOTA Glycoside hydrolase (GH13)
 c598537_g2_i2 0.00 20.09 inf gi|695542974|ref.|XP_009543687.1| Glycoside hydrolase family 13 protein
 c600093_g2_i1 0.00 2.50 inf gi|646308860|gb|KDQ30003.1| Glycoside hydrolase family 13 protein
 c598962_g2_i1 0.00 4.02 inf gi|691791220|emb|CDO73299.1| Glycoside Hydrolase Family 13 protein
 c546152_g1_i1 0.00 7.98 inf tr|F8PDS7|F8PDS7_SERL9 Glycoside hydrolase family 13/GT5 protein
 c594633_g1_i2 0.11 50.90 449.23 gi|751693072|gb|KIM43056.1| Glycoside hydrolase family 131 protein
 c569099_g1_i1 0.00 6.22 inf gi|595767974|ref.|XP_007262530.1| Glycoside hydrolase family 16 protein
 c601155_g2_i1 0.00 3.25 inf gi|751697951|gb|KIM47928.1| Glycoside hydrolase family 16 protein
 c601155_g2_i2 0.00 9.44 inf gi|751718111|gb|KIM67108.1| Glycoside hydrolase family 16 protein
 c601339_g1_i1 0.00 8.66 inf tr|M2QB49|M2QB49_CERS8 Glycoside hydrolase family 3 protein
 c594608_g1_i1 0.00 4.13 inf tr|S7Q7X9|S7Q7X9_GLOTA Glycoside hydrolase family 38 protein
 c601768_g1_i2 0.00 4.18 High gi|749771114|gb|KII95444.1| Glycoside hydrolase family 5 protein
 c601768_g1_i3 0.22 2.91 13.51 gi|749771114|gb|KII95444.1| Glycoside hydrolase family 5 protein
 c598880_g1_i5 0.04 104.28 2617.19 gi|660966484|gb|KEP50967.1| Barwin-like endoglucanase GH45
 c600699_g2_i2 0.00 5.19 inf gi|761954826|gb|KIY74457.1| Glycoside hydrolase family 45 protein
 c600240_g5_i1 0.04 37.05 862.09 gi|597903192|ref|XP_007298895.1| Glycoside hydrolase family 72 protein
 c597573_g1_i2 0.00 4.93 inf tr|M2RHY3|M2RHY3_CERS8 Glycosyltransferase family 1 protein
 c601034_g1_i3 0.00 5.05 inf gi|751699172|gb|KIM49104.1| Glycosyltransferase family 15 protein
 c601818_g1_i1 0.00 6.08 inf tr|F8NSE4|F8NSE4_SERL9 Glycosyltransferase family 2 protein
 c601727_g2_i2 0.00 4.46 inf gi|646307867|gb|KDQ29011.1| Glycosyltransferase family 2 protein
 c602102_g1_i1 0.00 1.47 inf gi|749763786|gb|KII88520.1| Glycosyltransferase family 2 protein
 c602018_g4_i1 0.00 21.01 inf gi|761950386|gb|KIY70060.1| Glycosyltransferase family 20 protein
 c593342_g2_i1 0.00 33.59 inf gi|754372083|gb|KIP04804.1| Glycosyltransferase family 4 protein
 c586703_g1_i3 0.00 7.27 inf gi|751716241|gb|KIM65247.1| Glycosyltransferase family 48 protein
 c593828_g1_i1 0.00 4.05 inf tr|G4T6Z6|G4T6Z6_PIRID Pectate lyase 1
 c576776_g1_i2 0.05 2.53 50.56 tr|R7SST1|R7SST1_DICSQ Galactose oxidase (AA5)
 c594647_g2_i1 0.20 25.38 127.24 gi|752370879|gb|KIO28638.1| Carbohydrate esterase family 12 protein
 c592601_g1_i1 0.03 13.15 414.76 gi|749760957|gb|KII85859.1| Carbohydrate esterase family 4 protein
 c600395_g1_i1 0.00 3.82 inf gi|691792079|emb|CDO72533.1| Carbohydrate-binding module family 1/GH18
 c600797_g1_i1 0.00 21.07 inf tr|V2WEI0|V2WEI0_MONRO Carbohydrate-binding module family 12 protein
 c600797_g1_i4 0.00 6.68 inf gi|695558353|ref.|XP_009547634.1| Carbohydrate-binding module family 12 protein
 c590812_g2_i2 0.00 7.48 inf gi|751000067|gb|KIK42253.1| Carbohydrate-binding module family 50 protein
EM pathway
 c598496_g1_i1 0.00 15.04 inf tr|E2M098|E2M098_MONPE Glucose-6-phosphate isomerase
 c596025_g1_i2 0.00 7.96 inf tr|S7Q9Q0|S7Q9Q0_GLOTA Glucokinase regulator
 c594601_g1_i2 0.00 13.43 inf gi|751180168|gb|KIL66119.1| Hexokinase
 c585806_g1_i1 0.02 18.89 1107.17 gi|646397316|gb|KDQ61522.1| Phosphoglucomutase
 c602057_g2_i2 0.00 11.14 High gi|646396300|gb|KDQ60552.1| Phosphoglycerate kinase
 c602057_g2_i3 0.07 11.10 151.91 tr|V2XST0|V2XST0_MONRO Phosphoglycerate kinase
 c598088_g2_i2 0.00 5.55 inf gi|749895786|gb|KIJ63485.1| Phosphoglycerate mutase-like protein
 c600469_g2_i1 0.00 10.71 inf gi|749764415|gb|KII89090.1| Phosphoglycerate mutase-like protein
 c572773_g2_i1 0.00 51.66 inf gi|695531349|ref.|XP_009540596.1| Enolase
 c596540_g1_i2 0.00 4.59 inf gi|646309757|gb|KDQ30900.1| Pyruvate kinase
 c600228_g1_i1 0.00 15.88 inf A0A0C9X171|A0A0C9X171_9AGAR Fructose-1,6-bisphosphatase
 c600228_g2_i1 0.00 3.03 inf gi|807746795|ref|XP_012178192.1| Fructose-1,6-bisphosphatase
Trehalose and glycogen metabolism
 c593922_g1_i3 0.01 2.87 238.65 tr|A8NBB7|A8NBB7_COPC7 Trehalose-6-phosphate phosphatase
 c593922_g1_i2 0.01 1.75 233.45 tr|A8NBB7|A8NBB7_COPC7 Trehalose-6-phosphate phosphatase
 c590104_g1_i2 0.00 5.27 inf gi|576992104|gb|EUC64784.1| Alpha,alpha-trehalose-phosphate synthase
 c601514_g2_i2 0.00 8.92 inf gi|636619097|ref|XP_008040683.1| Glycogen phosphorylase
 c601447_g1_i3 0.00 24.27 High tr|S7PZV3|S7PZV3_GLOTA Glycogen synthase
 c601447_g1_i4 0.02 5.34 267.52 tr|R7S2M9|R7S2M9_PUNST Glycogen synthase
Pentose phosphate pathway
 c599283_g2_i1 0.06 23.65 403.23 tr|S7QHH6|S7QHH6_GLOTA Glucose-6-phosphate 1-dehydrogenase
 c593556_g1_i1 0.00 4.43 inf tr|F8PCX3|F8PCX3_SERL9 6-Phosphogluconolactonase
 c579299_g1_i2 0.00 4.57 inf gi|695543481|ref|XP_009543815.1| 6-Phosphogluconate dehydrogenase
 c596260_g2_i1 0.00 6.07 inf tr|S7QN86|S7QN86_GLOTA 6-Phosphogluconate dehydrogenase, decarboxylating
 c599261_g6_i1 0.40 29.50 73.50 laccaria|B0DN26|B0DN26_LACBS Transketolase
 c586684_g1_i2 0.00 9.94 inf gi|807755903|ref|XP_012182746.1| Transaldolase
Ethanol
 c595474_g1_i1 0.00 16.64 inf gi|754377558|gb|KIP10174.1| Pyruvate decarboxylase
TCA cycle
 c578376_g1_i1 0.00 20.05 inf tr|A8N9T7|A8N9T7_COPC7 Pyruvate carboxylase
 c590892_g1_i1 0.00 16.91 inf gi|924125151|emb|CUA68456.1| Pyruvate dehydrogenase E1 component subunit alpha
 c602021_g6_i1 0.00 20.10 inf tr|D8PKQ0|D8PKQ0_SCHCM Acetyltransferase component of pyruvate dehydrogenase
 c569980_g1_i1 0.00 12.30 High tr|S8EDA9|S8EDA9_FOMPI ATP-utilising phosphoenolpyruvate carboxykinase
 c601865_g3_i1 0.00 21.12 inf tr|R7STC2|R7STC2_DICSQ ATP-utilising phosphoenolpyruvate carboxykinase
 c601865_g3_i2 0.00 9.71 inf tr|R7STC2|R7STC2_DICSQ ATP-utilising phosphoenolpyruvate carboxykinase
 c569980_g1_i2 0.09 16.00 168.90 gi|749767591|gb|KII92023.1| ATP-utilising phosphoenolpyruvate carboxykinase
 c596905_g1_i4 0.00 12.95 inf tr|F8ND69|F8ND69_SERL9 Malate dehydrogenase
 c596978_g1_i2 0.01 18.99 1489.83 gi|599119246|ref.|XP_007387111.1| NAD-malate dehydrogenase
 c596978_g1_i1 0.01 13.56 1360.27 gi|599119246|ref.|XP_007387111.1| NAD-malate dehydrogenase
 c601738_g1_i3 0.00 9.89 inf gi|751717279|gb|KIM66280.1| Succinyl-coa synthetase alpha chain, gdp-forming
 c600881_g1_i4 0.01 1.61 299.16 tr|M2RB43|M2RB43_CERS8 Succinyl-CoA synthetase beta chain SSC-beta
 c600756_g1_i1 0.00 11.35 inf gi|646392723|gb|KDQ57237.1| Homocitrate synthase
 c601939_g2_i2 0.05 13.42 261.20 gi|754372092|gb|KIP04812.1| Isocitrate dehydrogenase
 c583773_g1_i1 0.00 5.65 inf gi|636616019|ref|XP_008039144.1| Peroxysomal citrate synthase
 c585571_g1_i2 0.03 2.64 81.61 gi|751696020|gb|KIM45999.1| Aconitase
 c591611_g1_i1 0.00 10.96 inf gi|636618909|ref|XP_008040589.1| Aconitate hydratase
 c575147_g1_i1 0.00 5.73 inf gi|597981973|ref|XP_007363646.1| 2-Oxoglutarate dehydrogenase mitochondrial precursor
 c597062_g1_i2 0.00 16.03 inf gi|749834860|gb|KIJ12495.1| Succinate dehydrogenase
 c602048_g2_i2 0.00 5.52 inf gi|749830076|gb|KIJ08477.1| Succinate dehydrogenase
 c600915_g2_i1 0.07 13.16 190.79 tr|M2PCH1|M2PCH1_CERS8 Succinate dehydrogenase
 c600002_g1_i4 0.00 4.55 inf tr|D8Q9I2|D8Q9I2_SCHCM Fumarate reductase
 c600002_g1_i1 0.00 17.05 inf gi|752345450|gb|KIO04521.1| Fumarate reductase
Leading to AAs
 c601513_g2_i5 0.00 6.72 inf tr|M2PP80|M2PP80_CERS8 Glutamine sythetase
 c600930_g1_i1 0.00 9.88 inf tr|V2X687|V2X687_MONRO Glutamate synthase