TABLE 2.
New and old gene model assignments for NP-induced genes from P. chrysosporium and corresponding nutritional regulation information
| Genea | JGI gene ID
|
JGI protein ID (version 2) | P450 familyc | Nutritional regulation under LN vs HN conditionsd | |
|---|---|---|---|---|---|
| Version 1b | Version 2 | ||||
| P450 genes induced by NP in ME cultures | |||||
| PC-2 | ug.20.35.1 | e_gwh2.2.241.1 | 129114 | CYP63A2 | U(HN) |
| Pff 10a | pc.21.108.1 | e_gww2.9.198.1 | 132113 | CYP512H1 | U(HN) |
| Pff 129 | pc.81.21.1 | fgenesh1_pg.C_scaffold_4000627 | 3368 | CYP5141D1 | NR |
| Pff 141 | pc.1.6.1 | e_gww2.8.145.1 | 138737 | CYP5035A5 | NR |
| Pff 164a | ug.1.19.1 (pc.1.261.1) | e_gww2.5.195.1 | 130996 | CYP53C2 | U(HN) |
| Pff 164c | ug.1.25.1 | e_gwh2.5.180.1 | 121157 | CYP5037B2 | NR |
| Pff 169f | pc.83.7.1 | fgenesh1_pg.C_scaffold_1000770 | 770 | CYP5144A9 | U(HN) |
| Pff 173 | genewise2nd.66.11.1 (genscan.66.16.1) | fgenesh1_pg.C_scaffold_2000954 | 1976 | CYP5150B1 | U(HN) |
| Pff 205h | genewise2nd.24.9.1 (pc.24.11.1) | e_gww2.1.401.1 | 133311 | CYP5144A7 | U(HN) |
| Pff 252d | genewise2nd.24.17.1 (pc.24.19.1) | e_gww2.1.429.1 | 132914 | CYP5144D4 | U(LN) |
| Pff 311b | pc.142.11.1 | fgenesh1_pg.C_scaffold_9000456 | 5852 | CYP5136A2 | NR |
| Pff 311c | pc.142.5.1 | e_gww2.9.179.1 | 131921 | CYP5144C7 | NR |
| Pff 388a | pc.181.9.1 | Not assigned | CYP5141A1 | NR | |
| Pff 4a | pc.16.161.1 (genscan.16.7.1) | fgenesh1_pg.C_scaffold_8000176 | 5001 | CYP5136A3 | U(HN) |
| Pff 5 | ug.11.23.1 | fgenesh1_pg.C_scaffold_11000011 | 6326 | CYP5145A3 | NR |
| Pff 7 | genewise2nd.38.22.1 | e_gwh2.2.246.1 | 129675 | CYP5139A1 | NR |
| Pff 78 | ug.128.46.1 | e_gww2.3.561.1 | 137301 | CYP5036A3 | NR |
| Pff 82b | ug.43.44.1 | fgenesh1_pg.C_scaffold_22000065 | 9198 | CYP5035C1 | NR |
| P450 genes induced by NP under LN conditions | |||||
| foxy1 | ug.73.16.1 (pc.73.11.1) | e_gww2.3.23.1 | 137601 | CYP505D4 | U(HN) |
| pc-2 | ug.20.35.1 | e_gwh2.2.241.1 | 129114 | CYP63A2 | U(HN) |
| Pff 137a | pc.30.118.1 | fgenesh1_pg.C_scaffold_18000091 | 8720 | CYP512B5 | NR |
| Pff 15c | ug.50.27.1 | fgenesh1_pg.C_scaffold_5000216 | 3654 | CYP5147A1 | NR |
| Pff 169f | pc.83.7.1 | fgenesh1_pg.C_scaffold_1000770 | 770 | CYP5144A9 | U(HN) |
| Pff 205d | genewise2nd.24.5.1 (pc.24.8.1) | e_gww2.1.391.1 | 133327 | CYP5144A3 | NR |
| Pff 242b | ug.73.16.1 | e_gww2.3.23.1 | 137601 | CYP505D4 | U(HN) |
| Pff 242c | ug.73.15.1 (pc.73.10.1) | e_gww2.3.57.1 | 137435 | CYP505D3 | U(HN) |
| Pff 249a | ug.53.54.1 (genscan.53.52.1) | fgenesh1_pg.C_scaffold_20000051 | 8961 | CYP5035A3 | U(LN) |
| Pff 252a | pc.24.27.1 | gwh2.1.540.1 | 28946 | CYP5142A3 | U(HN) |
| Pff 361a | pc.73.4.1 | gww2.3.2.1 | 34980 | CYP505D2 | U(LN) |
| Pff 361b | ug.73.17.1 (pc.73.3.1) | Not assigned | CYP505D1 | U(HN) | |
| Pff 51 | pc.14.210.1 | fgenesh1_pg.C_scaffold_10000101 | 6018 | CYP5136A5 | NR |
| Pff 57 | pc.15.127.1 | gwh2.15.175.1 | 33411 | CYP5036A1 | U(HN) |
| Pff 7 | genewise2nd.38.22.1 | e_gwh2.2.246.1 | 129675 | CYP5139A1 | NR |
| Pff 86f | ug.20.43.1 (pc.20.56.1) | e_gwh2.2.406.1 | 129578 | CYP5142C1 | U(HN) |
| Pff 9 | ug.97.52.1 | fgenesh1_pg.C_scaffold_13000094 | 7306 | CYP5035A2 | NR |
| Peroxidase genes differentially regulated by NP under LN conditions | |||||
| lipA (M22720) | pc.85.52.1 | fgenesh1_pm.C_scaffold_19000014 | 10957 | ||
| lipC (M36815) | pc.85.38.1 | e_gww2.19.87.1 | 131738 | ||
| lipD (M18743) | pc.19.174.1 | fgenesh1_pg.C_scaffold_11000496 | 6811 | ||
| lipF (M80213) | pc.21.40.1 | e_gwh2.9.293.1 | 122202 | ||
| lipH (M24082) | pc.85.15.1 | e_gwh2.19.97.1 | 121806 | ||
| lipJ (AF140062) | genewise2nd.85.6.1 | e_gww2.19.111.1 | 131709 | ||
| lpoB (M37701) | pc.85.50.1 | e_gwh2.19.98.1 | 121822 | ||
| mnp1 (M60672) | pc.15.23.1 | e_gww2.15.98.1 | 140708 | ||
| mnp3 (U10306) | pc.27.12.1 | fgenesh1_pg.C_scaffold_1000878 | 878 | ||
| Transcription factor genes and signal transduction genes/gene homologs differentially regulated by NP in ME or LN cultures | |||||
| agal-A (AF246262) | pc.11.202.1 | e_gwh2.11.209.1 | 125033 | ||
| xynB-A (AF301904) | pc.120.11.1 | e_gww2.6.463.1 | 133788 | ||
| POR (AAG31349.1) | pc.51.97.1 | fgenesh1_kg.C_scaffold_12000002 | 11093 | ||
| cbhI-2 (S40817) | ug.139.1.1 | e_gww2.14.106.1 | 137042 | ||
| CDH (U46081) | pc.5.157.1 | fgenesh1_kg.C_scaffold_12000007 | 11098 | ||
| YAP2 (S68847) | genscan.183.4.1 | fgenesh1_pg.C_scaffold_5000600 | 4038 | ||
| TEC1 (M32797) | pc.100.54.1 | e_gwh2.13.284.1 | 126075 | ||
| Cellulose binding protein gene ac2 (AJ003224) | pc.47.15.1 | e_gwh2.2.646.1 | 129325 | ||
| gstA (AF425746) | pc.3.88.1 | fgenesh1_pg.C_scaffold_1000503 | 503 | ||
| OSM1 (Af184980) | pc.31.2.1 | e_gww2.13.222.1 | 135546 | ||
| pbs2 (NP_012407) | pc.200.8.1 | e_gww2.15.132.1 | 140816 | ||
| creA (AJ272151) | genewise2nd.23.8.1 | fgenesh1_pg.C_scaffold_8000320 | 5145 | ||
| uap (AB083397) | pc.93.60.1 | e_gwh2.22.25.1 | 121582 | ||
| glx1 (L47286) | pc.52.9.1 | fgenesh1_kg.C_scaffold_6000005 | 11068 | ||
| CBHI.1 (Z22528) | pc.139.26.1 | e_gwh2.14.89.1 | 127029 | ||
| STE12 (X16112) | pc.56.6.1 | gwh2.9.410.1 | 33036 | ||
a
NCBI accession numbers are shown in parentheses. Pff gene numbering is the same as that used in reference 7; the Pff numbering corresponds to the original scaffold numbers used by David Nelson on his cytochrome P450 webpage (http://drnelson.utmem.edu/whiterot.fasta.html).
b
Gene ID assigned in JGI genome annotation version 1. Numbers in parentheses represent the original (prerevision) JGI gene models of the draft genome as used by Doddapaneni and Yadav (7); these gene models were subsequently replaced by the revised JGI version 1 gene models.
c
Designations were assigned by the International Nomenclature Committee.
d
Nutritional regulation information was derived from Doddapaneni and Yadav (7). U(HN) indicates gene induction under HN conditions, U(LN) indicates gene induction under LN conditions, and NR means nonregulated.