Table 1.
List of the top 20 upregulated Leptosphaeria maculans genes during the compatible interaction with canola cultivar Topas-wild at each of the four sampling points.
| Gene name | Gene ID | Locus | FPKM | SE | *Log2 (FC) | Padj | Functional annotations |
|---|---|---|---|---|---|---|---|
| 3 dpi | |||||||
| Gene_11912 | Lema_T061640 | lm_SuperContig_8_v2:1610355–1610701 | 12276 | 1400.46 | 13.04 | 0.00E+00 | Hypothetical protein |
| Gene_4884 | Lema_T109090 | lm_SuperContig_18_v2:862571–862990 | 14727 | 2585.81 | 10.89 | 0.00E+00 | Hypothetical protein |
| Gene_9702 | Lema_T050310 | lm_SuperContig_5_v2:114784–120578 | 1424 | 229.89 | 10.79 | 0.00E+00 | Chitin binding/Carbohydrate-Binding Module Family 18 |
| Gene_1799 | Lema_T087550 | lm_SuperContig_11_v2:702412–703074 | 8854 | 1176.77 | 10.36 | 0.00E+00 | Hypothetical protein (CSEP) |
| Gene_8310 | Lema_T032040 | lm_SuperContig_2_v2:2602620–2603501 | 1040 | 261.13 | 10.24 | 7.00E-159 | Hypothetical protein |
| Gene_11624 | Lema_T058760 | lm_SuperContig_8_v2:828284–829346 | 1890 | 257.48 | 10 | 0.00E+00 | Hypothetical protein SSP(Effector) |
| Gene_6862 | Lema_T118070 | lm_SuperContig_21_v2:752639–754522 | 1097 | 214.03 | 9.74 | 0.00E+00 | G-protein coupled receptor activity |
| Gene_2936 | Lema_T094030 | lm_SuperContig_14_v2:218210–219154 | 1330 | 153.58 | 9.56 | 0.00E+00 | Hypothetical protein |
| Gene_9395 | Lema_T042140 | lm_SuperContig_4_v2:1136979–1138783 | 1911 | 277.28 | 9.48 | 0.00E+00 | Alcohol dehydrogenase |
| Gene_6482 | Lema_T114270 | lm_SuperContig_20_v2:529112–533279 (-) | 6078 | 667.23 | 8.52 | 0.00E+00 | Hypothetical protein |
| Gene_8982 | Lema_T038010 | lm_SuperContig_3_v2:2203740–2205537 | 1054 | 150.79 | 8 | 0.00E+00 | Transporter activity |
| Gene_11976 | Lema_T062280 | lm_SuperContig_8_v2:1760041–1760879 | 2812 | 828.34 | 7.86 | 0.00E+00 | Fasciclin and related adhesion glycoproteins |
| Gene_7649 | Lema_T025430 | lm_SuperContig_2_v2:804099–805458 | 1215 | 335.02 | 7.7 | 0.00E+00 | Predicted transporter |
| Gene_11804 | Lema_T060560 | lm_SuperContig_8_v2:1317923–1319474 | 1108 | 232.60 | 7.65 | Hypothetical protein SSP(Effector) | |
| Gene_5070 | Lema_T110950 | lm_SuperContig_19_v2:299282–300301 | 1331 | 384.38 | 7.19 | 9.90E-111 | Hypothetical protein |
| Gene_3811 | Lema_T093240 | lm_SuperContig_15_v2:1293850–1295649 | 1757 | 427.33 | 7.14 | 0.00E+00 | Transporter activity |
| Gene_5572 | Lema_T015460 | lm_SuperContig_1_v2:975571–976381 | 1529 | 191.58 | 6.44 | 0.00E+00 | Hypothetical protein |
| Gene_6173 | Lema_T021470 | lm_SuperContig_1_v2:2566440–2566907 | 1504 | 256.68 | 6.41 | 5.90E-221 | Hypothetical protein |
| Gene_2652 | Lema_T079530 | lm_SuperContig_13_v2:633177–634702 | 2616 | 398.51 | 6.26 | 0.00E+00 | Hypothetical protein |
| Gene_1331 | Lema_T073560 | lm_SuperContig_10_v2:445682–445936 | 1122 | 371.94 | 6.22 | 0.00E+00 | Hypothetical protein |
| 5 dpi | |||||||
| Gene_4884 | Lema_T109090 | lm_SuperContig_18_v2:862571–862990 | 33992 | 1715.82 | 13.06 | 0.00E+00 | Hypothetical protein |
| Gene_10161 | Lema_T054900 | lm_SuperContig_5_v2:1424583–1425111 | 1399 | 427.40 | 12.98 | 2.50E-90 | Hypothetical protein |
| Gene_2216 | Lema_T084480 | lm_SuperContig_12_v2:827863–828642 | 1931 | 368.22 | 11.52 | 3.90E-96 | Predicted protein SSP(Effector) |
| Gene_10273 | Lema_T056020 | lm_SuperContig_5_v2:1712896–1714128 | 1282 | 381.49 | 11.44 | 0.00E+00 | Transcription factor |
| Gene_8310 | Lema_T032040 | lm_SuperContig_2_v2:2602620–2603501 | 1143 | 435.53 | 11.34 | 2.20E-214 | Oxidoreductase activity |
| Gene_9395 | Lema_T042140 | lm_SuperContig_4_v2:1136979–1138783 | 1072 | 263.45 | 9.61 | 0.00E+00 | Alcohol dehydrogenase |
| Gene_11804 | Lema_T060560 | lm_SuperContig_8_v2:1317923–1319474 | 2104 | 547.85 | 9.55 | 0.00E+00 | Hypothetical protein (CSEP) |
| Gene_6173 | Lema_T021470 | lm_SuperContig_1_v2:2566440–2566907 | 4527 | 730.72 | 8.97 | 0.00E+00 | Hypothetical protein |
| Gene_6375 | Lema_T113200 | lm_SuperContig_20_v2:228262–228840 | 1117 | 482.45 | 8.47 | 1.60E-196 | Hypothetical protein (CSEP) |
| Gene_1799 | Lema_T087550 | lm_SuperContig_11_v2:702412–703074 | 1209 | 279.42 | 8.46 | 1.70E-289 | Hypothetical protein (CSEP) |
| Gene_11976 | Lema_T062280 | lm_SuperContig_8_v2:1760041–1760879 | 1441 | 225.72 | 7.87 | 0.00E+00 | Fasciclin and related adhesion glycoproteins |
| Gene_6483 | Lema_T114280 | lm_SuperContig_20_v2:534387–534664 | 1243 | 384.15 | 7.2 | 0.00E+00 | Hypothetical protein |
| Gene_8491 | Lema_T033100 | lm_SuperContig_3_v2:491445–491728 | 1283 | 356.20 | 6.66 | 3.50E-20 | Hypothetical protein |
| Gene_1613 | Lema_T076380 | lm_SuperContig_10_v2:1509441–1509941 | 2525 | 1043.94 | 6.4 | 7.30E-75 | Hypothetical protein (CSEP) |
| Gene_616 | Lema_T006160 | lm_SuperContig_0_v2:2286680–2287371 | 1062 | 295.59 | 6.35 | 5.50E-208 | Hypothetical protein |
| Gene_7940 | Lema_T028340 | lm_SuperContig_2_v2:1614035–1614898 | 4379 | 1327.86 | 6.33 | 0.00E+00 | Transporter activity |
| Gene_415 | Lema_T004150 | lm_SuperContig_0_v2:1345345–1345518 | 1090 | 232.24 | 6.14 | 0.00E+00 | Aminotransferase/Catalytic activity |
| Gene_6466 | Lema_T114110 | lm_SuperContig_20_v2:490947–492054 | 1030 | 361.07 | 5.94 | 1.90E-196 | Ion channel activity |
| Gene_2652 | Lema_T079530 | lm_SuperContig_13_v2:633177–634702 | 1060 | 337.82 | 5.92 | 4.20E-292 | Hypothetical protein |
| Gene_234 | Lema_T002340 | lm_SuperContig_0_v2:882882–883215 | 1670 | 221.35 | 5.58 | 1.00E-18 | Hypothetical protein |
| 7 dpi | |||||||
| Gene_6534 | Lema_T114790 | lm_SuperContig_20_v2:655034–655196 | 18463 | 3470.09 | 18.02 | 1.30E-126 | Predicted protein |
| Gene_10161 | Lema_T054900 | lm_SuperContig_5_v2:1424583–1425111 | 2763 | 185.07 | 13.08 | 1.30E-130 | Hypothetical protein |
| Gene_2216 | Lema_T084480 | lm_SuperContig_12_v2:827863–828642 | 5389 | 739.19 | 12.12 | 3.80E-162 | Predicted protein SSP(Effector) |
| Gene_1515 | Lema_T075400 | lm_SuperContig_10_v2:1026907–1027349 | 1157 | 262.25 | 11.46 | 2.50E-193 | Hypothetical protein |
| Gene_8929 | Lema_T037480 | lm_SuperContig_3_v2:1850027–1850254 | 3062 | 510.96 | 11.38 | 6.90E-256 | Hypothetical protein |
| Gene_11912 | Lema_T061640 | lm_SuperContig_8_v2:1610355–1610701 | 2410 | 453.43 | 10.77 | 1.20E-221 | Hypothetical protein |
| Gene_2066 | Lema_T082980 | lm_SuperContig_12_v2:398032–399219 | 2890 | 507.44 | 10.73 | 7.10E-274 | Hypothetical protein |
| Gene_8487 | Lema_T033060 | lm_SuperContig_3_v2:287922–288676 | 5468 | 1962.05 | 10.62 | 0.00E+00 | Hypothetical protein (CSEP) |
| Gene_10780 | Lema_T049660 | lm_SuperContig_6_v2:1607018–1607681 | 3553 | 316.20 | 9.31 | 0.00E+00 | Hypothetical protein (AvrLm1) |
| Gene_170 | Lema_T001700 | lm_SuperContig_0_v2:571327–571980 | 1695 | 466.93 | 9.31 | 0.00E+00 | Hypothetical protein (CSEP) |
| Gene_6375 | Lema_T113200 | lm_SuperContig_20_v2:228262–228840 | 3556 | 1067.76 | 9.26 | 0.00E+00 | Hypothetical protein (CSEP) |
| Gene_9004 | Lema_T038230 | lm_SuperContig_3_v2:2336899–2337410 | 23963 | 3704.18 | 9.06 | 0.00E+00 | Hypothetical protein (CSEP) |
| Gene_616 | Lema_T006160 | lm_SuperContig_0_v2:2286680–2287371 | 9230 | 1311.26 | 8.58 | 0.00E+00 | Hypothetical protein |
| Gene_4884 | Lema_T109090 | lm_SuperContig_18_v2:862571–862990 | 1940 | 697.48 | 8.04 | 4.40E-135 | Hypothetical protein |
| Gene_2397 | Lema_T086290 | lm_SuperContig_12_v2:1374587–1375064 | 2131 | 209.12 | 8.04 | 0.00E+00 | Hypothetical protein (AvrLm4-7) |
| Gene_1613 | Lema_T076380 | lm_SuperContig_10_v2:1509441–1509941 | 11945 | 2426.45 | 7.76 | 0.00E+00 | Hypothetical protein (CSEP) |
| Gene_7362 | Lema_T123070 | lm_SuperContig_25_v2:296506–296973 | 1952 | 519.68 | 7.66 | 5.40E-226 | Hypothetical protein (CSEP) |
| Gene_234 | Lema_T002340 | lm_SuperContig_0_v2:882882–883215 | 12153 | 4475.87 | 7.56 | 0.00E+00 | Hypothetical protein |
| Gene_1799 | Lema_T087550 | lm_SuperContig_11_v2:702412–703074 | 1064 | 240.87 | 7.38 | 0.00E+00 | Hypothetical protein (CSEP) |
| Gene_6961 | Lema_T119060 | lm_SuperContig_22_v2:294086–294450 | 6654 | 1114.42 | 6.32 | 0.00E+00 | Hypothetical protein (AvrLm11) |
| Gene_11177 | Lema_T070880 | lm_SuperContig_7_v2:982889–983113 | 6770 | 895.39 | 5.79 | 0.00E+00 | Hypothetical protein (AvrLmJ1) |
| 11 dpi | |||||||
| Gene_9481 | Lema_T043000 | lm_SuperContig_4_v2:1367322–1368521 | 2280 | 179.23 | 13.5 | 0.00E+00 | Vacuolar protein sorting-associated protein |
| Gene_10161 | Lema_T054900 | lm_SuperContig_5_v2:1424583–1425111 | 1760 | 173.39 | 12.26 | 6.50E-123 | Hypothetical protein |
| Gene_7308 | Lema_T122530 | lm_SuperContig_25_v2:145516–147997 | 1128 | 265.94 | 10.79 | 0.00E+00 | Glucose dehydrogenase |
| Gene_2216 | Lema_T084480 | lm_SuperContig_12_v2:827863–828642 | 1906 | 121.93 | 10.46 | 1.50E-131 | Predicted protein SSP(Effector) |
| Gene_11875 | Lema_T061270 | lm_SuperContig_8_v2:1510198–1511697 | 1484 | 458.66 | 10.25 | 0.00E+00 | Peptidase S26A, signal peptidase I/Proteolysis |
| Gene_2066 | Lema_T082980 | lm_SuperContig_12_v2:398032–399219 | 1316 | 182.72 | 9.44 | 1.20E-212 | Hypothetical protein |
| Gene_11099 | Lema_T070100 | lm_SuperContig_7_v2:754032–755352 | 2233 | 136.92 | 9.05 | 0.00E+00 | Peptidoglycan-binding LysM (Lm5LysM) |
| Gene_170 | Lema_T001700 | lm_SuperContig_0_v2:571327–571980 | 1377 | 101.99 | 8.84 | 0.00E+00 | Hypothetical protein (CSEP) |
| Gene_12054 | Lema_T063060 | lm_SuperContig_9_v2:365423–366979 | 1857 | 106.76 | 8.42 | 0.00E+00 | 3-dehydroquinate synthase activity |
| Gene_10765 | Lema_T049510 | lm_SuperContig_6_v2:1209331–1209753 | 15579 | 1656.89 | 8.12 | 1.40E-127 | Hypothetical protein |
| Gene_616 | Lema_T006160 | lm_SuperContig_0_v2:2286680–2287371 | 5059 | 356.09 | 7.55 | 0.00E+00 | Hypothetical protein |
| Gene_10767 | Lema_T049530 | lm_SuperContig_6_v2:1211326–1212274 | 2212 | 253.35 | 7.23 | 0.00E+00 | Glucose/ribitol dehydrogenase |
| Gene_1012 | Lema_T010120 | lm_SuperContig_0_v2:3437723–3438128 | 1319 | 310.89 | 7.13 | 2.50E-235 | Hypothetical protein (CSEP) |
| Gene_9092 | Lema_T039110 | lm_SuperContig_4_v2:302019–302430 | 12896 | 2333.41 | 7.08 | 4.20E-155 | Response to stress |
| Gene_304 | Lema_T003040 | lm_SuperContig_0_v2:1104438–1107822 | 1149 | 150.74 | 6.8 | 2.70E-294 | Haloacid dehalogenase-like hydrolase |
| Gene_11976 | Lema_T062280 | lm_SuperContig_8_v2:1760041–1760879 | 1061 | 112.38 | 6.37 | 6.70E-263 | Fasciclin and related adhesion glycoproteins |
| Gene_7609 | Lema_T025030 | lm_SuperContig_2_v2:575802–582958 | 3787 | 960.67 | 6.09 | 1.10E-83 | Hypothetical protein |
| Gene_6173 | Lema_T021470 | lm_SuperContig_1_v2:2566440–2566907 | 1252 | 141.60 | 6.06 | 4.20E-177 | Hypothetical protein |
| Gene_9004 | Lema_T038230 | lm_SuperContig_3_v2:2336899–2337410 | 2751 | 214.78 | 5.78 | 0.00E+00 | Hypothetical protein (CSEP) |
| Gene_368 | Lema_T003680 | lm_SuperContig_0_v2:1246649–1246843 | 1027 | 216.39 | 5.24 | 4.00E-198 | Hypothetical protein (CSEP) |
| Gene_1613 | Lema_T076380 | lm_SuperContig_10_v2:1509441–1509941 | 2195 | 113.31 | 5.15 | 6.30E-275 | Hypothetical protein (CSEP) |
| Gene_3471 | Lema_T089840 | lm_SuperContig_15_v2:160448–161311 | 746 | 150.76 | 7.37 | 1.30E-257 | Cutinase/catalytic activity |
*
The fold change was estimated by comparing in planta gene expression at 3, 5, 7, and 11 days post inoculation (dpi) with axenic cultures of L. maculans.
Analyses were performed with five biological replicates. dpi, days post inoculation; FPKM, Fragments per kilobase of transcript per million mapped reads; FC, fold-change; SE, Standard error for FPKM.