Supplemental Table 1: Detected duplicate gene IDs BBOV_I000150 BBOV_I000160 BBOV_I000540 BBOV_I001100 BBOV_I001110 BBOV_I001790 BBOV_I001810 BBOV_I001830 BBOV_I001860 BBOV_I003860 BBOV_I004200 BBOV_I004220 BBOV_I005020 BBOV_I005030 BBOV_I005050 BBOV_I005060 BBOV_I005080 BBOV_I005100 BBOV_II000170 BBOV_II001870 BBOV_II001950 BBOV_II002010 BBOV_II002600 BBOV_II002840 BBOV_II004160 BBOV_II007340 BBOV_II007350 BBOV_II007360 BBOV_II007370 BBOV_II007410 BBOV_II007420 BBOV_II007430 BBOV_II007440 BBOV_III001140 BBOV_III001170 BBOV_III001250 BBOV_III001350 BBOV_III002500 BBOV_III003070 BBOV_III003080 BBOV_III003640 BBOV_III003670 BBOV_III005000 BBOV_III005010 BBOV_III005020 BBOV_III005030 BBOV_III005040 BBOV_III005050 BBOV_III005650 BBOV_III006050 BBOV_III006060 BBOV_III006900 BBOV_III006910 BBOV_III006930 BBOV_III007100 BBOV_III007120 BBOV_III007130 BBOV_III007450 BBOV_III007460 BBOV_III007480 BBOV_III007490 BBOV_III007870 BBOV_III007880 BBOV_III009800 BBOV_III011280 BBOV_III011730 BBOV_III011740 BBOV_IV000670 BBOV_IV000960 BBOV_IV001030 BBOV_IV001580 BBOV_IV001590 BBOV_IV002150 BBOV_IV002190 BBOV_IV003230 BBOV_IV003240 BBOV_IV003440 BBOV_IV003770 BBOV_IV003780 BBOV_IV003790 BBOV_IV003800 BBOV_IV003810 BBOV_IV003820 BBOV_IV003830 BBOV_IV003840 BBOV_IV003850 BBOV_IV003860 BBOV_IV007130 BBOV_IV007410 BBOV_IV007460 BBOV_IV008310 BBOV_IV008320 BBOV_IV008500 BBOV_IV009470 BBOV_IV009480 BBOV_IV009860 BBOV_IV009870 BBOV_IV010620 BBOV_IV010630 BBOV_IV010820 BBOV_IV010830 BBOV_IV011400 CMU_000690 CMU_001350 CMU_002800 CMU_003450 CMU_004450 CMU_004460 CMU_004920 CMU_005020 CMU_010000 CMU_010020 CMU_010280 CMU_013110 CMU_013310 CMU_014140 CMU_014160 CMU_014620 CMU_014670 CMU_014680 CMU_015010 CMU_015800 CMU_015960 CMU_016270 CMU_016400 CMU_017730 CMU_018010 CMU_019790 CMU_019900 CMU_020850 CMU_021910 CMU_022010 CMU_022540 CMU_023990 CMU_024000 CMU_024170 CMU_025150 CMU_026330 CMU_026800 CMU_027820 CMU_028070 CMU_028080 CMU_028990 CMU_031840 CMU_032020 CMU_032190 CMU_032750 CMU_032830 CMU_033790 CMU_035710 CMU_037520 CMU_038070 CMU_038340 CMU_038940 CMU_039600 CMU_040500 CMU_042320 CMU_042540 cgd1_2240 cgd1_3690 cgd1_3800 cgd1_990 cgd2_1520 cgd2_3260 cgd2_3270 cgd2_3410 cgd2_3550 cgd2_4120 cgd2_70 cgd2_90 cgd3_1580 cgd3_2180 cgd3_2360 cgd3_2730 cgd3_3560 cgd3_3870 cgd3_4030 cgd3_410 cgd3_4200 cgd3_4210 cgd3_4260 cgd3_4270 cgd3_640 cgd3_860 cgd4_2680 cgd4_2900 cgd4_2960 cgd4_2970 cgd4_3670 cgd4_3680 cgd4_4440 cgd5_1380 cgd5_2200 cgd5_2870 cgd5_3200 cgd5_3350 cgd5_3560 cgd5_4070 cgd5_4480 cgd5_4490 cgd6_130 cgd6_140 cgd6_3860 cgd6_5500 cgd7_1630 cgd7_1760 cgd7_4020 cgd7_4480 cgd7_810 cgd8_10 cgd8_1220 cgd8_1420 cgd8_2330 cgd8_2770 NCLIV_000140 NCLIV_001070 NCLIV_001180 NCLIV_001440 NCLIV_001670 NCLIV_001690 NCLIV_001950 NCLIV_001970 NCLIV_002550 NCLIV_004290 NCLIV_004490 NCLIV_004830 NCLIV_004860 NCLIV_005250 NCLIV_007220 NCLIV_007430 NCLIV_007460 NCLIV_007540 NCLIV_007930 NCLIV_008250 NCLIV_008840 NCLIV_009440 NCLIV_009890 NCLIV_009980 NCLIV_009990 NCLIV_010050 NCLIV_010060 NCLIV_010440 NCLIV_011870 NCLIV_012990 NCLIV_013610 NCLIV_013620 NCLIV_014180 NCLIV_014520 NCLIV_014530 NCLIV_015290 NCLIV_015830 NCLIV_017220 NCLIV_017230 NCLIV_017560 NCLIV_017630 NCLIV_017780 NCLIV_018170 NCLIV_019170 NCLIV_019380 NCLIV_019900 NCLIV_019970 NCLIV_019990 NCLIV_020690 NCLIV_021050 NCLIV_021470 NCLIV_021480 NCLIV_021890 NCLIV_022140 NCLIV_022320 NCLIV_022330 NCLIV_022420 NCLIV_022430 NCLIV_022440 NCLIV_023150 NCLIV_024000 NCLIV_024520 NCLIV_024850 NCLIV_024860 NCLIV_024960 NCLIV_026720 NCLIV_027330 NCLIV_027640 NCLIV_027650 NCLIV_028530 NCLIV_028690 NCLIV_031040 NCLIV_031770 NCLIV_032330 NCLIV_032770 NCLIV_033850 NCLIV_036340 NCLIV_037700 NCLIV_038690 NCLIV_038770 NCLIV_039280 NCLIV_039290 NCLIV_039490 NCLIV_039580 NCLIV_039590 NCLIV_041220 NCLIV_041870 NCLIV_042690 NCLIV_042790 NCLIV_042810 NCLIV_042910 NCLIV_043550 NCLIV_044270 NCLIV_044470 NCLIV_046550 NCLIV_046720 NCLIV_048280 NCLIV_048330 NCLIV_048780 NCLIV_049770 NCLIV_049780 NCLIV_049970 NCLIV_049980 NCLIV_050620 NCLIV_052160 NCLIV_052930 NCLIV_052940 NCLIV_053600 NCLIV_053810 NCLIV_053840 NCLIV_054425 NCLIV_054450 NCLIV_056480 NCLIV_058250 NCLIV_060590 NCLIV_060600 NCLIV_060730 NCLIV_060740 NCLIV_061340 NCLIV_061500 NCLIV_061720 NCLIV_062790 NCLIV_065220 NCLIV_066170 NCLIV_066910 NCLIV_067180 NCLIV_068320 NCLIV_068340 NCLIV_068400 NCLIV_068410 NCLIV_068450 NCLIV_068460 NCLIV_068470 NCLIV_068640 NCLIV_068740 NCLIV_069090 NCLIV_069110 NCLIV_069520 NCLIV_069530 NCLIV_069570 NCLIV_069580 NCLIV_069620 PBANKA_000230 PBANKA_000370 PBANKA_010010 PBANKA_010020 PBANKA_020090 PBANKA_021510 PBANKA_021540 PBANKA_021550 PBANKA_030920 PBANKA_030930 PBANKA_031650 PBANKA_031670 PBANKA_031680 PBANKA_041770 PBANKA_052270 PBANKA_060120 PBANKA_060130 PBANKA_061590 PBANKA_080030 PBANKA_080430 PBANKA_081240 PBANKA_081420 PBANKA_090230 PBANKA_090240 PBANKA_091750 PBANKA_091760 PBANKA_093130 PBANKA_093240 PBANKA_093290 PBANKA_100030 PBANKA_100040 PBANKA_100050 PBANKA_101400 PBANKA_101710 PBANKA_102620 PBANKA_111100 PBANKA_111110 PBANKA_113330 PBANKA_113340 PBANKA_121890 PBANKA_123005 PBANKA_123010 PBANKA_131020 PBANKA_131030 PBANKA_132170 PBANKA_132700 PBANKA_143190 PBANKA_146070 PBANKA_146430 PBANKA_146440 PCHAS_000250 PCHAS_000650 PCHAS_000760 PCHAS_000860 PCHAS_010060 PCHAS_011400 PCHAS_021340 PCHAS_030230 PCHAS_041860 PCHAS_050030 PCHAS_050050 PCHAS_052290 PCHAS_061760 PCHAS_080020 PCHAS_080460 PCHAS_081270 PCHAS_081450 PCHAS_091140 PCHAS_091190 PCHAS_091300 PCHAS_100100 PCHAS_101480 PCHAS_101790 PCHAS_102700 PCHAS_104140 PCHAS_104150 PCHAS_104160 PCHAS_110910 PCHAS_113280 PCHAS_113290 PCHAS_121960 PCHAS_122090 PCHAS_130310 PCHAS_132500 PCHAS_133040 PCHAS_133060 PCHAS_133080 PCHAS_133130 PCHAS_140060 PCHAS_140250 PCHAS_143390 PCHAS_146300 PCHAS_146730 PCHAS_146810 MAL13P1.475 MAL13P1.480 MAL13P1.59 MAL7P1.178 MAL7P1.206 MAL7P1.231 MAL7P1.92 MAL8P1.206 MAL8P1.210 PF08_0022 PF08_0099 PF10_0020 PF10_0023 PF10_0025 PF10_0161 PF10_0162 PF10_0383 PF11_0033 PF11_0036 PF11_0037 PF11_0157 PF11_0174 PF11_0486 PF13_0073 PF13_0304 PF13_0305 PF14_0015 PF14_0164 PF14_0254 PF14_0286 PF14_0749 PF14_0755 PFA0360c PFA0365c PFB0926c PFB0950w PFB0953w PFB0970c PFB0976w PFC0420w PFC0870w PFD0090c PFD0095c PFD0610w PFD1050w PFD1200c PFD1205w PFE0075c PFE0080c PFE0230w PFF0075c PFF0080c PFF0520w PFF1505w PFF1510w PFI0130c PFI0180w PFI0550w PFI0645w PFL0780w PFL2290w PFL2560c PKH_000320 PKH_000510 PKH_000590 PKH_010510 PKH_031930 PKH_040040 PKH_052580 PKH_052820 PKH_060020 PKH_062300 PKH_070002 PKH_070090 PKH_071050 PKH_072680 PKH_073430 PKH_080650 PKH_082030 PKH_082140 PKH_083510 PKH_090010 PKH_091190 PKH_091410 PKH_094540 PKH_094560 PKH_100040 PKH_101180 PKH_103020 PKH_110040 PKH_111390 PKH_111400 PKH_112410 PKH_112930 PKH_112990 PKH_120710 PKH_123630 PKH_124250 PKH_124260 PKH_125860 PKH_131090 PKH_131130 PKH_131960 PKH_132290 PKH_133070 PKH_134550 PKH_134580 PKH_142580 PKH_143030 PKH_143330 PKH_145630 PKH_146510 PVX_002510 PVX_002515 PVX_002525 PVX_003680 PVX_003985 PVX_004505 PVX_004515 PVX_074695 PVX_081540 PVX_081545 PVX_083140 PVX_083145 PVX_084145 PVX_084160 PVX_084875 PVX_084880 PVX_085005 PVX_085160 PVX_085625 PVX_085855 PVX_086885 PVX_087875 PVX_088025 PVX_088030 PVX_089470 PVX_089473 PVX_089850 PVX_089852 PVX_090155 PVX_090330 PVX_091095 PVX_091380 PVX_091465 PVX_092645 PVX_092650 PVX_094265 PVX_095135 PVX_095255 PVX_096030 PVX_096035 PVX_096040 PVX_096055 PVX_096410 PVX_096980 PVX_096985 PVX_097025 PVX_098630 PVX_099005 PVX_099095 PVX_099795 PVX_099800 PVX_101280 PVX_101590 PVX_103160 PVX_105200 PVX_106730 PVX_110895 PVX_112715 PVX_114830 PVX_114832 PVX_115990 PVX_117305 PVX_117310 PVX_117995 PVX_118570 PVX_119355 PVX_121350 PVX_121860 PVX_121865 PVX_121885 PVX_123360 PVX_123490 PVX_123630 PVX_123820 PVX_124085 PVX_187290 PVX_209290 PVX_214290 PVX_215290 PVX_220290 PVX_227290 PVX_231290 PVX_235290 PVX_249300 PVX_250300 PVX_252300 PVX_253300 PVX_254300 TA02480 TA02485 TA02750 TA02995 TA03060 TA03860 TA04055 TA04060 TA04105 TA05535 TA06225 TA06245 TA06630 TA06640 TA07490 TA07495 TA10535 TA10545 TA10920 TA10925 TA11890 TA11900 TA11905 TA11910 TA12175 TA12185 TA13230 TA13235 TA13250 TA13255 TA13650 TA13875 TA13905 TA14665 TA14680 TA15665 TA15690 TA15710 TA15870 TA15875 TA15895 TA15900 TA16045 TA16980 TA16985 TA17545 TA18875 TA18910 TA18915 TA18970 TA19115 TA19800 TA19810 TA20083 TA20090 TA20265 TA20270 TA20445 TP04_0921 TP04_0917 TP04_0890 TP04_0889 TP04_0814 TP04_0813 TP04_0793 TP04_0792 TP04_0692 TP04_0691 TP04_0677 TP04_0675 TP04_0628 TP04_0627 TP04_0606 TP04_0605 TP04_0520 TP04_0519 TP04_0406 TP04_0352 TP04_0279 TP04_0278 TP04_0247 TP04_0212 TP04_0211 TP04_0128 TP04_0126 TP04_0095 TP04_0014 TP03_0895 TP03_0887 TP03_0868 TP03_0841 TP03_0840 TP03_0669 TP03_0668 TP03_0621 TP03_0620 TP03_0591 TP03_0590 TP03_0572 TP03_0557 TP03_0556 TP03_0357 TP03_0348 TP03_0340 TP03_0338 TP03_0306 TP03_0253 TP03_0252 TP03_0194 TP03_0193 TP03_0064 TP03_0063 TP02_0956 TP02_0954 TP02_0930 TP02_0929 TP02_0927 TP02_0926 TP02_0915 TP02_0914 TP02_0911 TP02_0910 TP02_0883 TP02_0878 TP02_0857 TP02_0819 TP02_0770 TP02_0706 TP02_0703 TP02_0618 TP02_0593 TP02_0592 TP02_0591 TP02_0571 TP02_0567 TP02_0562 TP02_0528 TP02_0527 TP02_0438 TP02_0437 TP02_0309 TP02_0274 TP02_0260 TP02_0257 TP02_0151 TP02_0150 TP02_0099 TP02_0098 TP02_0055 TP02_0054 TP02_0043 TP02_0038 TP02_0037 TP02_0024 TP02_0023 TP01_1229 TP01_1226 TP01_1225 TP01_1224 TP01_1222 TP01_1077 TP01_1076 TP01_0993 TP01_0894 TP01_0890 TP01_0835 TP01_0834 TP01_0692 TP01_0605 TP01_0604 TP01_0577 TP01_0576 TP01_0552 TP01_0520 TP01_0485 TP01_0484 TP01_0482 TP01_0470 TP01_0469 TP01_0417 TP01_0415 TP01_0388 TP01_0387 TP01_0384 TP01_0383 TP01_0274 TP01_0273 TP01_0265 TP01_0264 TP01_0119 TP01_0059 TP01_0058 TP01_0045 TP01_0043 TP01_0022 TP01_0021 TGME49_121630 TGME49_121500 TGME49_121490 TGME49_121470 TGME49_121440 TGME49_120260 TGME49_119700 TGME49_118650 TGME49_118130 TGME49_118120 TGME49_116780 TGME49_116640 TGME49_116440 TGME49_116430 TGME49_115560 TGME49_115190 TGME49_115180 TGME49_114240 TGME49_114230 TGME49_113900 TGME49_113630 TGME49_113610 TGME49_113140 TGME49_109560 TGME49_109160 TGME49_107870 TGME49_107860 TGME49_107850 TGME49_107840 TGME49_107570 TGME49_106640 TGME49_106630 TGME49_105310 TGME49_105300 TGME49_105160 TGME49_102350 TGME49_101890 TGME49_101210 TGME49_100370 TGME49_100170 TGME49_099060 TGME49_097240 TGME49_096440 TGME49_095950 TGME49_095750 TGME49_095710 TGME49_095700 TGME49_094820 TGME49_094800 TGME49_094440 TGME49_093190 TGME49_092600 TGME49_092280 TGME49_092270 TGME49_092110 TGME49_092010 TGME49_092000 TGME49_091990 TGME49_091980 TGME49_091290 TGME49_091180 TGME49_091040 TGME49_090940 TGME49_090920 TGME49_090720 TGME49_089620 TGME49_088800 TGME49_088420 TGME49_088410 TGME49_087730 TGME49_087530 TGME49_087520 TGME49_087510 TGME49_086420 TGME49_084420 TGME49_084200 TGME49_083730 TGME49_082940 TGME49_081050 TGME49_081040 TGME49_081030 TGME49_080820 TGME49_077270 TGME49_077240 TGME49_076920 TGME49_075690 TGME49_073870 TGME49_073120 TGME49_073110 TGME49_071480 TGME49_071470 TGME49_070590 TGME49_070580 TGME49_070320 TGME49_069720 TGME49_069710 TGME49_068650 TGME49_068200 TGME49_067490 TGME49_067410 TGME49_066760 TGME49_066750 TGME49_066450 TGME49_066440 TGME49_066420 TGME49_064070 TGME49_063410 TGME49_062960 TGME49_061920 TGME49_061800 TGME49_061190 TGME49_061080 TGME49_060310 TGME49_059200 TGME49_058400 TGME49_057720 TGME49_056040 TGME49_055860 TGME49_055750 TGME49_055250 TGME49_054560 TGME49_053930 TGME49_053510 TGME49_052880 TGME49_052460 TGME49_052180 TGME49_051870 TGME49_047540 TGME49_045880 TGME49_045770 TGME49_045510 TGME49_044620 TGME49_043440 TGME49_042790 TGME49_042630 TGME49_042620 TGME49_042600 TGME49_042450 TGME49_042430 TGME49_042400 TGME49_039020 TGME49_037900 TGME49_037810 TGME49_036570 TGME49_036400 TGME49_036290 TGME49_036050 TGME49_036040 TGME49_034920 TGME49_034700 TGME49_033540 TGME49_032830 TGME49_032350 TGME49_031630 TGME49_030520 TGME49_030360 TGME49_030350 TGME49_029170 TGME49_028170 TGME49_028160 TGME49_026410 TGME49_026220 TGME49_024790 TGME49_024750 TGME49_024220 TGME49_023700 TGME49_022830 TGME49_022720 TGME49_021830 TGME49_021320 TGME49_021270 TGME49_019140 TGME49_018880 TGME49_018560 TGME49_017950 TGME49_017230 TGME49_016140 TGME49_016050 TGME49_015170 TGME49_014410 TGME49_014400 TGME49_012880 TGME49_012740 TGME49_012730 TGME49_012720 TGME49_012420 TGME49_010980 TGME49_010720 TGME49_010700 TGME49_010330 TGME49_010320 TGME49_010260 TGME49_009790 TGME49_007650 TGME49_007480 TGME49_007100 TGME49_007090 TGME49_006590 TGME49_005700 TGME49_005680 TGME49_004560 TGME49_004050 TGME49_003030 TGME49_002770 TGME49_002510 TGME49_002500 TGME49_002490 TGME49_002130 TGME49_002120 TGME49_002070 TGME49_002060 TGME49_001700 TGME49_001690 TGME49_001520 TGME49_001410 TGME49_001250