Horizontal gene transfer drives adaptive colonization of apple trees by the fungal pathogen Valsa mali. Zhiyuan Yin, Baitao Zhu, Hao Feng, Lili Huang*

Supplementary Information Horizontal gene transfer drives adaptive colonization of apple trees by the fungal pathogen Valsa mali Zhiyuan Yin, Baitao Zhu, Hao Feng, Lili Huang* State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712, Shaanxi, China *Corresponding author Lili Huang, e-mail: huanglili@nwsuaf.edu.cn

Supplementary Figures Supplementary Figure S1. Dead tissues of apple bark caused by Valsa mali in the fields.

Supplementary Figure S2. Bleomycin resistance assays of three fungi under different levels of bleomycin stress. were grown on the potato dextrose agar (PDA) media at 25 C in the dark for two days.

Supplementary Figure S3. Generation of gene deletion mutants. (a) Gene replacement strategy of hygromycin-resistant cassette. (b) Gene replacement strategy of G418-resistant cassette.

Supplementary Tables Supplementary Table S1. The genes involved in lysine biosynthesis in V. mali Gene Description Ortholog/homolog in V.mali a Genes involved in α-aminoadipate (AAA) pathway b LYS20/LYS21 Homocitrate synthase VM1G_07016 LYS4 Homoaconitase VM1G_10252 LYS12 Homoisocitrate VM1G_06170 dehydrogenase LYS2 α-aminoadipate reductase VM1G_02319, VM1G_105, VM1G_06405, VM1G_03154, VM1G_05645 LYS9 Saccharopine reductase VM1G_06828 LYS1 Saccahropine dehydrogenase VM1G_01424 Genes involved in succinylase (DAP) pathway c Ask Aspartate kinase VM1G_06620 Asd Aspartate semialdehyde VM1G_082 dehydrogenase DapA Dihydrodipicolinate VM1G_02804 synthase DapB Dihydrodipicolinate NA reductase DapD THDPA succinylase NA DapC succinyl-dap VM1G_011 aminotransferase DapE succinyl-dap VM1G_00056 desuccinylase DapF DAP epimerase NA LysA DAP decarboxylase VM1G_069 a Orthologs to genes involved in AAA pathway of Saccharomyces cerevisiae were identified by orthagogue (Ekseth O K, Kuiper M, Mironov V. orthagogue: an agile tool for the rapid prediction of orthology relations. Bioinformatics, 2013: btt582.); homologs to genes involved in DAP pathway were identified by blastp searches using known bacterial genes. b Refer to "Xu H, Andi B, Qian J, et al. The α-aminoadipate pathway for lysine biosynthesis in fungi. Cell biochemistry and biophysics, 2006, 46(1): 43-64." c Refer to "Liu Y, White R H, Whitman W B. Methanococci use the diaminopimelate aminotransferase (DapL) pathway for lysine biosynthesis. Journal of bacteriology, 2010, 192(13): 3304-3310."

Supplementary Table S2. Primers used for gene deletion and qrt-pcr. Names Sequences (5'-3') HGT32-1F CCATTGCGGAGAAGGTTAG HGT32-2R CAGATACGGCAGAGAAATCGCAACCTCCAAATGCTGCGTGGGTAA HGT32-3F GTTTAGATTCCAAGTGTCTACTGCTGGCTGGGTAGCGTTGTAGTTGT ATG HGT32-4R TGAGAAGGGAGCCAGCAT HGT32-5F ACGAATAACTCGCCTGTGG HGT32-6R AGCCGGGTCCTGAAATG HGT32-7F GCCAGAGCCAAGTCAACC HGT32-8R GCCCGTCCAGTATGTAATCA HGT32-CF GCAACAACCGAAGACGAAA HGT32-CR CTGACAAGGCAGGAGGAGA G852-F TCGGCTATGACTGGGCACAACA G850-R GAGCGGCGATACCGTAAAGCAC G856-F GAATGGTCAAATCAAACTGCTAGATAT G855-F TGTTGGGTTTGAGCTAGGTGGG HGT32-qPCR-F TGGACGATGTAGACGAGGTAT HGT32-qPCR-R TCCTGAAATGTCACAGTCCTAAC HGT14-1F GGCTCCAAATCCCCTCG HGT14-2R TTGACCTCCACTAGCTCCAGCCAAGCCAATACCACTGCTAATACAA TGCTG HGT14-3F GAATAGAGTAGATGCCGACCGCGGGTTGGGAAAGACTACGCCGAA TG HGT14-4R GCGTCCATAGAGCGGAAGAT HGT14-5F CGTCACTGCCCGTCTCA HGT14-6R TCCTCAACAGTCAAGTCCCTC HGT14-CF TCTAGCGAGCCGATTACAGT HGT14-CR CCCACATTGACCACCCAC H852 ATGTTGGCGACCTCGTATTGG H850 TTCCTCCCTTTATTTCAGATTCAA H855-R GCTGATCTGACCAGTTGC H856-F GTCGATGCGACGCAATCGT HGT14-qPCR-F GTGGGAGATATCGAGACGAAAC HGT14-qPCR-R ATCTGCCAGCCCTTGATTAC G6PDH-F TCAGAACAAGTTCGAGGGCGACAA G6PDH-R TGAGGGCAATAGAGGGCTTGTTCA

WP_028053142_Sinorhizobium_meliloti XP_0012171_Aspergillus_terreus WP_044541183_Bradyrhizobium_sp WP_008134725_Bradyrhizobium_sp WP_0475172_Methylobacterium_sp WP_016558781_Rhizobium_grahamii XP_0132750_Rhinocladiella_mackenziei WP_0550112_Bosea_thiooxidans KQR77015_Burkholderia_sp KGO54378_Penicillium_expansum XP_007831531_Pestalotiopsis_fici AIC2_Rhizobium_etli KIH762_Sporothrix_brasiliensis KEQ566_Aureobasidium_melanogenum XP_013264452_Exophiala_aquamarina WP_055727246_Bosea_thiooxidans XP_013427578_Aureobasidium_namibiae KFX361_Pseudogymnoascus_pannorum WP_040140511_Rhizobium_etli XP_013317900_Exophiala_xenobiotica KJR86105_Sporothrix_schenckii KKY16813_Phaeomoniella_chlamydospora WP_0518385_Bosea_sp KIW133_Exophiala_spinifera XP_0079280_Pseudocercospora_fijiensis WP_0190155_Elioraea_tepidiphila XP_0075482_Capronia_epimyces CRL21828_Penicillium_camemberti CEJ10414_bacterium_YEK KEQ90_Aureobasidium_pullulans VM1G_00056_Valsa_mali KIW34027_Cladophialophora_immunda XP_002482557_Talaromyces_stipitatus CDX52783_Mesorhizobium_plurifarium XP_013348217_Aureobasidium_subglaciale KQU83927_Mesorhizobium_sp CRG84517_Talaromyces_islandicus WP_019015338_Elioraea_tepidiphila GAM33785_Talaromyces_cellulolyticus XP_013280332_Fonsecaea_pedrosoi XP_008715541_Cyphellophora_europaea KRE00578_Bosea_sp EPE08060_Ophiostoma_piceae ERS919_Sporothrix_schenckii WP_038571221_Paenibacillus_odorifer GAD627_Byssochlamys_spectabilis KRE06713_Bosea_sp WP_023743264_Mesorhizobium_sp XP_007681567_Baudoinia_panamericana 60 92 80 88 79 77 67 88 88 71 76 77 63 80 64 56 48 Bordetella_spp. Fusarium_spp. VM1G_00056

WP037508279_Sphingobium_yanoikuyae EYE663_Aspergillus_ruber WP051913433_Kutzneria_albida XP0075381_Colletotrichum_fioriniae KKO503_Trichoderma_harzianum WP0581819_Terracidiphilus_gabretensis KMS54549_Sphingobium_czechense WP0240192_Sphingobium_sp WP0185169_Streptomyces_sp WP0515262_Caulobacter_henricii WP055877466_Sphingomonas_sp CAK41643_Aspergillus_niger WP056479065_Sphingomonas_sp WP039287456_Novosphingobium_malaysiense WP018364_Streptomyces_sp XP007705768_Bipolaris_sorokiniana XP003855274_Zymoseptoria_tritici KOC10800_Aspergillus_flavus WP046762340_Sphingobium_chungbukense WP0567751_Novosphingobium_sp XP008027713_Setosphaeria_turcica WP0519103_Caulobacter_henricii WP056438490_Caulobacter_sp WP007710609_Sphingobium_sp EWM18849_Kutzneria_sp GAA86910_Aspergillus_kawachii EAU69263_Stigmatella_aurantiaca XP0013382_Aspergillus_niger KKY241_Diaporthe_ampelina GAM05656_Novosphingobium_sp WP055840713_Sphingomonas_sp KFY42778_Pseudogymnoascus_sp WP052310620_Granulicella_mallensis WP0064300_Sphingobium_japonicum WP006275380_Asticcacaulis_biprosthecium XP007707913_Bipolaris_zeicola WP037444261_Shewanella_sp CCT70624_Fusarium_fujikuroi XP0052906_Pantholops_hodgsonii GAP82757_Rosellinia_necatrix WP0487408_Sphingobium_yanoikuyae CEJ83726_Torrubiella_hemipterigena WP056081617_Rhodanobacter_sp XP009262641_Fusarium_pseudograminearum XP00859_Beauveria_bassiana WP056607412_Rhodanobacter_sp WP013377414_Stigmatella_aurantiaca WP023360913_Actinoplanes_friuliensis XP0072776_Colletotrichum_gloeosporioides KLO763_Fusarium_fujikuroi EZP83146_Novosphingobium_resinovorum WP0207036_Caulobacter_sp EHA27409_Aspergillus_niger WP056665665_Rhizobacter_sp KNG444_Stemphylium_lycopersici KJK67468_Aspergillus_parasiticus WP025356805_Kutzneria_albida WP054437009_Novosphingobium_sp KMS50525_Novosphingobium_barchaimii EMF10247_Sphaerulina_musiva ABZ728_Caulobacter_sp WP056870571_Pedobacter_sp XP681701_Aspergillus_nidulans WP007082610_Rhodanobacter_fulvus WP0523274_Kutzneria_sp VM1G_00616_Valsa_mali XP0076879_Bipolaris_oryzae KEQ82843_Aureobasidium_pullulans XP007839039_Pestalotiopsis_fici KGQ057_Beauveria_bassiana AEU37208_Granulicella_mallensis WP0438409_Novosphingobium_sp KJX524_Zymoseptoria_brevis WP004208502_Sphingobium_yanoikuyae WP051761416_Microbispora_rosea WP056687091_Sphingobium_sp WP021233304_Novosphingobium_lindaniclasticum WP0521203_Methylibium_sp WP020638161_Amycolatopsis_balhimycina XP0010715_Pyrenophora_tritici WP008832861_Sphingomonas_sp WP056458907_Caulobacter_sp WP0513372_Caulobacter_sp WP051586764_Novosphingobium_resinovorum XP002384552_Aspergillus_flavus XP0133390_Aureobasidium_subglaciale WP051035186_Sphingomonas-like KEQ67483_Aureobasidium_melanogenum WP007677879_Novosphingobium_sp WP010338081_Sphingobium_yanoikuyae EQB52649_Colletotrichum_gloeosporioides WP017500926_alpha_proteobacterium XP0072916_Marssonina_brunnea KIS30550_Novosphingobium_sp XP003301361_Pyrenophora_teres WP041539077_Caulobacter_sp XP001792566_Parastagonospora_nodorum XP013432022_Aureobasidium_namibiae XP0145584_Bipolaris_victoriae WP0350008_Hassallia_byssoidea XP0113274_Fusarium_graminearum 83 59 59 86 55 37 92 27 62 92 87 70 82 92 88 52 57 87 78 47 45 85 60 81 56 18 92 83 VM1G_00616

KKY35092_Diaporthe_ampelina WP_01111_Rhodopirellula_baltica WP_015845757_Paenibacillus_sp WP_0516030_Verrucomicrobium_sp WP_0035877_Rhodopirellula_baltica WP_0136209_Rubinisphaera_brasiliensis KLU07046_Rhodopirellula_sp WP_002648541_Gimesia_maris WP_00308_Rhodopirellula_baltica WP_035614887_Haloferula_sp XP_0026808_Naegleria_gruberi WP_00228_Paenibacillus_sp WP_053061056_Rhodopirellula_sp WP_038167922_Verrucomicrobium_sp WP_044183010_Pirellula_staleyi EMI25847_Rhodopirellula_europaea WP_007413557_Pedosphaera_parvula WP_00913_Verrucomicrobium_spinosum EPX57826_Cystobacter_fuscus WP_0090037_Rhodopirellula_sp WP_007131155_Paenibacillus_lactis WP_0060829_Chthoniobacter_flavus WP_020475059_Zavarzinella_formosa WP_051256691_Cystobacter_fuscus WP_008701458_Rhodopirellula_maiorica WP_050028687_Verrucomicrobium_sp ADG68792_Planctopirus_limnophila WP_0025841_Rhodopirellula_baltica ADB15537_Pirellula_staleyi WP_051425275_Paenibacillus_sp WP_0152470_Singulisphaera_acidiphila WP_015845758_Paenibacillus_sp VM1G_00776_Valsa_mali WP_0523015_Planctopirus_limnophila WP_0372520_Rhodopirellula_europaea WP_0156928_Paenibacillus_sp WP_0516032_Verrucomicrobium_sp WP_0026523_Blastopirellula_marina WP_008660827_Rhodopirellula_europaea 89 52 79 41 78 51 89 35 31 49 92 87 61 92 72 49 41 M1G_00776

EKX68546_Streptomyces_ipomoeae XP_0077583_Eutypa_lata VM1G_01172_Valsa_mali AAA67510_Streptomyces_glaucescens AGP609_Streptomyces_rapamycinicus KIM364_Oidiodendron_maius WP_055554004_Streptomyces_sp KIM9_Oidiodendron_maius WP_0414118_Streptomyces_caatingaensis WP_030472125_Lechevalieria_aerocolonigenes KJK50809_Lechevalieria_aerocolonigenes WP_044580209_Streptomyces_iranensis CEL20688_Kibdelosporangium_sp WP_0414488_Streptomyces_caatingaensis CDM28614_Penicillium_roqueforti WP_030451751_Herbidospora_cretacea WP_051581436_Pseudonocardia_acaciae WP_030430268_Allokutzneria_albata WP_00403_Saccharopolyspora_erythraea AFU90406_Streptomyces_sp WP_0054866_Streptomyces_bottropensis WP_0488178_Streptomyces_ipomoeae WP_051823529_Streptomyces_sp WP_052407890_Allokutzneria_albata WP_01870_Streptomyces_purpureus WP_014058002_Streptomyces_violaceusniger WP_046086371_Streptomyces_sp XP_007831810_Pestalotiopsis_fici WP_0020878_Streptomyces_himastatinicus WP_0435824_Mycobacterium_llatzerense WP_0048267_Streptomyces_mobaraensis WP_0377719_Streptomyces_sp WP_043777869_Amycolatopsis_rifamycinica AFV25479_Streptomyces_sp WP_01436_Streptomyces_sulphureus WP_0542160_Kibdelosporangium_phytohabitans WP_013003265_Streptomyces_scabiei WP_047856040_Archangium_gephyra WP_0308376_Streptomyces_hygroscopicus 67 61 72 70 90 48 86 91 78 68 60 81 58 Mycobacterium_spp Mycobacterium_spp VM1G_01172

WP_039287675_Novosphingobium_malaysiense WP_008831132_Sphingomonas_sp KOP40348_Madurella_mycetomatis XP_007790307_Eutypa_lata WP_0287570_Sphingomonas_phyllosphaerae WP_01681_Sphingomonas_sp XP_007781537_Coniosporium_apollinis WP_0260631_Sphingomonas-like WP_0116366_Sphingomonas_sp KMS52368_Sphingobium_czechense WP_0432285_Novosphingobium_sp WP_0116073_Sphingomonas_sp KKY366_Diaporthe_ampelina WP_011542842_Sphingopyxis_alaskensis WP_036526828_Novosphingobium_resinovorum WP_047867289_Sphingomonas_paucimobilis WP_0390924_Novosphingobium_sp XP_007914885_Togninia_minima WP_0464064_Sphingomonas_sp KFA55220_Stachybotrys_chartarum WP_004212890_Sphingomonadaceae XP_003176580_Microsporum_gypseum WP_010164270_Sphingomonas_sp XP_013343190_Aureobasidium_subglaciale KMS54367_Novosphingobium_barchaimii WP_0424691_Sphingomonas_paucimobilis WP_010217468_Sphingomonas_sp WP_053556571_Sphingopyxis_sp WP_024022119_Sphingobium_sp WP_0134315_Sphingomonas_sp WP_04385_Novosphingobium_sp WP_007683121_Novosphingobium_sp EKG044_Macrophomina_phaseolina WP_054436516_Novosphingobium_sp WP_0545614_Novosphingobium_sp WP_007015386_Sphingomonadaceae WP_0089115_Novosphingobium_sp WP_021233326_Novosphingobium_lindaniclasticum WP_013832163_Novosphingobium_sp WP_008827648_Sphingomonas_sp KEQ619_Aureobasidium_melanogenum WP_041043236_Tolypothrix_campylonemoides VM1G_01377_Valsa_mali XP_0074854_Capronia_epimyces 33 39 82 49 75 88 72 44 55 92 40 57 63 75 87 88 92 Sphingomonas_spp. Fusarium_spp. Pseudogymnoascus_spp. VM1G_01377

WP_046566018_Micromonospora_sp WP_0116880_Candidatus_Solibacter KRB77082_Nocardioides_sp WP_014263653_Granulicella_mallensis WP_014910753_Nocardiopsis_alba WP_045511028_bacterium_UASB WP_0264450_Acidobacteriaceae_bacterium KKY217_Diaporthe_ampelina WP_017556421_Nocardiopsis_baichengensis WP_0474891_Terriglobus_sp WP_0500613_Acidobacteriaceae_bacterium WP_0175327_Nocardiopsis_alba WP_0175366_Nocardiopsis_potens WP_030338225_Micromonospora_parva WP_011520852_Candidatus_Koribacter XP_0030392_Nectria_haematococca WP_0491333_Acidobacterium_sp KQP78010_Aeromicrobium_sp WP_026388329_Acidobacteria_bacterium WP_035350004_Edaphobacter_aggregans WP_012922627_Kribbella_flavida WP_020711462_Acidobacteriaceae_bacterium ACO33744_Acidobacterium_capsulatum WP_020715449_Acidobacteriaceae_bacterium WP_013581785_Granulicella_tundricola KQP26891_Aeromicrobium_sp WP_020720442_Acidobacteriaceae_bacterium VM1G_01892_Valsa_mali WP_0175363_Nocardiopsis_halophila WP_026392688_Acidobacteriaceae_bacterium XP_007834859_Pestalotiopsis_fici WP_0418365_Acidobacterium_capsulatum WP_014784690_Terriglobus_roseus WP_0422857_Nocardiopsis_sp WP_017623657_Nocardiopsis_chromatogenes 83 71 86 71 83 69 89 78 77 Streptomyces_spp VM1G_01892

KJJ21279_Penicillium_solitum XP_006461545_Agaricus_bisporus VM1G_02284_Valsa_mali KIY62258_Cylindrobasidium_torrendii XP_0132758_Rhinocladiella_mackenziei CAI43283_Malassezia_sympodialis XP_0037020_Auricularia_subglabra KGO75825_Penicillium_italicum KIJ090_Laccaria_amethystina CEH18770_Ceraceosorus_bombacis EEB884_Moniliophthora_perniciosa KIW63858_Capronia_semiimmersa CEJ58114_Penicillium_brasilianum EKV115_Penicillium_digitatum XP_0078511_Moniliophthora_roreri XP_00260_Agaricus_bisporus CRG84226_Talaromyces_islandicus XP_0037726_Auricularia_subglabra XP_00272_Agaricus_bisporus KOS16334_Malassezia_pachydermatis XP_007878320_Anthracocystis_flocculosa KOS16335_Malassezia_pachydermatis KPV76585_Rhodotorula_graminis XP_013242305_Tilletiaria_anomala XP_0044212_Auricularia_subglabra XP_007728224_Capronia_coronata XP_0078465_Moniliophthora_roreri XP_0012090_Malassezia_globosa KIW34086_Cladophialophora_immunda CDI54338_Melanopsichium_pennsylvanicum KGO420_Penicillium_expansum KIW42617_Exophiala_oligosperma CDI554_Melanopsichium_pennsylvanicum XP_003029253_Schizophyllum_commune XP_011391368_Ustilago_maydis EMS260_Rhodosporidium_toruloides ETS65339_Pseudozyma_aphidis GAK65507_Pseudozyma_antarctica CBQ6_Sporisorium_reilianum GAK684_Pseudozyma_antarctica XP_0133222_Exophiala_xenobiotica KIY44082_Fistulina_hepatica CDM35827_Penicillium_roqueforti XP_0012157_Malassezia_globosa XP_0030355_Schizophyllum_commune CCF50110_Ustilago_hordei GAC024_Pseudozyma_antarctica KKY36776_Diaporthe_ampelina ETS61786_Pseudozyma_aphidis GAD92055_Byssochlamys_spectabilis KIY70183_Cylindrobasidium_torrendii KIW17623_Exophiala_spinifera XP_012187255_Pseudozyma_hubeiensis XP_0012158_Malassezia_globosa XP_0121808_Pseudozyma_hubeiensis EST09215_Pseudozyma_brasiliensis GAC71446_Pseudozyma_antarctica XP_007878618_Anthracocystis_flocculosa KIK66615_Gymnopus_luxurians EGU12718_Rhodotorula_glutinis XP_002148263_Talaromyces_marneffei KDQ31492_Pleurotus_ostreatus GAM40240_Talaromyces_cellulolyticus XP_0025652_Penicillium_rubens KIY01127_Fonsecaea_multimorphosa KOS37086_Penicillium_nordicum XP_009153623_Exophiala_dermatitidis CRL26481_Penicillium_camemberti KIV78046_Exophiala_sideris XP_0073140_Capronia_epimyces XP_002482522_Talaromyces_stipitatus 83 86 56 78 58 67 69 71 42 74 71 74 62 83 32 59 77 91 88 Basidiomycota Basidiomycota Ascomycota VM1G_02284

WP_0518349_Streptomyces_sp GAM366_Talaromyces_cellulolyticus KOS44646_Penicillium_nordicum XP_013267670_Rhinocladiella_mackenziei XP_008722525_Cladophialophora_carrionii CCD565_Botrytis_cinerea KGO68501_Penicillium_italicum KIW350_Cladophialophora_bantiana XP_007788870_Eutypa_lata WP_022613653_Vibrio_nigripulchritudo GAM832_fungal_sp WP_028671217_Saccharospirillum_impatiens KMO772_Mycobacterium_obuense XP_007592883_Colletotrichum_fioriniae XP_007753077_Cladophialophora_yegresii EPE030_Ophiostoma_piceae XP_007290357_Marssonina_brunnea KIW024_Capronia_semiimmersa CEJ516_Penicillium_brasilianum XP_001559066_Botrytis_cinerea KIW16780_Exophiala_spinifera KQY06207_Mycobacterium_sp CDK28010_Kuraishia_capsulata KKY27433_Diplodia_seriata KEY74755_Stachybotrys_chartarum KKP037_Trichoderma_harzianum WP_004923045_Streptomyces_griseoflavus KIX3_Fonsecaea_multimorphosa KQR7_Williamsia_sp XP_007726655_Capronia_coronata KIW34586_Cladophialophora_immunda KIW00318_Verruconis_gallopava ETW9_Candidatus_Entotheonella XP_0015740_Sclerotinia_sclerotiorum KIV82153_Exophiala_sideris KFY76565_Pseudogymnoascus_pannorum CRG85410_Talaromyces_islandicus CDM27871_Penicillium_roqueforti WP_0455515_Streptomyces_sp KGO40120_Penicillium_expansum KFZ104_Pseudogymnoascus_pannorum VM1G_02549_Valsa_mali XP_007827705_Pestalotiopsis_fici WP_0127581_Limnohabitans_sp CRL18751_Penicillium_camemberti XP_0141717_Grosmannia_clavigera XP_007784224_Coniosporium_apollinis WP_029106224_Mycobacterium_sp XP_013330523_Rasamsonia_emersonii KJJ10128_Penicillium_solitum WP_011580156_Chelativorans_sp KPI35356_Phialophora_attae KKY18201_Phaeomoniella_chlamydospora XP_002145663_Talaromyces_marneffei KIW880_Cladophialophora_bantiana KFX42121_Talaromyces_marneffei WP_046364536_Mycobacterium_obuense XP_007747150_Cladophialophora_psammophila ETR7_Trichoderma_reesei XP_002565743_Penicillium_rubens XP_013285500_Fonsecaea_pedrosoi WP_048422864_Mycobacterium_obuense XP_013310106_Exophiala_xenobiotica XP_013278448_Fonsecaea_pedrosoi EMR87546_Botrytis_cinerea WP_0364418_Mycobacterium_vulneris ESZ586_Sclerotinia_borealis XP_007913054_Togninia_minima XP_0077672_Eutypa_lata KPI424_Phialophora_attae KFA45846_Stachybotrys_chartarum WP_037926253_Streptomyces_toyocaensis 89 20 49 64 89 74 61 43 47 84 61 28 91 71 87 27 89 67 29 77 68 63 52 60 89 83 89 83 74 Bordetella_spp. Acinetobacter_spp. VM1G_02549

KIW16782_Exophiala_spinifera KEC78234_Sinorhizobium_americanum WP_0334574_Bordetella_bronchiseptica WP_03723_Rhodococcus_wratislaviensis WP_053740490_Streptomyces_sp KIW00312_Verruconis_gallopava WP_003814501_Bordetella_bronchiseptica XP_007581902_Neofusicoccum_parvum XP_00702_Pseudocercospora_fijiensis WP_0282317_Burkholderia_mimosarum WP_048680362_Bacillus_sp KFX42120_Talaromyces_marneffei WP_025420472_Sodalis_praecaptivus XP_0132676_Rhinocladiella_mackenziei WP_004752139_Acinetobacter_sp WP_052223540_Novosphingobium_malaysiense WP_0129165_Streptomyces_scabiei WP_014231725_Vibrio_sp WP_030417717_Streptomyces_sp WP_054188629_Rhodococcus_sp WP_0030112_Mycobacterium_vaccae WP_007086582_Bacillus_bataviensis AAW28146_Rhizobium_sp XP_0079130_Togninia_minima WP_019068143_Streptomyces_sp WP_037672378_Streptomyces_griseus WP_004901645_Acinetobacter_brisouii WP_036527808_Novosphingobium_resinovorum GAM368_Talaromyces_cellulolyticus EPE023_Ophiostoma_piceae WP_0436625_Streptomyces_xylophagus WP_0008802_Streptomyces_ipomoeae WP_050747292_Sodalis_glossinidius WP_034888352_Erwinia_typographi WP_021471208_Arthrobacter_sp WP_0385310_Sinorhizobium_americanum WP_0407920_Nocardia_higoensis WP_004181676_Klebsiella_pneumoniae WP_033840446_Bordetella_bronchiseptica WP_025036279_Bradyrhizobium_sp XP_007827707_Pestalotiopsis_fici WP_038676339_Pimelobacter_simplex KKO72846_Kerstersia_gyiorum KEY74761_Stachybotrys_chartarum XP_002145661_Talaromyces_marneffei WP_029112541_Mycobacterium_sp WP_026187581_Ensifer_sp WP_0135830_Hyphomicrobium_sp WP_055611366_Streptomyces_phaeochromogenes XP_007726659_Capronia_coronata WP_0503717_Streptomyces_acidiscabies VM1G_02555_Valsa_mali KFA81538_Stachybotrys_chartarum WP_0458567_Raoultella_terrigena EGD06287_Burkholderia_sp WP_033470245_Bordetella_bronchiseptica WP_017524424_Pusillimonas_noertemannii KKY16861_Phaeomoniella_chlamydospora WP_045555454_Streptomyces_sp XP_0077666_Eutypa_lata WP_010929200_Bordetella_parapertussis WP_0265645_Bacillus_sp WP_010360538_Streptomyces_acidiscabies WP_026582866_Bacillus_sp WP_028471543_Nocardioides_alkalitolerans WP_052371903_Amycolatopsis_taiwanensis KPI35307_Phialophora_attae XP_014171920_Grosmannia_clavigera WP_050655584_Rhodococcus_sp WP_017523084_Pusillimonas_noertemannii 36 80 37 90 70 83 32 88 81 77 81 62 86 70 49 55 55 30 55 Achromobacter_spp Photorhabdus_spp VM1G_02555

KDQ13290_Botryobasidium_botryosum CEL57465_Rhizoctonia_solani KDQ58426_Jaapia_argillacea EUC53763_Rhizoctonia_solani KIO242_Tulasnella_calospora XP_0084366_Punctularia_strigosozonata KIO24292_Tulasnella_calospora XP_0078605_Gloeophyllum_trabeum VM1G_02910_Valsa_mali CCO26677_Rhizoctonia_solani EJU02432_Dacryopinax_sp XP_0055390_Auricularia_subglabra CUA77546_Rhizoctonia_solani KIO24291_Tulasnella_calospora XP_007270418_Fomitiporia_mediterranea KII87568_Plicaturopsis_crispa KLO122_Schizopora_paradoxa KIO24307_Tulasnella_calospora KLO13341_Schizopora_paradoxa XP_007927005_Pseudocercospora_fijiensis XP_0040609_Auricularia_subglabra KIO216_Tulasnella_calospora KIO26062_Tulasnella_calospora KIO24280_Tulasnella_calospora CED84805_Xanthophyllomyces_dendrorhous KIM123_Serendipita_vermifera CCA74032_Piriformospora_indica 70 82 80 53 80 72 45 Cryptococcus_spp Basidiomycota Basidiomycota Ascomycota VM1G_02910

EYE023_Aspergillus_ruber KGO304_Penicillium_expansum KIV762_Exophiala_sideris EUN26561_Bipolaris_victoriae XP_007406645_Melampsora_larici XP_007840418_Pestalotiopsis_fici XP_007281785_Colletotrichum_gloeosporioides KGO75074_Penicillium_italicum KOS478_Penicillium_nordicum KDN66752_Colletotrichum_sublineola AF181866_synthetic_construct XP_456462_Debaryomyces_hansenii XP_00829_Punctularia_strigosozonata KIV86820_Exophiala_sideris XP_013343258_Aureobasidium_subglaciale XP_002477846_Talaromyces_stipitatus XP_007703311_Bipolaris_sorokiniana XP_0080261_Setosphaeria_turcica 4RSL_A_4RSL_A XP_0030411_Nectria_haematococca CEJ56755_Penicillium_brasilianum KGO47403_Penicillium_expansum XP_002484168_Talaromyces_stipitatus XP_0006188_Stereum_hirsutum KKY34247_Diaporthe_ampelina EQB58906_Colletotrichum_gloeosporioides BAD00185_Penicillium_terrenum XP_013422318_Aureobasidium_namibiae XP_0032444_Pyrenophora_teres CRL24868_Penicillium_camemberti EPE02569_Ophiostoma_piceae XP_0133163_Exophiala_xenobiotica KIW10542_Exophiala_spinifera XP_003047168_Nectria_haematococca XP_014171052_Grosmannia_clavigera XP_009153156_Exophiala_dermatitidis XP_0075814_Neofusicoccum_parvum BAE140_Ulocladium_sp XP_014079006_Bipolaris_maydis XP_013320914_Exophiala_xenobiotica KII88422_Plicaturopsis_crispa KIY458_Fistulina_hepatica XP_007708512_Bipolaris_zeicola ENH83077_Colletotrichum_orbiculare XP_681392_Aspergillus_nidulans XP_0077547_Eutypa_lata XP_003327623_Puccinia_graminis CDK252_Kuraishia_capsulata CDZ665_Xanthophyllomyces_dendrorhous CDM34716_Penicillium_roqueforti XP_007686371_Bipolaris_oryzae XP_0018761_Pyrenophora_tritici XP_777019_Cryptococcus_neoformans KNZ529_Puccinia_sorghi VM1G_020_Valsa_mali GAM35130_Talaromyces_cellulolyticus KNE892_Puccinia_striiformis XP_0017711_Parastagonospora_nodorum KEZ43556_Scedosporium_apiospermum XP_0052692_Heterobasidion_irregulare KDQ51628_Jaapia_argillacea XP_00255_Penicillium_rubens KEQ614_Aureobasidium_melanogenum XP_007722025_Capronia_coronata KJJ23348_Penicillium_solitum CEP22126_Cyberlindnera_jadinii XP_568763_Cryptococcus_neoformans KEQ80229_Aureobasidium_pullulans BAD00186_Coniochaeta_sp XP_0080854_Colletotrichum_graminicola XP_012047727_Cryptococcus_neoformans XP_003027756_Schizophyllum_commune XP_0078609_Gloeophyllum_trabeum XP_011276769_Wickerhamomyces_ciferrii 68 27 88 92 78 41 76 86 56 86 55 77 76 81 27 40 86 66 85 38 91 90 33 79 34 Fusarium_spp Cryptococcus_spp Basidiomycota Ascomycota VM1G_020

WP_028224824_Burkholderia_sp AJC22888_Pandoraea_pulmonicola WP_035518721_Burkholderia_sp WP_038201680_Xenophilus_azovorans WP_0062650_Rhodococcus_sp KIM700_Oidiodendron_maius WP_051243811_Azohydromonas_australica WP_0114126_Burkholderia_xenovorans WP_043374609_Comamonas_testosteroni WP_0511283_Nocardia_jiangxiensis WP_0247163_Rhodococcus_sp WP_0527645_Streptomyces_europaeiscabiei KPI23374_Actinobacteria_bacterium KRB187_Hydrogenophaga_sp WP_031470863_Sciscionella_sp WP_021245320_Sphingobium_baderi WP_038357689_Bosea_sp KMS61908_Sphingobium_baderi WP_0186817_Amorphus_coralli KEY74811_Stachybotrys_chartarum KFA4_Stachybotrys_chartarum GAO20820_Alicycliphilus_sp WP_028603815_Ottowia_thiooxydans EIF318_Burkholderia_sp WP_052267612_Pandoraea_pulmonicola KRB85535_Sphingomonas_sp WP_051059071_Burkholderia_sp WP_053555626_Sphingopyxis_sp WP_0204047_Sciscionella_marina EYS85102_Cupriavidus_sp AJW201_Sphingomonas_sp XP_008823_Colletotrichum_graminicola XP_0080266_Setosphaeria_turcica WP_036168362_Massilia_sp WP_007182687_Burkholderia_sp WP_049019177_Burkholderia_multivorans KGO63929_Penicillium_italicum WP_0334638_Burkholderia_multivorans EIF32032_Burkholderia_sp WP_051591807_Cupriavidus_sp XP_0132532_Rhinocladiella_mackenziei WP_011600445_Rhodococcus_jostii VM1G_03090_Valsa_mali AKP92220_Achromobacter_xylosoxidans 91 56 74 89 92 72 41 56 91 47 54 48 66 76 67 VM1G_03090

0.3 KQV30626_Rhizobium_sp WP_031445849_Arenibacter_algicola KFZ12530_Pseudogymnoascus_pannorum EWG42788_Fusarium_verticillioides KPA45902_Fusarium_langsethiae WP_011684915_Candidatus_Solibacter WP_01623_Eudoraea_adriatica WP_026337085_Acidobacteriaceae_bacterium KFY43621_Pseudogymnoascus_pannorum CRK16278_Verticillium_longisporum KFY710_Pseudogymnoascus_pannorum XP_002850586_Arthroderma_otae KKY31257_Diaporthe_ampelina WP_02615_Rhizobium_leguminosarum KIL912_Fusarium_avenaceum KFY30424_Pseudogymnoascus_pannorum WP_0267102_Flavobacterium_filum XP_0075926_Colletotrichum_fioriniae XP_0056857_Verticillium_dahliae EXM07238_Fusarium_oxysporum VM1G_03108_Valsa_mali WP_055445581_Lacinutrix_himadriensis WP_0186746_Arenitalea_lutea WP_052535513_Candidatus_Phaeomarinobacter WP_0222775_Xanthomonas_sp KFX86644_Pseudogymnoascus_pannorum XP_009254460_Fusarium_pseudograminearum XP_0030022_Verticillium_alfalfae ENH68826_Fusarium_oxysporum XP_0078755_Anthracocystis_flocculosa CRK14657_Verticillium_longisporum WP_050058090_Acidobacteriaceae_bacterium WP_008582349_Niabella_soli XP_008716440_Cyphellophora_europaea CRL17750_Penicillium_camemberti KFH68184_Mortierella_verticillata GAO88553_Neosartorya_udagawae WP_0052892_Corynebacterium_genitalium WP_016552353_Rhizobium_grahamii ALM086_Sediminicola_sp CCT66908_Fusarium_fujikuroi EMT68080_Fusarium_oxysporum XP_0070320_Pseudocercospora_fijiensis XP_007411880_Melampsora_larici EWZ727_Fusarium_oxysporum WP_0522008_Terriglobus_sp XP_0031771_Microsporum_gypseum WP_02903_Rhizobium_leguminosarum KFX2_Pseudogymnoascus_pannorum KLO632_Fusarium_fujikuroi XP_011324523_Fusarium_graminearum WP_0466907_Sphingobacterium_sp 57 57 79 75 86 76 86 23 76 50 50 91 82 91 44 27 88 85 79 86 78 76 88 80 Chryseobacterium_spp VM1G_03108

XP001803248_Parastagonospora_nodorum XP0012554_Neosartorya_fischeri WP056222432_Chryseobacterium_sp GAM319_Talaromyces_cellulolyticus GAD648_Byssochlamys_spectabilis CEJ62862_Penicillium_brasilianum WP021337456_Lactobacillus_plantarum KIY01641_Fonsecaea_multimorphosa KIV86245_Exophiala_sideris KIV87176_Exophiala_sideris KJK64811_Aspergillus_parasiticus XP007911352_Phaeoacremonium_minimum XP0061702_Dichomitus_squalens WP055751546_Frankia_sp WP040857625_Nocardia_niigatensis GAQ11743_Aspergillus_lentulus CAJ62281_Frankia_alni XP00752_Eutypa_lata CRL172_Penicillium_camemberti XP0080868_Colletotrichum_graminicola GAO858_Neosartorya_udagawae KFY420_Pseudogymnoascus_sp XP008086616_Glarea_lozoyensis XP0078022_Capronia_epimyces WP025357426_Kutzneria_albida GAM35249_Talaromyces_cellulolyticus WP0570326_Algoriphagus_sp EMR911_Botrytis_cinerea XP7449_Aspergillus_fumigatus XP014072629_Bipolaris_maydis WP054655555_Lactobacillus_silagei KJK63712_Aspergillus_parasiticus WP0072514_WP_0072514.1 WP0406162_Nocardia_vinacea KLP06860_Fusarium_fujikuroi XP007725605_Capronia_coronata KIV78870_Exophiala_sideris KKZ655_Emmonsia_crescens VM1G_03556_Valsa_mali KJJ25285_Penicillium_solitum WP04176_Frankia_alni XP013271914_Rhinocladiella_mackenziei WP025718519_Paenibacillus_sp XP007727103_Capronia_coronata KIW012_Exophiala_spinifera CRL24591_Penicillium_camemberti XP001545304_Botrytis_cinerea XP007854117_Moniliophthora_roreri XP013313089_Exophiala_xenobiotica KDN71869_Colletotrichum_sublineola XP002480320_Talaromyces_stipitatus XP008715582_Cyphellophora_europaea XP003654012_Thielavia_terrestris KOS216_Escovopsis_weberi GAM43929_Talaromyces_cellulolyticus XP007839172_Pestalotiopsis_fici KOS482_Penicillium_nordicum WP033236876_Rhodococcus_rhodochrous XP008728502_Cladophialophora_carrionii XP007602036_Colletotrichum_fioriniae XP009156188_Exophiala_dermatitidis XP002381900_Aspergillus_flavus KJA23206_Hypholoma_sublateritium CRG83420_Talaromyces_islandicus WP0101203_Sphingomonas_sp XP007284617_Colletotrichum_gloeosporioides 51 89 52 87 64 90 75 80 86 85 74 62 59 91 55 45 76 85 62 70 Ascomycota Ascomycota Basidiomycota VM1G_03556

WP_005202792_Gordonia_sputi WP_051761685_Microbispora_rosea VM1G_04133_Valsa_mali WP_013585784_Microbacterium_testaceum WP_023515101_Shinella_sp WP_02001_Mycobacterium_sp WP_04701_Nonomuraea_sp WP_02681_Mycobacterium_sp KQM34063_Rhizobium_sp WP_030487625_Micromonospora_chokoriensis WP_0316378_Microbacterium_hominis WP_029006549_Azorhizobium_doebereinerae WP_007241146_Gordonia_otitidis KQQ534_Rhizobium_sp WP_055505010_Nonomuraea_sp WP_029121389_Mycobacterium_sp ESY88146_Mesorhizobium_sp WP_014784429_Terriglobus_roseus WP_0291123_Mycobacterium_sp WP_050744208_Shinella_sp WP_0514425_Mesorhizobium_sp WP_0433926_Mycobacterium_llatzerense WP_0407428_Nocardia_higoensis WP_055506838_Nonomuraea_sp WP_007414650_Pedosphaera_parvula WP_026218354_Streptomyces_scabrisporus WP_043390600_Mycobacterium_sp WP_031248647_Mesorhizobium_sp XP_0076778_Baudoinia_panamericana 68 88 92 84 71 60 51 VM1G_04133

WP_0284380_Rhizobium_leguminosarum XP_0061342_Nicotiana_sylvestris WP_0306634_Streptomyces_cellulosae WP_054405172_Paenibacillus_sp WP_026554331_Arthrobacter_sp XP_0010288_Nicotiana_tomentosiformis XP_0133754_Ogataea_parapolymorpha ABR16229_Picea_sitchensis XP_012839034_Erythranthe_guttatus AFZ84925_Physcomitrella_patens KCW88013_Eucalyptus_grandis WP_028526659_Runella_limosa KCW88014_Eucalyptus_grandis WP_010347135_Paenibacillus_peoriae CDK279_Kuraishia_capsulata WP_0368225_Photobacterium_sanctipauli EFL20921_Streptomyces_himastatinicus WP_010272453_Paenibacillus_senegalensis EIF45186_Brettanomyces_bruxellensis WP_015206226_Cylindrospermum_stagnale WP_051400605_Clostridiales_bacterium WP_0421618_Paenibacillus_sp XP_0042513_Solanum_lycopersicum WP_0228092_Corynebacterium-like WP_053490884_Bacillus_sp XP_010228384_Brachypodium_distachyon AFZ84926_Physcomitrella_patens WP_035031753_Devosia_sp XP_007911220_Togninia_minima BAJ480_Candidatus_Caldiarchaeum XP_010912743_Elaeis_guineensis WP_0302275_Streptomyces_violaceoruber KON30581_miscellaneous_Crenarchaeota WP_0506411_Eubacterium_sp WP_0355501_Halomonas_salina BAJ471_Candidatus_Caldiarchaeum WP_004072790_Clostridium_sp AFZ84924_Physcomitrella_patens WP_042160752_Paenibacillus_sp WP_0249238_Mesorhizobium_sp AFZ84927_Physcomitrella_patens XP_001771662_Physcomitrella_patens WP_046260205_Streptomyces_sp WP_025654547_Clostridiales_bacterium AFZ84928_Physcomitrella_patens KPN14136_Bacillus_sp VM1G_04190_Valsa_mali WP_0232108_Scytonema_hofmanni WP_0343233_Bacillus_sp XP_006688763_Candida_tenuis 82 79 80 92 66 55 69 51 61 69 78 80 77 Viridiplantae Viridiplantae VM1G_04190

0.09 XP_008091551_Colletotrichum_graminicola XP_007837540_Pestalotiopsis_fici XP_008904024_Phytophthora_parasitica KKY13676_Diplodia_seriata ETM415_Phytophthora_parasitica XP_0088679_Phytophthora_parasitica ETL31091_Phytophthora_parasitica CEJ56904_Penicillium_brasilianum EKV05820_Penicillium_digitatum XP_664276_Aspergillus_nidulans XP_002904300_Phytophthora_infestans XP_0072856_Colletotrichum_gloeosporioides ETO70679_Phytophthora_parasitica KGO77832_Penicillium_italicum ETI48538_Phytophthora_parasitica KPM40080_Neonectria_ditissima CCX34009_Pyronema_omphalodes EME43478_Dothistroma_septosporum EKG17_Macrophomina_phaseolina KJX177_Zymoseptoria_brevis ENH83916_Colletotrichum_orbiculare XP_00140_Phytophthora_sojae EQB47601_Colletotrichum_gloeosporioides EMF12245_Sphaerulina_musiva XP_007585183_Neofusicoccum_parvum XP_0033419_Phytophthora_sojae XP_0025686_Penicillium_rubens ETL88722_Phytophthora_parasitica CRL22911_Penicillium_camemberti XP_003044743_Nectria_haematococca XP_008909123_Phytophthora_parasitica XP_0028090_Phytophthora_infestans XP_0074128_Melampsora_larici XP_0037901_Phytophthora_sojae XP_0028635_Phytophthora_infestans XP_007601812_Colletotrichum_fioriniae CCF36503_Colletotrichum_higginsianum KGO46541_Penicillium_expansum ETO306_Phytophthora_parasitica XP_0015305_Phytophthora_sojae XP_007927589_Pseudocercospora_fijiensis XP_0028611_Phytophthora_infestans KDN63372_Colletotrichum_sublineola VM1G_04692_Valsa_mali XP_0033133_Puccinia_graminis KJJ039_Penicillium_solitum ETI44692_Phytophthora_parasitica KOS396_Penicillium_nordicum 24 40 52 44 87 59 25 87 47 50 62 92 35 91 60 52 84 67 87 55 58 92 27 70 79 52 70 84 89 31 28 Fusarium_spp Ascomycota Ascomycota Basidiomycota Oomycetes VM1G_04692

WP_046708143_Streptomyces_europaeiscabiei ELQ35678_Magnaporthe_oryzae WP_033529082_Streptomyces_galbus KPI324_Actinobacteria_bacterium XP_007912745_Togninia_minima WP_029163109_Clostridium_scatologenes WP_0517846_Rhodococcus_rhodnii XP_007790812_Eutypa_lata VM1G_04714_Valsa_mali WP_053170466_Streptomyces_sp WP_0438279_Micromonospora_carbonacea WP_037705209_Streptomyces_scabiei ELP70762_Streptomyces_turgidiscabies WP_005475302_Streptomyces_bottropensis WP_0133490_Verrucosispora_maris KLU857_Magnaporthiopsis_poae WP_033383766_Kibdelosporangium_aridum WP_046767147_Jiangella_alkaliphila GAP83078_Rosellinia_necatrix XP_003843216_Leptosphaeria_maculans XP_0037163_Magnaporthe_oryzae WP_0556167_Streptomyces_phaeochromogenes KRD202_Streptomyces_sp EKX634_Streptomyces_ipomoeae WP_037671454_Streptomyces_griseus WP_048818700_Streptomyces_turgidiscabies KKY35501_Diaporthe_ampelina WP_043488778_Streptomyces_bingchenggensis WP_052762853_Jiangella_alkaliphila WP_051426158_Jiangella_gansuensis WP_051765927_Streptomyces_sp WP_030453123_Herbidospora_cretacea WP_020518221_Actinoplanes_globisporus WP_037677121_Streptomyces_afghaniensis XP_009222647_Gaeumannomyces_graminis ELQ63839_Magnaporthe_oryzae WP_053205240_Jiangella_muralis ADI039_Streptomyces_bingchenggensis WP_048821013_Streptomyces_ipomoeae KPM46055_Neonectria_ditissima KFF211_Streptomyces_scabiei WP_053203882_Jiangella_muralis WP_053207702_Jiangella_muralis WP_034272539_Actinospica_robiniae WP_0520376_Clostridium_drakei WP_0288062_Streptomyces_sp WP_045562247_Streptomyces_sp EPJ42815_Streptomyces_afghaniensis WP_03331_Streptomyces_yerevanensis WP_055637517_Streptomyces_griseoruber 80 9 58 41 42 78 45 92 45 90 85 80 55 66 82 VM1G_04714

KFY72129_Pseudogymnoascus_pannorum WP_027603547_Pseudomonas_sp WP_024076438_Pseudomonas_sp WP_034512789_Agrobacterium_rhizogenes GAD0_Byssochlamys_spectabilis EQB50603_Colletotrichum_gloeosporioides EXK762_Fusarium_oxysporum XP_003041254_Nectria_haematococca VM1G_05155_Valsa_mali XP_003042148_Nectria_haematococca XP_007285204_Colletotrichum_gloeosporioides KFY12076_Pseudogymnoascus_pannorum WP_013078876_Caulobacter_segnis WP_0319858_Acinetobacter_baumannii KGO69138_Penicillium_expansum WP_0547504_Paenibacillus_sp KFY05889_Pseudogymnoascus_pannorum XP_007587276_Neofusicoccum_parvum WP_012654221_Agrobacterium_vitis KIL86485_Fusarium_avenaceum WP_0246155_Pseudomonas_fluorescens XP_013327456_Rasamsonia_emersonii WP_021015152_Serratia_sp WP_0241323_Rhodococcus_sp WP_025418326_Rhizobium_leguminosarum KFZ05818_Pseudogymnoascus_pannorum WP_0252121_Pseudomonas_brassicacearum EXL915_Fusarium_oxysporum XP_0075415_Colletotrichum_fioriniae WP_0547667_Paenibacillus_sp KGO47902_Penicillium_expansum XP_003042149_Nectria_haematococca KGO617_Penicillium_expansum 77 87 53 70 Ascomycota Ascomycota VM1G_05155

0.3 WP_000522842_Bacillus_thuringiensis VM1G_05405_Valsa_mali EGV00186_Mycoplasma_columbinum KIR032_Lachnospiraceae_bacterium EMR90169_Botrytis_cinerea XP_0015079_Sclerotinia_sclerotiorum ESZ91503_Sclerotinia_borealis EWC47146_Drechslerella_stenobrocha WP_04660_Bacillus_cereus XP_002837481_Tuber_melanosporum AET42542_Emiliania_huxleyi WP_011290355_Mycoplasma_hyopneumoniae WP_048722_Bacillus_cytotoxicus CNS05861_Salmonella_enterica AET610_Emiliania_huxleyi CCX04588_Pyronema_omphalodes WP_0134751_Mycoplasma_bovis XP_003054765_Micromonas_pusilla WP_000522844_Bacillus_cereus WP_040544532_Mycoplasma_anatis WP_043538453_Ruminococcus_albus WP_013022060_Mycoplasma_agalactiae WP_048558552_Bacillus_cereus AKU788_Spiroplasma_turonicum KKY246_Diaporthe_ampelina WP_000052106_Bacillus_cereus KPU55275_Bacillus_cereus CDC49071_Clostridium_sp WP_023789016_Spiroplasma_apis CCA68150_Piriformospora_indica WP_01782_Ruminococcus_flavefaciens EGS282_Mycoplasma_anatis WP_051527230_WP_051527230.1 WP_000052105_Bacillus_cereus WP_0291852_Mycoplasma_columbinum WP_050801909_Mycoplasma_columbinum WP_004023828_Mycoplasma_agalactiae WP_02338_Mycoplasma_glycophilum WP_002851376_Ruminococcus_albus WP_020835859_Mycoplasma_hyopneumoniae WP_052587769_Bacillus_thuringiensis WP_000522843_Bacillus_cereus XP_001551802_Botrytis_cinerea XP_0111105_Dactylellina_haptotyla CCD50810_Botrytis_cinerea WP_044284700_Mycoplasma_hyopneumoniae CCD50809_Botrytis_cinerea WP_016340370_Spiroplasma_syrphidicola WP_049112424_Bacillus_cereus YP_0030136_Cafeteria_roenbergensis AKA50185_Mycoplasma_gallinaceum WP_002557700_Mycoplasma_flocculare XP_011124586_Arthrobotrys_oligospora WP_023789215_Spiroplasma_apis KPI390_Phialophora_attae WP_0485666_Bacillus_cereus 59 41 67 55 40 30 56 37 59 67 37 65 66 31 61 66 91 90 61 82 82 86 64 91 Ascomycota VM1G_05405

VM1G_05720 WP_0235309_Streptomycetaceae_bacterium 85 WP_018385646_Streptomyces_vitaminophilus WP_030054716_Streptomyces_peruviensis 83 WP_053200603_Streptomyces_viridochromogenes 74 WP_048582755_Streptomyces_viridochromogenes 67 WP_030557113_Streptomyces_aureofaciens WP_020550180_Streptomyces_scabrisporus 80 WP_020540641_Nonomuraea_coxensis KRF34641_Nocardioides_sp KRE443_Nocardioides_sp 84 KGO636_Penicillium_italicum KJJ26316_Penicillium_solitum 42 KGO43380_Penicillium_expansum KGO5_Penicillium_expansum 64 KIN08901_Oidiodendron_maius 75 VM1G_05720_Valsa_mali XP_0134220_Aureobasidium_namibiae GAM913_fungal_sp WP_01291_Kribbella_flavida WP_0203087_Kribbella_catacumbae WP_042538244_WP_042538244.1

WP_004579154_Marinobacter_nanhaiticus KPV61707_Bathyarchaeota_archaeon ESN65425_Serratia_sp EKG16230_Macrophomina_phaseolina WP_0125430_Thermoanaerobacter_italicus WP_005587021_Clostridium_sp WP_052382138_Bifidobacterium_reuteri ADI02052_Syntrophothermus_lipocalidus WP_014256091_Clostridium_sp WP_0133764_Stigmatella_aurantiaca WP_041433479_Syntrophothermus_lipocalidus WP_038290705_Clostridium_sp WP_025640236_Clostridium_sp XP_007828774_Pestalotiopsis_fici EAU64700_Stigmatella_aurantiaca WP_042833261_Thermoanaerobacter_sp WP_003867672_Thermoanaerobacter_ethanolicus WP_0486322_Brenneria_goodwinii WP_009052490_Thermoanaerobacter_sp WP_054564146_Frankia_sp WP_027852618_Marinobacterium_litorale KFA45684_Stachybotrys_chartarum WP_014063006_Thermoanaerobacter_wiegelii WP_024831490_Clostridium_sp WP_051391431_Serratia_sp WP_005604241_Butyrivibrio_crossotus XP_014174339_Grosmannia_clavigera KEY71523_Stachybotrys_chartarum XP_007911356_Togninia_minima WP_0208133_Clostridium_sp WP_0536778_Clostridiaceae_bacterium KFI83206_Bifidobacterium_reuteri WP_006541704_Frankia_sp XP_007581483_Neofusicoccum_parvum KFA6_Stachybotrys_chlorohalonata WP_027620302_Pseudomonas_sp KFA71331_Stachybotrys_chartarum WP_0256526_Desulfotomaculum_thermocisternum VM1G_05918_Valsa_mali WP_0038626_Thermoanaerobacter_sp WP_0333888_Clostridium_argentinense WP_011025828_Caldanaerobacter_subterraneus CCY766_Butyrivibrio_crossotus KKY26283_Phaeomoniella_chlamydospora XP_00713_Capronia_epimyces WP_010248415_Acetivibrio_cellulolyticus WP_031515334_Desulfotomaculum_alkaliphilum WP_003518853_Ruminiclostridium_thermocellum WP_0534815_Clostridiales_bacterium 78 75 77 66 91 87 91 86 85 82 59 70 67 92 VM1G_05918

KPI44658_Phialophora_attae XP008714385_Cyphellophora_europaea VM1G_07081_Valsa_mali KIW13928_Exophiala_spinifera CCF657_Nocardia_cyriacigeorgica ADI11806_Streptomyces_bingchenggensis WP051791556_Amycolatopsis_jejuensis WP03192_Nocardia_otitidiscaviarum XP002487172_Talaromyces_stipitatus WP011211753_Nocardia_farcinica WP036434328_Mycobacterium_mageritense WP048834444_Nocardia_cyriacigeorgica XP0130333_Trichoderma_atroviride XP001243166_Coccidioides_immitis EJZ13104_Mycobacterium_fortuitum CRZ15879_Mycobacterium_neworleansense WP038566274_Mycobacterium_sp KMU87049_Coccidioides_immitis CRG873_Talaromyces_islandicus WP036540657_Nocardia_cyriacigeorgica XP013264629_Exophiala_aquamarina XP003070214_Coccidioides_posadasii WP052741045_Rhodococcus_erythropolis CEO59207_Penicillium_brasilianum WP043492345_Streptomyces_bingchenggensis 52 43 49 84 90 48 Fusarium_spp Mycobacterium_spp Mycobacterium_spp VM1G_07081

WP_004383847_Prevotella_veroralis WP_0182206_Methyloversatilis_universalis WP_0471488_Mesorhizobium_sp WP_037553335_Sphingopyxis_sp WP_036865240_Prevotella_melaninogenica WP_0561269_Pelomonas_sp WP_013561234_Anaerolinea_thermophila WP_0248890_Sphingomonas_sp WP_0568891_Nocardioides_sp WP_0034540_Prevotella_sp WP_04854_Tetrasphaera_japonica ABQ71016_Sphingomonas_wittichii WP_0032331_Mycobacterium_vaccae WP_0068700_Prevotella_multiformis CDA82828_Bacteroides_sp WP_0557909_Frigoribacterium_sp WP_003181470_Pseudomonas_fluorescens WP_056603387_Nocardioides_sp WP_0403168_Bacteroides_sp WP_056926488_Nocardioides_sp WP_0183610_Prevotella_nanceiensis WP_0434544_Georgenia_sp CRK15713_Verticillium_longisporum WP_02782_Anaerobiospirillum_succiniciproducens WP_009012323_Prevotella_sp EFC729_Prevotella_melaninogenica WP_0444826_Pseudomonas_sp WP_036285601_Methylocystis_sp WP_056355644_Sphingomonas_sp VM1G_088_Valsa_mali WP_0446567_Mycobacterium_goodii WP_008060600_Methyloversatilis_universalis WP_055811854_Frigoribacterium_sp WP_0541711_Sphingopyxis_macrogoltabida WP_020085090_Hyphomicrobium_zavarzinii WP_0554510_Curtobacterium_sp WP_036922530_Prevotella_sp WP_018910288_Prevotella_veroralis WP_0264721_Alkanindiges_illinoisensis WP_0305221_Phycicoccus_jejuensis WP_008644456_Bacteroides_sp WP_040157054_Mobilicoccus_sp KOR33108_Achromatium_sp CUO758_Bacteroides_xylanisolvens WP_0552354_Bacteroides_xylanisolvens WP_0306404_Pseudomonas_tuomuerensis WP_0083646_Mobilicoccus_pelagius WP_042728649_Pseudomonas_fluorescens WP_0483519_Candidatus_Achromatium AIV40612_Curtobacterium_sp WP_0475492_Pseudomonas_chlororaphis WP_025311410_Roseibacterium_elongatum WP_05641_Sphingomonas_sp 51 72 65 54 69 74 71 43 89 54 60 69 67 53 67 43 75 60 74 44 82 48 61 78 77 55 45 VM1G_088

WP_013626478_Rubinisphaera_brasiliensis WP_055241132_Turicibacter_sanguinis WP_01134_Hahella_chejuensis KGZ109_Raoultella_planticola KPL13614_Bacteroides_sp WP_0026444_Gimesia_maris WP_002655157_Blastopirellula_marina WP_020562346_Methylosarcina_fibrata WP_055164580_Turicibacter_sanguinis KIW16080_Exophiala_spinifera WP_0535676_Helicobacter_ailurogastricus WP_0555363_Streptomyces_neyagawaensis AIT56388_uncultured_bacterium XP_0132270_Rhinocladiella_mackenziei WP_037710455_Streptomyces_mirabilis ADB40010_Spirosoma_linguale WP_0504802_Raoultella_planticola WP_044886174_Frankia_sp WP_007513803_Frankia_sp WP_020508908_Actinoplanes_globisporus CRF52922_Helicobacter_ailurogastricus XP_0077191_Capronia_coronata WP_011437149_Frankia_sp WP_051400402_Amycolatopsis_halophila XP_0091588_Exophiala_dermatitidis WP_035912617_Frankia_sp WP_0175905_Nocardiopsis_potens KIV80839_Exophiala_sideris WP_0006659_Turicibacter_sp WP_046707020_Streptomyces_europaeiscabiei KJE22112_Frankia_sp ADO74692_Stigmatella_aurantiaca WP_005483556_Streptomyces_bottropensis WP_050500321_Raoultella_sp KFD06387_Raoultella_planticola VM1G_09114_Valsa_mali WP_002609279_Stigmatella_aurantiaca KKY36417_Diaporthe_ampelina WP_017664669_Porphyrobacter_sp KQM04280_Frankia_sp WP_051350625_Caloramator_sp WP_006784821_Turicibacter_sanguinis 67 56 61 88 43 72 57 72 54 74 79 46 67 56 68 54 VM1G_09114

0.1 WP_054162343_Rhodopseudomonas_sp WP_031627251_Pandoraea_sp WP_047853353_Burkholderia_contaminans WP_022721801_Rhodopseudomonas_sp WP_045203862_Burkholderiaceae_bacterium WP_026131711_Pandoraea_sp WP_027820844_Burkholderia_bannensis VM1G_10126_Valsa_mali WP_0433565_Cupriavidus_basilensis WP_013500206_Rhodopseudomonas_palustris WP_029047159_Cupriavidus_sp WP_040_Rhodopseudomonas_palustris AHB77920_Pandoraea_sp WP_0282327_Burkholderia_mimosarum WP_012405446_Burkholderia_phymatum WP_01129_Cupriavidus_pinatubonensis WP_011439207_Rhodopseudomonas_palustris WP_021156819_Burkholderia_sp WP_044404138_Rhodopseudomonas_palustris WP_02539_Pandoraea_pnomenusa WP_027923722_Pseudomonas_sp AHN788_Pandoraea_pnomenusa 76 68 81 82 81 56 79 90 76 66 46 VM1G_10126

WP_046741332_Lampropedia_sp KKY15566_Phaeomoniella_chlamydospora XP_007692102_Bipolaris_oryzae ESW512_Rhodobacter_sp WP_0228017_Ochrobactrum_sp CDE50821_Faecalibacterium_sp KKY13883_Diplodia_seriata WP_008725919_unclassified_Clostridiales XP_013318127_Exophiala_xenobiotica WP_025092082_Ochrobactrum_intermedium CCD47517_Botrytis_cinerea WP_046741416_Lampropedia_sp XP_007718182_Bipolaris_zeicola ABP50426_Pyrobaculum_arsenaticum ABO08726_Pyrobaculum_calidifontis WP_047510_Rhizobium_sp XP_0107875_Notothenia_coriiceps WP_007812667_Rhizobium_sp BAN8_Aeropyrum_camini AFA320_Pyrobaculum_oguniense XP_010787572_Notothenia_coriiceps WP_005006925_Nitrospina_gracilis WP_007864923_WP_007864923.1 XP_0071628_Capronia_epimyces WP_0121863_Caldivirga_maquilingensis XP_0078840_Cladophialophora_psammophila WP_013562723_Desulfurococcus_mucosus ESZ587_Sclerotinia_borealis WP_007812657_Rhizobium_sp XP_012775920_Maylandia_zebra XP_013287559_Fonsecaea_pedrosoi CDX58527_Mesorhizobium_plurifarium WP_0365718_Ochrobactrum_anthropi WP_014127285_Thermoproteus_tenax WP_0371067_Rhizobium_alamii KIW71727_Capronia_semiimmersa XP_0140311_Salmo_salar XP_00761_Bipolaris_sorokiniana BAA79068_Aeropyrum_pernix WP_011763153_Pyrobaculum_islandicum XP_0022639_Selaginella_moellendorffii WP_055408061_Pyrodictium_delaneyi KIV85086_Exophiala_sideris ACB407_Pyrobaculum_neutrophilum WP_037106809_Rhizobium_alamii KIX314_Fonsecaea_multimorphosa EEQ130_Ochrobactrum_intermedium VM1G_10361_Valsa_mali WP_0112710_Ochrobactrum_anthropi XP_002610203_Branchiostoma_floridae KNG44746_Stemphylium_lycopersici WP_045680131_Martelella_endophytica XP_007725314_Capronia_coronata AAL64263_Pyrobaculum_aerophilum WP_014026482_Pyrolobus_fumarii WP_0106600_Ochrobactrum_sp KJS17081_Hoeflea_sp WP_006468457_Ochrobactrum_intermedium XP_008727271_Cladophialophora_carrionii WP_0284379_Rhizobium_leguminosarum XP_013142091_Papilio_polytes CDK24869_Kuraishia_capsulata ERM02390_Ochrobactrum_intermedium XP_0126051_Aplysia_californica XP_0133556_Ogataea_parapolymorpha WP_006472483_Ochrobactrum_intermedium WP_041375681_Alphaproteobacteria WP_025092084_Ochrobactrum_intermedium WP_021588192_Ochrobactrum_sp WP_048078750_Desulfurococcus_mobilis WP_056345859_Arthrobacter_sp AKT35671_Pyrobaculum_sp KIW464_Exophiala_oligosperma EUN231_Bipolaris_victoriae KIW368_Cladophialophora_bantiana XP_013277786_Rhinocladiella_mackenziei KJS17077_Hoeflea_sp KIY45135_Fistulina_hepatica ADM28010_Ignisphaera_aggregans WP_0456848_Martelella_endophytica ADZ72558_Polymorphum_gilvum XP_0032132_Pyrenophora_teres AJY45479_Martelella_endophytica KIW25045_Cladophialophora_immunda WP_021588188_Ochrobactrum_sp XP_014084148_Bipolaris_maydis XP_007833566_Pestalotiopsis_fici KPQ17907_Rhodobacteraceae_bacterium WP_052214169_Rhizobium_sp WP_020560907_Thiothrix_flexilis WP_006782779_Hungatella_hathewayi KIW15468_Exophiala_spinifera XP_001591272_Sclerotinia_sclerotiorum XP_003842872_Leptosphaeria_maculans XP_014172305_Grosmannia_clavigera XP_008026446_Setosphaeria_turcica XP_007755875_Cladophialophora_yegresii KGK40729_Pichia_kudriavzevii WP_043871404_Celeribacter_indicus AJE45757_Celeribacter_indicus WP_0106604_Ochrobactrum_anthropi 52 64 39 71 64 50 64 92 72 90 85 41 90 60 83 52 48 82 78 87 67 79 67 50 28 81 79 72 46 46 42 85 30 89 91 /Archaea VM1G_10361

0.3 WP_02663_Nocardia_brasiliensis KJR86022_Sporothrix_schenckii ERS929_Sporothrix_schenckii WP_043576855_Actinopolyspora_erythraea WP_0015861_Gordonia_effusa WP_0144508_Nocardia_brasiliensis WP_0441035_Mycobacterium_abscessus WP_0424210_Streptacidiphilus_anmyonensis WP_024445482_Mycobacterium_iranicum WP_0517414_Streptomyces_xylophagus WP_042261206_Nocardia_brasiliensis WP_0118886_Mycobacterium_gilvum WP_036342171_Mycobacterium_aromaticivorans XP_0079130_Togninia_minima WP_048631712_Mycobacterium_aurum WP_025351170_Nocardia_nova WP_0033160_Mycobacterium_vaccae WP_017669225_Sandarakinorhabdus_sp KIH915_Sporothrix_brasiliensis WP_043675115_Nocardia_vulneris KDE0_Mycobacterium_aromaticivorans WP_030022670_Streptomyces_monomycini VM1G_10685_Valsa_mali 87 87 84 57 84 84 50 74 47 VM1G_10685

WP_0270871_Clostridiales_bacterium WP_0533716_Clostridiales_bacterium KON206_miscellaneous_Crenarchaeota WP_011391756_Moorella_thermoacetica WP_0426715_Anaerosalibacter_sp WP_004068910_Thermococcus_litoralis WP_0040924_Acetonema_longum WP_012186863_Caldivirga_maquilingensis WP_010885136_Pyrococcus_horikoshii CBK79287_Coprococcus_catus WP_0042258_Lysinibacillus_fusiformis WP_033140009_Blautia_producta WP_0361301_Lysinibacillus_sphaericus VM1G_109_Valsa_mali KON29082_miscellaneous_Crenarchaeota WP_032111112_bacterium_OL WP_036118713_Lysinibacillus_sphaericus WP_009164586_Pyramidobacter_piscolens WP_0185072_Blautia_producta WP_045432866_bacterium_UASB WP_00526_Blautia_hydrogenotrophica WP_036825807_Photobacterium_sanctipauli WP_0515850_Clostridiales_bacterium WP_020611386_Spirochaeta_bajacaliforniensis WP_0137471_Pyrococcus_sp WP_0092005_Anaerobaculum_hydrogeniformans 66 81 72 78 31 37 77 89 90 89 41 89 22 67 41 Outgroup Outgroup /Archaea VM1G_109