"Primers and taxa";"Sequences and mismatches" "I. ITS primers"; "ITS1F (original: Gardes and Bruns 1993)";CTTGGTCATTTAGAGGAAGTAA "ITSOF-T (Taylor and McCormick 2008)";AACTTGGTCATTTAGAGGAAGT "ITSOF (Tedersoo et al. 2008)";ACTTGGTCATTTAGAGGAAGT "ITS1Fngs (this study)";GGTCATTTAGAGGAAGTAA "Tulasnellaceae p.parte";****C**C***************C "Cantharellus p.parte";****G***T*************** "Eurotiomycetes, Dothideomycetes, Sordariomycetes p.parte";****C******************* "Trichocomaceae p.parte";***CC******************* "Dothideomycetes p.parte";*******************T**** Dothioraceae;****CC****************** Botryosphaeriaceae;****AC****************** Psoraceae;**********C************* "Valsaceae, Entomophthoromycotina";******A***************** "Chytridiomycota, Magnaporthales, Suillus, Paraglomerales, Mucorales, Rhizinaceae p.parte";*********G************** "Chytridiomycota p.parte, Saccharomycetes";********************C*** Mucorales;****A**CT*************** Viridiplantae;*****TA**************G*G Metazoa;****K*A***************W* "ITS5 (original: White et al. 1990)";GGAAGTAAAAGTCGTAACAAGG "Tulasnella p.parte";******WC************** "Tremellomycetes, Ustilaginomycetes p.parte";*******M*****A******** Dothideaceae;***T****************** "Saccharomycetales, Chytridiomycota p.parte";****C***************** "Microsporidia, Entomophthoromycotina, Chytridiomycota p.parte";*******C************** Metazoa;******W*************** Viridiplantae;*****G*G************** ; "ITS1 (original: White et al. 1990)";TCCGTAGGTGAACCTGCGG "ITS1ngs (this study)";TCCGTAGGTGAACCTGC Sordariomycetes;*****T********A**** Microsporidia;G*W*****W********M* "Viridiplantae, Metazoa";******************* ; "gITS7 (Ihrmark et al. 2012, used here)";GTGARTCATCGARTCTTTG "fITS7 (Ihrmark et al. 2012)";GTGARTCATCGAATCTTTG "ITS86F (Turenne et al. 1999)";GTGAATCATCGAATCTTTGAA Cantharellus;*C**********G******** "Tulasnellaceae, Microsporidia";"no match" Antherospora;*********T****T****** "Pucciniales p.parte";*********TC**GT****** Ophiostoma;*C**RY*************** "Eurotiales p.parte";************G******** Cordyceps;**A**CT***********A** Dipodascus;**********-********** Leptosphaeria;**************T****** Pichia;************G*TC***** Candida;*********T-***T****** Neocallismatigales;**********A******C*** Lobulomycetales;*********TA********** "Acaulospora, Glomus intraradices";**********A********** Gigaspora;**********A***T****** "Cokeromyces, Rhizopus";************G******** Entomophthorales;************G*T****** Angiospermae;*Y***Y******G******** Gymnospermae;************G*T****** "Metazoa p.parte";A*T*A***CA*********** "Metazoa p.parte";****A*TGCA*G*CACA*K** Straminipila;****R*****R*RWY****** "ITS3 (original: White et al. 1990; ITS2 primer is reverse complement)";GCATCGATGAAGAACGCAGC "58A1F (Martin and Rygiewicz 2005)";GCATCGATGAAGAACGC "58A2F (Martin and Rygiewicz 2005)";ATCGATGAAGAACGCAG "ITS3-Kyo1 (Toju et al. 2012)";AHCGATGAAGAACRYAG "ITS3-Kyo3 (Toju et al. 2012)";GATGAAGAACGYAGYRAA "ITS3mix (Tedersoo et al. 2014; mix1-5 used here; consensus)";CANCGATGAAGAACGYRG Cantharellus;*******************Y*W* Tulasnellaceae;"no match" Mycenaceae;CY********************* "Amanita p.parte, Antrodia";***************R******* Gomphales;************R****C***** "Sebacinales p.parte";***C******************* "Tremellales, Yarrowia";A********************** "Pucciniomycetes p.parte";AY*************A***T*** Puccinia;R**C***********R******* Tilletiales;C********************** Ophiocordyceps;****TA**A************** Onygenales;A********************** "Dothideomycetes p.parte";***A******************* "Sordariomycetes p.parte";***A******************* "Sordariales p.parte";******************G**** "Pezizaceae p.parte";*******************T*** "Saccharomycetales p.parte";*************G********* "Candida p.parte";*T**************T****** "Thecaphora, Thysanophora";*T********************* "Glomeraceae p.parte";****************T****** "Glomeraceae p.parte";********A************** "Mucorales p.parte";*T********************* "Mucorales p.parte, Waitea, Microbotryum";****************T****** "Chytridiomycota p.parte";***A******************* Neocallimastigomycota;*A********************* Microsporidia;*TGA*********WY*TT** "Nuclearida, Aphelidea";***A**************** Viridiplantae;****************Y**Y "Amoebozoa p.parte";*TRA**************** "Amoebozoa p.parte";AT*A*********G*AT*** "Amoebozoa p.parte";AA***********C**T*** "Amoebozoa p.parte";**T****Y*****G*****T "Apusozoa p.parte";*Y*A**************** "Apusozoa p.parte";A**A*********C**TG** "Alveolata p.parte";A**A********GR****** "Alveolata p.parte";***C*TN*****GG****** "Alveolata p.parte";AT*A************T*** Bacillariophyta;A**A**************** Bryophyta;***A**************** "Chlorophyta p.parte";***A**************** "Chlorophyta p.parte";*YG*******G*****T*** "Chlorophyta p.parte";*Y*N**************** "Euglenozoa p.parte";ATT**T************Y* "Euglenozoa p.parte";CAG*********G****G** Eustigmatophyta;A**A**************** Haptophyta;***A**************** Marchandiophyta;***A**************** Platyhelminthes;*YG**********GW***** "Nematoda p.parte";AGN***************** "Nematoda p.parte";GGG********R*******T "Nematoda p.parte";RGN********R****GG** "Nematoda p.parte";*T*********A******** "Nematoda p.parte";TGG********A****GT** "Insecta p.parte";GGG****************T "Insecta p.parte";*G*******G********** "Insecta p.parte";GGR**********C****** Placozoa;*T**************T*** Annelida;*TG**********G****** Mollusca;GGG**********G****** Cnidaria;*Y**************Y*** Porifera;*T*C*********G****** "Acari p.parte";TGG*************Y**T "Acari p.parte";AA*********A***AT**T "Acari p.parte";AA*G*******A***RT**T "Acari p.parte";CA**************T*** "Ichtyes p.parte";CGC***************** "Oomycota p.parte";A**Y*********M***T** "Oomycota p.parte";A****************T** Parabasalia;****************AC*T Phaeophyta;A*WA**************** Rapidophyta;A**W**************** "Rhizaria p.parte";R**A**************** "Rhizaria p.parte";***A*************GT* "Rhizaria p.parte";*YR*************Y*T* Rhodophyta;RY*W************Y*** Synurophyta;AY*A**************** "ITS4 (original: White et al. 1990)";TCCTCCGCTTATTGATATGC "ITS4ngs (Tedersoo et al. 2014, used here)";TCCTSCGCTTATTGATATGC Chaetothyriales;****G*************** Archaeorhizomycetes;*****GC************* "Tulasnellaceae p.parte";*********G*W*A****** Microsporidia;****S*Y******M****** "Viridiplantae, Amoebozoa, Rhizaria";******************** Apusozoa;*************R****** "Alveolata p.parte";***K*******M*T****** "Alveolata p.parte";**T***A****A*T****** "Alveolata p.parte";**TG*******G*T****** "Alveolata p.parte";***********A*A****** "Bacillariophyta p.parte";***********A*T****** "Chlorophyta p.parte";***********A******** Euglenozoa;*********C*R*A****** Eustigmatophyta;***********G*T****** Haptophyta;***********G******** Marchandiophyta;***********G******** Rotifera;***********K*T****** Platyhelminthes;***********K******** "Nematoda p.parte";*********W*N******** "Nematoda p.parte";********C**G*A****** "Insecta p.parte";******C**C***A****** Ichtyes;***********G*A****** Annelida;*************A****** Acari;***********A*A****** Mollusca;***********Y******** Crustacea;*************A****** "Cnidaria p.parte";****G*T****G*A****** "Cnidaria p.parte";***********K*A****** "Cnidaria p.parte";********C**G******** Oomycota;******************** Parabasalia;***********A***G**** Phaeophyta;***********G*T****** Rapidophyta;***********A*T****** "Rhizaria p.parte";*****G*******A****** Rhodophyta;***W*******R*W****** Synurophyta;***********G*T****** Nucleariida;***********C******** "ITS4B (Gardes and Bruns 1993)";CAGGAGACTTGTACACGGTCCAG "Hygrophoraceae, Corticiales";**A******************** Schizophyllaceae;**********A************ Armillaria;**********************A "Inocybaceae, Amanitaceae";***************Y******* Psathyrellaceae;**********R*******K**GA Amylocorticiales;**********A**********GA Atheliales;***A*****************GA Boletales;******R*Y*R*******K**RK Suillineae;*****A****A************ Russulales;************G********** Polyporales;**A***************G*TG* "Tomentella, Thelephora";**A**R****K******R****R "Pseudotomentella, Phellodon, Tomentellopsis";**A*G****************** Hydnellum;*CA******************** Hymenochaetales;**A*************R****RA Phallomycetidae;**RRR********R****Y**RR "Clavulina, Sistotrema";*****A**********A****** Ceratobasidiaceae;**A************T******* "Sebacinales p.parte";****GA*T**A*GTGT*****GA "Sebacinales p.parte";****GA***************GA "Tremellales p.parte";**A*G*****RG*********** Auriculariales;**A*G****************G* Puccinomycetes;**AC***T*************R* Ustilaginomycetes;**********AGG*WT*****GW "Dacrymycetales, Cantharellus, Tulasnella";"<40% identical" "Other fungal phyla, Plantae, Metazoa";"<40% identical" ; "LB-w (Tedersoo et al. 2008)";CTTTTCATCTTTCCCTCACGG Cantharellus;TA**************TG*** Sistotrema;*****************G*** Tulasnella;*******C*********G*** Coniophoraceae;*******C************* Ustilaginomycetes;**************A****T* Ascomycota;*************GA****TC Saccharomycetes;**************W****W* "Glomeromycota, Mucoromycota, Chytridiomycota";********************* Gigasporaceae;**************A****T* Viridiplantae;*****************G*** "II. LSU primers"; "LR0R (Hopple and Vilgalys 1994)";ACCCGCTGAACTTAAGC "LR0Rngs (this study)";ACSCGCTGAACTTAAGC Tulasnellaceae;**G*C**NR*Y****** Chaetothyriales;**G************** Archaeorhizomycetes;***GC************ Microsporidia;MMMKSY**R******** Viridiplantae;**********T****** ; "LF402Fmix1 (this study; LF402 is a reverse complement)";GTGAAATTGYTRAAAGGGAA "LF402Fmix3 (this study)";GTGAAATTGTCAAAAGGGAA "Most fungi";*********TTG******** Cantharellus;************CG**A*** "Tulasnellaceae p.parte";**********Y*GTR***** "Agaricaceae, Boletaceae";*********C********** Ceratobasidiaceae;***************T**** "Cystofilobasidiaceae, Corticiaceae";***********A******** Ustilaginaceae;*********CCA******** Schizosaccharomycetaceae;*********C****R***** "Glomerellaceae, Verticillium, Dothideomycetes";********A*********** "Candida p.parte";********A****T*CW*** Falcocladium;*********C*A******** "Mucoraceae p.parte";***********A******** "Neocallimastigales, Chytridiomycota";**********CR******** Viridiplantae;T*********C*GG****** ; "TW13 (original: T.J. White, unpublished)";GGTCCGTGTTTCAAGACG "LR3 (original: Hopple and Vilgalys 1994; LR3R is reverse complement)";CCGTGTTTCAAGACGGG "Saccharomycetales p.parte";*****A************** "Microsporidia, Viridiplantae, Metazoa";******************** Dictyostelids;RR**YR*R***T****TA** ; "LR5-Fung (Tedersoo et al. 2008)";CGATCGATTTGCACGTCAGA Tulasnellaceae;********Y*********** "Cordycipitaceae p.parte";*********C********** "Straminipila, Metazoa";******************** "Viridiplantae, Alveolata, Rhizaria";***A***************T ; "LR5 (original: Hopple and Vilgalys 1994)";TCCTGAGGGAAACTTCG "TW14 (T.J. White et al. unpublished)";GCTATCCTGAGGGAAACTTC "Microsporidia, Metazoa, Viridiplantae";********************* "Candida p.parte";***********A********* "Apicomplexa p.parte";**G********A**TCT**** Straminipila;****************Y**** "III. SSU primers"; "SSU515F (original: Turner et al. 1999)";GTGCCAGCANCCGCGGTAA "SSU515Fngs (this study)";GCCAGCAGCCGCGGTAA "Saccharomycetes, Pezizomycotina p.parte (I, intron site)";*I***************** Archaeorhizomycetes;*********C********* Microsporidia;*********T********* "Viridiplantae, Metazoa";******************* ; "Euk742R (this study)";AAATCCAAGAATTTCACCTCT "Many fungal groups";NR******************* Cantharellus;TGG**ACT*G********C** Tulasnellaceae;GGR**ANM*R********Y** "Baeomycetales p.parte";*****************Y*** "Eurotiales p.parte";NR***************Y*Y* Harpellales;TGG*T****T********A** "Dothideomycetes p.parte";CG*******G********C** Lecanorales;RW**NMN*********Y**** "Saccharomycetales, Hypocreales";NNR**Y*************** "Chytridiomycota, Neocallimastigomycota, Blastocladiomycota";*****Y*************** ; "SSU817F (original: Borneman and Hartin 2000)";TTAGCATGGAATAATRRAATAGGA Cantharellus;*********G****CSG*WWC*** Tulasnellaceae;*************RCWN*TKGACN "Sebacinales p.parte";*********G************** Gomphales;**************C********* Phallales;*********************R** "Agaricostilbales p.parte";AC********************** "Dacrymycetales p.parte";**************K********* "Ustilaginales p.parte";**************C********* "Pucciniales p.parte";*******************C*A** "Coryneliales p.parte";*********************A** "Helotiales p.parte";************R******N*N*M "Microascales p.parte";"W Y**********************" "Pleosporales p.parte";NY***W*****************R "Saccharomycetales p.parte";NN*T********G*CAGG*CC*YT "Saccharomycetales p.parte";NN************C***T*--** "Saccharomycetales p.parte";"W Y************N*********" Urocystidales;**************N****Y**** "Ramicandelaber, Falciformispora";*********G************** Zoopagomycota;**************C********* "Mucorales p.parte";*********************N** Entomophthoromycota;*******************K*N*W Chytridiomycota;*Y************Y********* "Microsporidia, Viridiplantae";"no match" "SSU1196R (original: Borneman and Hartin 2000)";TCTGGACCTGGTGAGTTTCC "SSU1196Rngs (this study)";TCTGGACCTGGTGAGTTT Cantharellus;**CT**************T* Tulasnellaceae;**CT*T***********GT* "Tremellales p.parte, Chytridiomycota";************A******* "Saccharomycetes p.parte";***************C*GT* "Pezizales p.parte";***************A**T* "Sordariales p.parte";**C*****C*********** "Glomeromycota p.parte";************R*****T* Microsporidia;NNNNNR**N***R**R*KT* Viridiplantae;************A******* ; "IV. Primer recommendations"; "Recommended primer mixes for the ITS1F family"; "ITS1Fngs-Mix1 (Fungi)";GGTCATTTAGAGGAAGTAA "ITS1Fngs-Mix2 (Tulasnellaceae)";GGCCATTTAGAGGAAGTAC "ITS1Fngs-Mix3 (Saccharomycetes)";GGTCATTTAGAGGAACTAA "ITS1Fngs-Mix4 (various groups)";GGTCGTTTAGAGGAAGTAA "ITS1Fngs-Mix5 (Mucorales)";GGCTATTTAGAGGAAGTAA ; "Recommended primer mixes for the ITS1 family"; "ITS1ngs-Mix1 (Most eukaryotes)";TCCGTAGGTGAACCTGC__ "ITS1ngs-Mix2 (Sordariomycetes)";TCCGTTGGTGAACCAGC__ ; "Recommended ITS1 and full ITS forward primer mixes for fungi"; "ITS1Fngs (except SSU 5’ intron containing groups)";GGTCATTTAGAGGAAGTAA "ITS1ngs (except Sordariomycetes)";TCCGTAGGTGAACCTGC ; "Recommended forward primer mixes for ITS2 barcode"; "ITS3-Mix1 (Fungi)";CATCGATGAAGAACGCAG_ "ITS3-Mix2 (Chytridiomycota)";CAACGATGAAGAACGCAG_ "ITS3-Mix3 (Sebacinales)";CACCGATGAAGAACGCAG_ "ITS3-Mix4 (Glomeromycota)";CATCGATGAAGAACGTAG_ "ITS3-Mix5 (Sordariales)";CATCGATGAAGAACGTGG_ ; "Recommended reverse primers for ITS2 and full ITS"; "ITS4-Mix1 (Fungi)";TCCTCCGCTTATTGATATGC "ITS4-Mix2 (Chaetothyriales)";TCCTGCGCTTATTGATATGC "ITS4-Mix3 (Archaeorhizomycetes)";TCCTCGCCTTATTGATATGC "ITS4-Mix4 (Tulasnellaceae)";TCCTCCGCTGAWTAATATGC "ITS4-Euk (all eukaryotes)";TCCTSSGCTTANTDATATGC ; "Recommended LF402 mixes for fungi"; "LF402f_mix1 (Fungi)";TTCCCTTTYARCAATTTCAC "LF402f_mix2 (Ceratobasidiaceae)";TTCCATTTCAACAATTTCAC "LF402f_mix3 (Chytridiomycota)";TTCCCTTTTGACAATTTCAC "LF402f_mix4 (Tulasnellaceae)";TTCCCYACCRACAATTTCAC "LF402f_mix5 (Cantharellus)";TTCTCCGTCAACAATTTCAC