0 %) (Table 2) In contrast, 40 6 % of OTUs amplified with ITS1/I

0 %) (Table 2). In contrast, 40.6 % of OTUs amplified with ITS1/ITS2, 22.7 % with ITS3/ITS4, 5.7 % with nrLSU-LR, 26.6 % with nrLSU-U, 34.4 % with mtLSU and 83.8 % with mtATP6 were not assignable to any organisms based on the BLAST searches (Table 2). Although most reads for mtATP6 were assigned to fungi, 96.2 % of these reads belonged to one OTU (Ceratobasidium sp. CBS 189.90). Table 2 Summary of sequencing reads and operational taxonomic

unit (OTU) numbers from all barcodes   ITS1/2 ITS3/4 this website nrLSU-LR nrLSU-U mtLSU mtATP6 Reads  Total 2,050,657 948,313 2,854,004 9,249,520 9,454,223 2,542,716  Processed to OTU 1,504,231 649,608 1,898,847 6,636,430 8,132,397 2,187,555  Fungi 1,294,385 513,844 385,244 6,018,234 5,670,611

2,171,475  Not assigned 149,192 26,313 2,735 551,261 746,746 15,482  Other kingdoms check details 60,654 109,451 1,510,868 66,935 1,715,040 598 OTU  Total 1,177 746 878 1,997 1,176 501  Fungi 512 (43.5 %) 364 (48.8 %) 287 (32.7 %) 1,189 (59.5 %) 387 (32.9 %) 60 (12.0 %)  Not assigned 478 (40.6 %) 169 (22.7 %) 50 (5.7 %) 532 (26.6 %) 404 (34.4 %) 420 (83.8 %)  Other kingdoms 187 (15.9 %) 213 (28.6 %) 541 (61.6 %) 276 (13.8 %) 385 (32.7 %) 21 (4.2 %) Fungal diversity in orchid roots detected with six barcoding markers Six phyla (Ascomycota, Basidiomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Neocallimastigomycota) and three subphyla (Kickxellomycotina, Mucoromycotina, Motierellomycotina) were detected in Phalaenopsis CBL-0137 molecular weight roots (Tables 3, S2). Both major phyla, Ascomycota and Basidiomycota, were detected by all markers, while the remaining

phyla/subphyla were only detected with the markers for the nrITS and nrLSU regions, revealing insufficiencies of Pyruvate dehydrogenase lipoamide kinase isozyme 1 mitochondrial markers. Glomeromycota, Neocallimastigomycota, and Kickxellomycotina were only observed with single markers, whereas Chytridiomycota, Entomophthoromycota, Mortierellomycotina, and Mucoromycotina were detected with two or more markers. As indicated, Ascomycota and Basidiomycota were dominant. All nrITS markers yielded a higher abundance of Ascomycota, while nrLSU and mitochondrial markers yielded a higher abundance of Basidiomycota (Fig. 1a). At the class level, the dominant classes were Dothideomycetes (Ascomycota), Eurotiomycetes (Ascomycota), Sordariomycetes (Ascomycota), and Agaricomycetes (Basidiomycota), which nevertheless displayed high variances in the relative abundance across markers (Fig. 1b). For example, the detection of Dothideomycetes was mostly restricted to ITS1/2, low abundance of the Sordariomycetes was observed when using nrLSU-LR, and the abundance of Agaricomycetes ranged from 20 to 94 % across five markers. At the order level, 34 orders were identified with markers of ITS1/2, 31 for nrLSU-LR, 35 for ITS3/4, 46 for nrLSU-U, 19 for mtLSU, and 6 orders for mtATP6.

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