Fig 1.
Ribosomal RNA primer map and alignment of LSU200-F/LSU481-R and LSU200A-F/LSU476A-R primers developed in this study.
A, Approximate location of LSU200-F/LSU481-R and LSU200A-F/LSU476A-R primers in relation to the D1/D2 variable domains within the LSU of Saccharomyces cerevisiae J01355 in relation to ITS1, ITS2, ITS4 from White et al. [35], NS31 from Simon et al. [36], AM1 from Helgason et al. [37], AMV4.5N-F and AMDG-R from Sato et al. [38], AML1 and AML2 from Lee et al. [39], WANDA from Dumbrell et al. [40], ITS3_KYO2 from Toju et al. [41], and ITS7o from Kohout et al. [42]. B, LSU200-F/LSU481-R and LSU200A-F/LSU476A-R alignments made using a custom reference sequence set, aligned using Muscle v 3.8.31 [31] and visualized using CLC Sequence Viewer (http://www.clcbio.com/), with S. cerevisiae J01355 included as positional reference.
Table 1.
Fungal nuclear large ribosomal primer targets (nu-LSU), with positions numbered relative to Saccharomyces cerevisiae (GenBank Accession #: J01355).
Table 2.
Summary data for all sample sets using LSU200-F/LSU481-R, and LSU200A-F/LSU476A-R (Ascomycota) primers developed in this study, and ITS3_KYO2/ITS4_KYO3 primers developed by Toju et al. [41].
Table 3.
List of genera and species recovered by LSU200-F/LSU481-R, LSU200A-F/LSU476A-R and ITS3_KYO2/ITS4_KYO3 primers.
Taxa were included only if the total read count across the three subsamples were >3, and are listed alphabetically by higher taxa (A = Ascomycota, B = Basidiomycota, C = Chytridiomycota, E = Entomophthoromycota, G = Glomeromycota, K = Kickxellomycotina, M = Mucoromycotina, Mi = Microsporidia, Z = Zoopagomycotina). (#) = Number of OTUs identified to that taxon.