Alignment of LSU rRNA sequences of fungi associated with the hindgut of carrion beetles (Coleoptera, Silphidae)

Genomic DNA was extracted from the hindguts of males and females of eight species of carrin beetles (Coleoptera, Silphidae), respectively, and part of the fungal large subunit ribosomal RNA gene (LSU) was amplified for the different species and sexes, respectively, with primers LS1 and LR5 (Gibson & Hunter 2009). Amplicons were cloned into E. coli using the StrataClone PCR Cloning Kit (Agilent Technologies, USA) according to the manufacturer’s instructions. For Ni. humator, Ni. vespillo, Ni. orbicollis, Ni. puctulatus, Ni. tomentosus, Ne. americana, and O. noveboracense, inserts of 16 clones per species were amplified with the flanking primers M13fwd and M13rev and sequenced bidirectionally with M13fwd and M13rev. For Ni. vespilloides, 53 clones were sequenced unidirectionally with primer M13fwd. All sequences were blasted against the NCBI nr database for taxonomy assignment. Representative sequences were aligned with SINA (Pruesse et al. 2012) and imported into ARB (Ludwig et al. 2004). Closely related fungal reference sequences were selected from the SILVA LSU reference database and included in the alignment.