SSU to the rescue: conserving the original partial SSU fragment ahead of the ITS1 sub-locus enhances the detection of putative chimeras and limits the formation of possibly spurious taxa in fungal metabarcoding. Abies balsamea fungal endophytes

The aim of this study was to evaluate if (1) conserving the original 5’ extremity of the fungal pyrosequences, usually the partial fragment of the ribosomal small sub-unit (pSSU) immediately adjacent to the ITS1F primer ahead of the ITS1 sub-locus, impacts the detection of chimeras; (2) as the pSSU displays a lower variability, its inclusion in addition to the ITS1 sub-locus might also buffer the variation due to putative sequencing errors, and reduce the formation of the singletons and doubletons; (3) performing ecological analyses based on pSSU-ITS1 leads to similar conclusions on the community structure as analyses based on ITS1. For this study we analysed the fungal endophytic community (endomycobiota) of a single individual of Abies balsamea (L.) Mill. based on 108 samples distributed among both the aerial and root systems.