Taxonomic assignment of arbuscular mycorrhizal fungi in an 18S metagenomic dataset: a case study with saltcedar (Tamarix aphylla)

Similar Arbuscular Mycorrhizal Fungal Communities in 31 Durum Wheat Cultivars (Triticum turgidum L. var. durum) Under Field Conditions in Eastern Canada

“…A total of 317 ASVs was recorded in the current study while 190 AM fungal OTUs were associated with durum wheat in the Prairies using a similarity threshold of 97% to cluster 18S AM fungal sequences. As discussed in Stefani et al. (2020) and in Schlaeppi et al.…”

“…A total of 317 ASVs was recorded in the current study while 190 AM fungal OTUs were associated with durum wheat in the Prairies using a similarity threshold of 97% to cluster 18S AM fungal sequences. As discussed in Stefani et al (2020) and in Schlaeppi et al (2016), 18S sequences from different AM fungal species are lumped together at a similarity threshold of 99%, making the ASVs approach the least inaccurate as a proxy for species for datasets based on the 18S sequences of the nuclear ribosomal DNA. However, using ASVs based on 18S sequences as a proxy for AM fungal species could overestimate species richness.…”

“…Each sample was rarefied to 5,000 sequences which retained 1,680,000 (32.9%) sequences in 336 (90.3%) samples and 303 (95.6%) of the amplicon sequence variants ( Figure S4 ). The taxonomic identification of each ASV was performed using a backbone phylogenetic tree as described in Stefani et al. (2020) .…”

“…Within-sample (alpha) diversity was calculated using the sample size- and coverage-based rarefaction and extrapolation (R/E) of the Hill numbers of species, i.e., richness (q = 0), Shannon diversity (q = 1, the exponential of Shannon entropy), and Simpson diversity (q = 2, the inverse of Simpson concentration), as implemented in the R package iNEXT version 2.0.19 ( Chao et al., 2014 ; Hsieh et al., 2016 ). The Faith’s phylogenetic diversity index ( Faith and Baker, 2006 ) was calculated using the QIIME 2 command qiime diversity alpha-phylogenetic on a RAxML phylogenetic tree that included 303 AM fungal ASVs as described in Stefani et al. (2020) .…”

“…Library preparation followed the protocol described in Stefani et al (2020). Briefly, the PCR products from the nested PCR were purified using Agencourt AMPure ® XP beads (Beckman Coulter Inc., Indianapolis, IN, USA), normalized to 1 to 2 ng/ml with the SequalPrep ™ Normalization Plate kit (ThermoFisher Scientific) and indexed using the Nextera index kit (Illumina, San Diego, CA, USA).…”