Environmental identification of arbuscular mycorrhizal fungi using the LSU rDNA gene region: an expanded database and improved pipeline

• DOI: 10.1007/s00572-022-01068-3
• Publication Date: 2022-01-31T05:03:41Z
• Authors: Camille S. Delavaux; Robert J. Ramos; Sidney L. Sturmer; James D. Bever
• Keywords: Amplicon; Glomeromycota; Identification

Arbuscular mycorrhizal fungi (AMF; Glomeromycota) are difficult to culture; therefore, establishing a robust amplicon-based approach taxa identification is imperative describe AMF diversity. Further, due low and biased sampling of taxa, molecular databases do not represent the breadth diversity, making database matching approaches suboptimal. Therefore, full description diversity requires tool determine sequence-based placement in Glomeromycota clade. Nonetheless, commonly used gene regions, including SSU ITS, enable reliable phylogenetic placement. Here, we present an improved pipeline for determination using amplicons from large subunit (LSU) rRNA gene. We improve our backbone tree by additional outgroup sequences. also existing bioinformatics aligning forward reverse reads separately, universal alignment all building, implementing BLAST screening prior building remove non-homologous Finally, script extract belonging 11 major families as well amplicon sequencing variant (ASV) version pipeline. test utility testing known AMF, non-AMF, Acaulospora sp. spore This work represents most comprehensive LSU sequences within