An updated LSU database and pipeline for environmental DNA identification of arbuscular mycorrhizal fungi. Journal Article uri icon

Overview

abstract

  • Recent work established a backbone reference tree and phylogenetic placement pipeline for identification of arbuscular mycorrhizal fungal (AMF) large subunit (LSU) rDNA environmental sequences. Our previously published pipeline allowed any environmental sequence to be identified as putative AMF or within one of the major families. Despite this contribution, difficulties in implementation of the pipeline remain. Here, we present an updated database and pipeline with (1) an expanded backbone tree to include four newly described genera and (2) several changes to improve ease and consistency of implementation. In particular, packages required for the pipeline are now installed as a single folder (conda environment) and the pipeline has been tested across three university computing clusters. This updated backbone tree and pipeline will enable broadened adoption by the community, advancing our understanding of these ubiquitous and ecologically important fungi.

publication date

  • July 1, 2024

has restriction

  • hybrid

Date in CU Experts

  • July 2, 2024 8:15 AM

Full Author List

  • Delavaux CS; Ramos RJ; Stürmer SL; Bever JD

author count

  • 4

Other Profiles

Electronic International Standard Serial Number (EISSN)

  • 1432-1890

Additional Document Info

start page

  • 369

end page

  • 373

volume

  • 34

issue

  • 4