PDF(Pubmed)
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.
摘要：
最近的工作建立了骨干参考树和系统发育放置管道，用于鉴定丛枝菌根真菌（AMF）大亚基（LSU）rDNA环境序列。我们先前发布的管道允许将任何环境序列确定为推定的AMF或在其中一个主要家族中。尽管有这样的贡献,管道的实施仍然存在困难。这里,我们提出了一个更新的数据库和管道（1）一个扩展的骨干树，包括四个新描述的属和（2）几个变化，以提高易用性和一致性的实现。特别是,管道所需的软件包现在作为单个文件夹（conda环境）安装，并且管道已在三个大学计算集群中进行了测试。这个更新的骨干树和管道将使社区广泛采用，提高我们对这些无处不在和生态重要的真菌的理解。
