An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
University of Colorado Boulder · Lawrence Berkeley National Laboratory · +6 more institutions
Abstract
Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a 'taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408,315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names…
Citation impact
- FWCI
- 46.82
- Percentile
- 100%
- References
- 35
Authors
9- DMDaniel McDonald
University of Colorado Boulder
- MNMorgan N. Price
Lawrence Berkeley National Laboratory
- JKJulia K. Goodrich
University of Colorado Boulder, Cornell University
- EPEric P. Nawrocki
Howard Hughes Medical Institute, Janelia Research Campus
- TZTodd Z. DeSantis
Cornell University, Second Genome (United States)
Topics & keywords
- Biology
- Taxonomy (biology)
- Metagenomics
- Bacterial taxonomy
- Phylum
- Phylogenetic tree
- Taxonomic rank
- Rank (graph theory)
- Industry, innovation and infrastructure
Funding
- HHHoward Hughes Medical InstituteAward: DE-AC02-05CH11231
- UDU.S. Department of EnergyAwards: -AC02-05CH11231, 05CH11231, AC02-05CH11231, DE-AC02, DE-AC02-05CH11231, DE-AC02-
- BABill and Melinda Gates Foundation
- NINational Institutes of HealthAward: DE-AC02-05CH11231
- OOOffice of ScienceAwards: AC02-05CH11231, -AC02-05CH11231, DE-AC02
- BABiological and Environmental ResearchAwards: 05CH11231, DE-AC02-05CH11231, AC02-05CH11231