The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks
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Abstract
SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources.
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The record
- Venue
- Nucleic Acids Research
- Topic
- Genomics and Phylogenetic Studies
- Field
- Biochemistry, Genetics and Molecular Biology
- Canadian institutions
- University of British Columbia
- Funders
- Max-Planck-Institut für Terrestrische MikrobiologieDeutsche Forschungsgemeinschaft
- Keywords
- BiologyTaxonomy (biology)TaxonPhylogenetic treeRibosomal RNAThree-domain systemPhylogeneticsEvolutionary biologyArchaeaEcologyGeneGenetics
- Has abstract in OpenAlex
- yes