The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

TLDR

SILVA is a comprehensive, quality‑controlled database of aligned ribosomal RNA gene sequences from Bacteria, Archaea, and Eukaryota, and it offers a manually curated taxonomy based on representative phylogenetic trees for the small and large subunit rRNA genes. The article reports on improvements made to the SILVA taxonomy over the past three years. The authors focus on the curation workflow, the resources employed, and compare the SILVA taxonomy with Greengenes and RDP‑II taxonomies. Comparisons show a reasonable overlap in taxa names but also significant differences in both names and numbers of taxa among the three resources.

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.