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

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

2014 | Pelin Yilmaz, Laura Wegener Parfrey, Pablo Yarza, Jan Gerken, Elmar Pruesse, Christian Quast, Timmy Schweer, Jörg Peplies, Wolfgang Ludwig, Frank Oliver Glöckner
The article discusses the SILVA and All-species Living Tree Project (LTP) taxonomic frameworks, which are essential for microbial classification. SILVA is a comprehensive resource for quality-controlled ribosomal RNA (rRNA) gene sequences from Bacteria, Archaea, and Eukaryota, providing a manually curated taxonomy based on phylogenetic trees. The study highlights improvements in the SILVA taxonomy over the past three years, including curation processes, resources used, and comparisons with Greengenes and RDP-II taxonomies. The SILVA taxonomy is based on Bergey's Taxonomic Outlines and is updated with information from LPSN (List of Prokaryotic Names with Standing in Nomenclature). The LTP taxonomy is also based on LPSN and provides a curated database for all three domains of life. The article emphasizes the importance of a taxonomic framework in microbiology, as most life on Earth is microbial, and traditional methods have underestimated microbial diversity. The use of rRNA gene sequences has been a major breakthrough in understanding microbial diversity and evolutionary relationships. SILVA uses a phylogenetic tree-guided manual curation approach for taxonomy, while LPSN provides a list of validly published names for prokaryotes. The SILVA taxonomy includes a wide range of taxa, including eukaryotic groups, and has been improved over the years. The eukaryotic taxonomy in SILVA has been significantly enhanced, with the help of the Eukaryotic Taxonomy Working Group (ETWG). The article also compares the SILVA, RDP-II, and Greengenes taxonomies, highlighting differences in the number of taxa and their names. SILVA has the highest number of unique taxa, including Candidatus taxa and taxa without standing in nomenclature. The study concludes that the SILVA and LTP taxonomies will continue to be maintained with high diligence, with a focus on improving eukaryotic groups. The SILVA-NGS pipeline is introduced for easy access to the SILVA taxonomy for the classification of rRNA gene amplicon data. The SILVA taxonomy curation is an open and transparent process, and input from users and experts is highly appreciated.The article discusses the SILVA and All-species Living Tree Project (LTP) taxonomic frameworks, which are essential for microbial classification. SILVA is a comprehensive resource for quality-controlled ribosomal RNA (rRNA) gene sequences from Bacteria, Archaea, and Eukaryota, providing a manually curated taxonomy based on phylogenetic trees. The study highlights improvements in the SILVA taxonomy over the past three years, including curation processes, resources used, and comparisons with Greengenes and RDP-II taxonomies. The SILVA taxonomy is based on Bergey's Taxonomic Outlines and is updated with information from LPSN (List of Prokaryotic Names with Standing in Nomenclature). The LTP taxonomy is also based on LPSN and provides a curated database for all three domains of life. The article emphasizes the importance of a taxonomic framework in microbiology, as most life on Earth is microbial, and traditional methods have underestimated microbial diversity. The use of rRNA gene sequences has been a major breakthrough in understanding microbial diversity and evolutionary relationships. SILVA uses a phylogenetic tree-guided manual curation approach for taxonomy, while LPSN provides a list of validly published names for prokaryotes. The SILVA taxonomy includes a wide range of taxa, including eukaryotic groups, and has been improved over the years. The eukaryotic taxonomy in SILVA has been significantly enhanced, with the help of the Eukaryotic Taxonomy Working Group (ETWG). The article also compares the SILVA, RDP-II, and Greengenes taxonomies, highlighting differences in the number of taxa and their names. SILVA has the highest number of unique taxa, including Candidatus taxa and taxa without standing in nomenclature. The study concludes that the SILVA and LTP taxonomies will continue to be maintained with high diligence, with a focus on improving eukaryotic groups. The SILVA-NGS pipeline is introduced for easy access to the SILVA taxonomy for the classification of rRNA gene amplicon data. The SILVA taxonomy curation is an open and transparent process, and input from users and experts is highly appreciated.
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Understanding The SILVA and %E2%80%9CAll-species Living Tree Project (LTP)%E2%80%9D taxonomic frameworks