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Syst Appl Microbiol. 2010 Oct;33(6):291-9. doi: 10.1016/j.syapm.2010.08.001.

Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses.

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  • 1Department of Ecology and Marine Resources, Institut Mediterrani d'Estudis Avançats (CSIC-UIB), Esporles, Illes Balears, Spain. pablo.yarza@uib.es

Abstract

The "All-Species Living Tree Project" (LTP) provides the scientific community with a useful taxonomic tool consisting of a curated database of type strain sequences, a universal and optimized alignment and a single phylogenetic tree harboring all the type strains of the hitherto classified species. On the website http://www.arb-silva.de/projects/living-tree an update has been regularly maintained by including the 1301 new descriptions that have appeared in the validation and notification lists of the IJSEM journal. The topology of the 16S rRNA-based tree was validated with a detailed comparison against a collection of taxa-specific and broad-range trees made using different approaches, subsets of sequences and alignments. Seven percent of the classified species is still missing, as their type strains do not have a good quality SSU sequence. In addition, a new database of type strains for which adequate 23S rRNA entries existed in public repositories was built. Among the 8602 species with validly published names until February 2010, we were able to find good quality LSU representatives for 792 type strains, whereas around 91% of the complete catalogue still remains unsequenced. Despite the scarce representation of some groups in LSU databases, we have devised a highly optimized alignment and a reliable LSU tree in order to set up a stable phylogenetic starting point for taxonomic purposes. The current release corresponds to the fourth update of the project (LTPs102), and contains additional features which increase usability and compatibility. Use the contact address living-tree@arb-silva.de to provide additional input for the development of this taxonomic tool.

Copyright © 2010 Elsevier GmbH. All rights reserved.

PMID:
20817437
[PubMed - indexed for MEDLINE]
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