Literature DB >> 34111737

Release LTP_12_2020, featuring a new ARB alignment and improved 16S rRNA tree for prokaryotic type strains.

Wolfgang Ludwig1, Tomeu Viver2, Ralf Westram3, Juan Francisco Gago2, Esteban Bustos-Caparros2, Katrin Knittel1, Rudolf Amann1, Ramon Rossello-Mora4.   

Abstract

The new release of the All-Species Living Tree Project (LTP) represents an important step forward in the reconstruction of 16S rRNA gene phylogenies, since we not only provide an updated set of type strain sequences until December 2020, but also a series of improvements that increase the quality of the database. An improved universal alignment has been introduced that is implemented in the ARB format. In addition, all low-quality sequences present in the previous releases have been substituted by new entries with higher quality, many of them as a result of whole genome sequencing. Altogether, the improvements in the dataset and 16S rRNA sequence alignment allowed us to reconstruct robust phylogenies. The trees made available through this current LTP release feature the best topologies currently achievable. The given nomenclature and taxonomic hierarchy reflect all the changes available up to December 2020. The aim is to regularly update the validly published nomenclatural classification changes and new taxa proposals. The new release can be found at the following URL: https://imedea.uib-csic.es/mmg/ltp/.
Copyright © 2021 Elsevier GmbH. All rights reserved.

Keywords:  16S rRNA gene; LTP; Living Tree Project; Phylogeny; Taxonomy

Year:  2021        PMID: 34111737     DOI: 10.1016/j.syapm.2021.126218

Source DB:  PubMed          Journal:  Syst Appl Microbiol        ISSN: 0723-2020            Impact factor:   4.022


  2 in total

1.  A positive correlation between GC content and growth temperature in prokaryotes.

Authors:  En-Ze Hu; Xin-Ran Lan; Zhi-Ling Liu; Jie Gao; Deng-Ke Niu
Journal:  BMC Genomics       Date:  2022-02-09       Impact factor: 3.969

2.  Microbiome Analysis via OTU and ASV-Based Pipelines-A Comparative Interpretation of Ecological Data in WWTP Systems.

Authors:  Jan Torsten Jeske; Claudia Gallert
Journal:  Bioengineering (Basel)       Date:  2022-03-29
  2 in total

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