Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
Jongsik Chun,Aharon Oren,Antonio Ventosa,Henrik Christensen,David R. Arahal,Milton S. da Costa,Alejandro P. Rooney,Hana Yi,Xue-Wei Xu,Sofie E. De Meyer,Martha E. Trujillo +10 more
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TLDR
The minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes are described.Abstract:
Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes.read more
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A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae.
Jinshui Zheng,Stijn Wittouck,Elisa Salvetti,Charles M. A. P. Franz,Hugh M. B. Harris,Paola Mattarelli,Paul W. O'Toole,Bruno Pot,Peter Vandamme,Jens Walter,Koichi Watanabe,Sander Wuyts,Giovanna E. Felis,Michael G. Gänzle,Michael G. Gänzle,Sarah Lebeer +15 more
TL;DR: This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences and proposed reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties.
Journal ArticleDOI
TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy
TL;DR: TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy and analysis connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information.
Journal ArticleDOI
UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction
TL;DR: This work presents the up-to-date bacterial core gene set, named UBCG, and software suites to accommodate necessary steps to generate and evaluate phylogenetic trees, successfully used to infer phylogenomic relationship of Escherichia and related taxa.
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A complete domain-to-species taxonomy for Bacteria and Archaea.
Donovan H. Parks,Maria Chuvochina,Pierre-Alain Chaumeil,Christian Rinke,Aaron J. Mussig,Philip Hugenholtz +5 more
TL;DR: This resource provides a complete domain-to-species taxonomic framework for bacterial and archaeal genomes, which will facilitate research on uncultivated species and improve communication of scientific results.
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Genome-Based Taxonomic Classification of the Phylum Actinobacteria
Imen Nouioui,Lorena Carro,Marina García-López,Jan P. Meier-Kolthoff,Tanja Woyke,Nikos C. Kyrpides,Rüdiger Pukall,Hans-Peter Klenk,Michael Goodfellow,Markus Göker +9 more
TL;DR: Good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features, underline the pitfalls inherent in phylogenies based upon single gene sequences.
References
More filters
Journal ArticleDOI
Base-calling of automated sequencer traces using Phred. I. accuracy assessment
TL;DR: In this article, a base-calling program for automated sequencer traces, phred, with improved accuracy was proposed. But it was not shown to achieve a lower error rate than the ABI software, averaging 40%-50% fewer errors in the data sets examined independent of position in read, machine running conditions, or sequencing chemistry.
Journal ArticleDOI
Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology
Erko Stackebrandt,B. M. Goebel +1 more
TL;DR: Amorphous metal alloys are employed in acoustic devices dependent upon the properties of low acoustic velocity and low attenuation, such as wire, strip and bulk delay lines.
Journal ArticleDOI
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
TL;DR: An objective measure of genome quality is proposed that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities and is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches.
Journal ArticleDOI
Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies.
TL;DR: An integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea, which is represented by quality-controlled 16S rRNA gene and genome sequences, with accompanying bioinformatics tools.
Journal ArticleDOI
Shifting the genomic gold standard for the prokaryotic species definition
TL;DR: The work package JSpecies is examined as a user-friendly, biologist-oriented interface to calculate ANI and the correlation of the tetranucleotide signatures between pairwise genomic comparisons, and results agreed with the use of ANI to substitute DDH.
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