Sammelbandbeitrag

Autorenliste: Blom, J; Juhre, T; Kreis, J; Hanel, PHG; Schrade, JG; Kämpfer, P; Goesmann, A

Erschienen in: Bergey's Manual of Systematics of Archaea and Bacteria

Herausgeberliste: Whitman, WB

Jahr der Veröffentlichung: 2019

eISBN: 978-1-118-96060-8

DOI Link: https://doi.org/10.1002/9781118960608.bm00038

Abstract: 

The deployment of next-generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is feasible to analyze not only single genomes, but also large groups of related genomes in a comparative approach. Whole genome sequencing of type strain genomes also holds huge potential for obtaining a higher resolution phylogenetic and taxonomic classification. In the past 9 years, the EDGAR platform has become one of the most established software tools in the field of comparative genomics. During this time, the software has been continuously improved, and a large number of new analysis features have been added. In recent years, the use of EDGAR for core-genome-based phylogenomic/taxonomic analysis has become a main application field of the software. With a focus on generating genome sequences of all type strains of prokaryotic species, the basic 16S rRNA gene sequence phylogeny can be significantly extended to a higher resolution core-genome-based taxonomy, and lab work intensive DNA–DNA hybridization (DDH) can be replaced by genome-sequence-based indices, which reflect the species borders in the same manner as the DDH.

The web-based user interface of EDGAR offers all tools required for phylogenomic inter- and intraspecies taxonomic analyses as needed for the proposal of novel species. EDGAR calculates core-genome-based phylogenetic trees with neighbor-joining and maximum-likelihood methods as well as amino acid identity (AAI) and average nucleotide identity (ANI) matrices. Furthermore, it offers convenient visualization features such as Venn diagrams, synteny plots, and a comparative view of the genomic neighborhood of orthologous genes. Recently, the software was extended to include various new features, such as statistical analyses, replicon grouping options, and second-level analyses of meta gene sets. Thus, the software enables a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes.

EDGAR also provides public databases with precomputed projects providing comparative genomics and phylogenomic results. The platform provides 322 genus-based public databases comprising 8,079 complete genomes. Besides those genus-based projects, in this article, we present 226 new public projects that are clustered on the family level and use type strains genomes, which also include draft genomes. These new public projects comprise a further 4,400 genomes. EDGAR is free for academic use and funded as a service by the German Network for Bioinformatics Infrastructure – de.NBI. EDGAR is available via the public web server http://edgar.computational.bio.

Harvard-Zitierstil: Blom, J., Juhre, T., Kreis, J., Hanel, P., Schrade, J., Kämpfer, P., et al. (2019) EDGAR: A Versatile Tool for Phylogenomics*, in Whitman, W. (ed.) Bergey's Manual of Systematics of Archaea and Bacteria. Hoboken, NJ: Wiley. https://doi.org/10.1002/9781118960608.bm00038

APA-Zitierstil: Blom, J., Juhre, T., Kreis, J., Hanel, P., Schrade, J., Kämpfer, P., & Goesmann, A. (2019). EDGAR: A Versatile Tool for Phylogenomics*. In Whitman, W. (Ed.), Bergey's Manual of Systematics of Archaea and Bacteria. Wiley. https://doi.org/10.1002/9781118960608.bm00038