10.3389/fmicb.2019.02083.s001
Marina García-López
Marina
García-López
Jan P. Meier-Kolthoff
Jan P.
Meier-Kolthoff
Brian J. Tindall
Brian J.
Tindall
Sabine Gronow
Sabine
Gronow
Tanja Woyke
Tanja
Woyke
Nikos C. Kyrpides
Nikos C.
Kyrpides
Richard L. Hahnke
Richard L.
Hahnke
Markus Göker
Markus
Göker
Data_Sheet_1_Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes.PDF
Frontiers
2019
G+C content
genome size
genome BLAST distance phylogeny
chemotaxonomy
morphology
phylogenetic systematics
phylogenomics
2019-09-23 13:43:49
Dataset
https://frontiersin.figshare.com/articles/dataset/Data_Sheet_1_Analysis_of_1_000_Type-Strain_Genomes_Improves_Taxonomic_Classification_of_Bacteroidetes_PDF/9891968
<p>Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.</p>