Genome sequences as the type material for taxonomic descriptions of prokaryotes

doi:10.1016/j.syapm.2015.02.003

Systematic and Applied Microbiology

Volume 38, Issue 4, June 2015, Pages 217-222

https://doi.org/10.1016/j.syapm.2015.02.003 Get rights and content

Abstract

Genome sequencing of type strains promises to revolutionize prokaryotic systematics by greatly improving the identification of species, elucidating the functional properties of taxonomic groups, and resolving many of the ambiguities in the phylogeny of the higher taxa. Genome sequences could also serve as the type material for naming prokaryotic taxa, which will greatly expand the nomenclature governed by the Bacteriological Code to include many fastidious and uncultured organisms and endosymbionts of great biological interest.

Section snippets

Genomics for species delineation

In the original proposal for the delineation of species based upon genome similarity [59], two measures of genetic relatedness were proposed to set the boundary for prokaryotic species. The first measure was the change in the melting temperature (or ΔT_m) of heteroduplex DNA formed upon annealing the DNAs from the two strains to be tested. The ΔT_m is directly related to the sequence identity of the DNAs, and a ΔT_m of about 5 °C, the cutoff proposed for prokaryotic species, corresponds to an

Genomics for identification of functional properties of taxonomic groups

In addition to setting the criteria for delineation of species, genomics can play an important role in how thresholds are applied. While thresholds are necessary to maintain uniformity in taxonomic ranks among phylogenetic lineages, there are many reasons why they should be applied flexibly [12], [35]. First, no matter what threshold is chosen, there will be certain groups that fall just below or above the threshold and would be inappropriately subdivided or grouped, respectively (Fig. 1). A

Genomics for delineation of higher taxa

The same concerns that exist at the species level also occur at the higher taxonomic ranks. In addition, the phylogeny of the taxonomic groups becomes critical at the higher taxonomic ranks where phylogenetic trees based upon single genes often fail to resolve the tree. For instance, 16S rRNA gene trees fail to resolve branching patterns of most of the orders within the class Actinobacteria [33]. Complete or draft genome sequences can overcome many of these limitations. Because many more genes

Genomics in the description of novel species

The opportunity genomics provides to microbial systematics is enormous, and we should expect that genome sequences will become common in descriptions of new species. The sequences are just too valuable not to determine. Moreover, the value of the sequences increases with the size of the data base of genome sequences. According to a search of the NCBI database, at the end of 2014 complete or draft genome sequences were available for about 3600 type strains of prokaryotes. The DOE-JGI

Genome sequence as type material

Therefore, it is recommended that the genome sequence be allowed serve as the type material when it has been obtained from either a clonal population or a single cell. In this case, samples of the DNA should be submitted to public culture collections to insure the authenticity of the sequence. When the genome sequence is not possible, as might be the case for obligate endosymbionts, multilocus sequence analyses would be a suitable alternative if it can be shown to provide an unambiguous

Recommendations

It is proposed that the sequence identity of homologous genes be accepted as the new criterion for delineation of species. Sequence identity could be based upon measures of the entire genome such as ANI and distance formula d₄ of the GGDC package, selections of specific genes such as specI or multilocus sequence analysis, or similar criteria deemed to be appropriate for each prokaryotic group. The similarity of gene content or DDH will then become a describable property of the species, as

Acknowledgements

This work was supported in part by a NSF Dimensions of Biodiversity grant OCE-1342694. I also thank Jongsik Chun, Michael Galperin, Radhey S. Gupta, Kuo Hong, Hans-Peter Klenk, Nikos Krypides, Haiwei Luo, Amrita Pati, and Tanja Woyke for helpful discussions.

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Genome sequences as the type material for taxonomic descriptions of prokaryotes

Abstract

Section snippets

Genomics for species delineation

Genomics for identification of functional properties of taxonomic groups

Genomics for delineation of higher taxa

Genomics in the description of novel species

Genome sequence as type material

Recommendations

Acknowledgements

Syst. Appl. Microbiol.

Res. Microbiol.

Syst. Appl. Microbiol.

FEMS Microbiol. Rev.

Syst. Appl. Microbiol.

Gene ontology: tool for the unification of biology

Nat. Genet.

Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs

Stand. Genom. Sci.

Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

Stand. Genom. Sci.

A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land

BMC Evol. Biol.

Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis

PLoS ONE

An expansion of age constraints for microbial clades that lack a conventional fossil record using phylogenomic dating

J. Mol. Evol.

Calibration of the change in thermal-stability of DNA duplexes and degree of base pair mismatch

J. Mol. Evol.

Genomics. Genome project standards in a new era of sequencing

Science

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

Int. J. Syst. Evol. Microbiol.

Polyphasic taxonomy of bacteria

Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol

Environ. Microbiol.

Opinion: re-evaluating prokaryotic species

Nat. Rev. Microbiol.

International Committee on Systematic Bacteriology XVIth International Congress of Microbiology: Minutes of the Meetings, 2, 3, and 5 July 1994, Prague, Czech Republic

Int. J. Syst. Bacteriol.

DNA–DNA hybridization values and their relationship to whole-genome sequence similarities

Int. J. Syst. Evol. Microbiol.

International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of the Chlamydiae: Minutes of the inaugural closed meeting, 21 March 2009, Little Rock, AR, USA

Int. J. Syst. Evol. Microbiol.

A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring

Proc. Natl. Acad. Sci. U.S.A.

Similarity analysis of DNAs

Similarity analysis of DNAs

Prokaryotic taxonomy in the sequencing era – the polyphasic approach revisited

Environ. Microbiol.

Large-scale evaluation of experimentally determined DNA G + C contents with whole genome sequences of prokaryotes

Syst. Appl. Microbiol.

Isolation of an autotrophic ammonia-oxidizing marine archaeon

Nature

Genomic insights that advance the species definition for prokaryotes

Proc. Natl. Acad. Sci. U.S.A.

Genomic encyclopedia of type strains. Phase I: the one thousand microbial genomes (KMG-I) project

Stand. Genom. Sci.

Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria

Biol. Dir.

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PLoS Biol.

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Int. J. Syst. Evol. Microbiol.