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Life 2015, 5(1), 50-64; doi:10.3390/life5010050

Does a Barcoding Gap Exist in Prokaryotes? Evidences from Species Delimitation in Cyanobacteria

Microbial Ecology Group, Institute of Ecosystem Study, National Research Council, Largo Tonolli 50, 28922 Verbania, Italy
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Academic Editors: John C. Meeks and Robert Haselkorn
Received: 31 October 2014 / Accepted: 19 December 2014 / Published: 31 December 2014
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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Abstract

The amount of information that is available on 16S rRNA sequences for prokaryotes thanks to high-throughput sequencing could allow a better understanding of diversity. Nevertheless, the application of predetermined threshold in genetic distances to identify units of diversity (Operative Taxonomic Units, OTUs) may provide biased results. Here we tests for the existence of a barcoding gap in several groups of Cyanobacteria, defining units of diversity according to clear differences between within-species and among-species genetic distances in 16S rRNA. The application of a tool developed for animal DNA taxonomy, the Automatic Barcode Gap Detector (ABGD), revealed that a barcoding gap could actually be found in almost half of the datasets that we tested. The identification of units of diversity through this method provided results that were not compatible with those obtained with the identification of OTUs with threshold of similarity in genetic distances of 97% or 99%. The main message of our results is a call for caution in the estimate of diversity from 16S sequences only, given that different subjective choices in the method to delimit units could provide different results. View Full-Text
Keywords: cyanobacteria; DNA barcoding; taxonomy; operational taxonomic units; species in prokaryotes cyanobacteria; DNA barcoding; taxonomy; operational taxonomic units; species in prokaryotes
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Eckert, E.M.; Fontaneto, D.; Coci, M.; Callieri, C. Does a Barcoding Gap Exist in Prokaryotes? Evidences from Species Delimitation in Cyanobacteria. Life 2015, 5, 50-64.

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