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Abstract
Although the 16S rRNA gene is frequently used as a phylogenetic marker in analysis of environmental DNA, this marker often fails to distinguish closely related species, including those in the genus Vibrio. Here, we investigate whether inclusion and analysis of 23S rRNA sequence can help overcome the intrinsic weaknesses of 16S rRNA analyses for the differentiation of Vibrio species. We construct a maximum likelihood 16S rRNA gene tree to assess the use of this gene to identify clades of Vibrio species. Within the 16S rRNA tree, we identify the putative informative bases responsible for polyphyly, and demonstrate the association of these positions with tree topology. We demonstrate that concatenation of 16S and 23S rRNA genes increases the number of informative nucleotide positions, thereby overcoming ambiguities in 16S rRNA-based phylogenetic reconstructions. Finally, we experimentally demonstrate that this approach considerably improves the differentiation and identification of Vibrio species in environmental samples.
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1 University of the Basque Country UPV/EHU, Department of Immunology, Microbiology and Parasitology, Leioa, Spain (GRID:grid.11480.3c) (ISNI:0000 0001 2167 1098); University of the Basque Country (UPV/EHU), Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE-UPV/EHU), Plentzia, Spain (GRID:grid.11480.3c) (ISNI:0000000121671098)
2 University of the Basque Country (UPV/EHU), Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE-UPV/EHU), Plentzia, Spain (GRID:grid.11480.3c) (ISNI:0000000121671098); University of the Basque Country (UPV/EHU), CBET Research Group, Department of Zoology and Animal Cell Biology, Leioa, Spain (GRID:grid.11480.3c) (ISNI:0000 0001 2167 1098)
3 University of the Basque Country, UPV/EHU, Department of Plant Biology and Ecology, Faculty of Sciences and Technology, Leioa, Spain (GRID:grid.11480.3c) (ISNI:0000 0001 2167 1098)
4 University of the Basque Country, UPV/EHU, Department of Plant Biology and Ecology, Faculty of Sciences and Technology, Leioa, Spain (GRID:grid.11480.3c) (ISNI:0000 0001 2167 1098); IKERBASQUE, Basque Foundation for Science, Bilbao, Spain (GRID:grid.424810.b) (ISNI:0000 0004 0467 2314); Scientific Campus of the University of the Basque Country, BC3 Basque Center for Climate Change, Leioa, Spain (GRID:grid.11480.3c) (ISNI:0000000121671098)
5 University of the Basque Country UPV/EHU, Department of Immunology, Microbiology and Parasitology, Leioa, Spain (GRID:grid.11480.3c) (ISNI:0000 0001 2167 1098); University of the Basque Country (UPV/EHU), Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE-UPV/EHU), Plentzia, Spain (GRID:grid.11480.3c) (ISNI:0000000121671098); IKERBASQUE, Basque Foundation for Science, Bilbao, Spain (GRID:grid.424810.b) (ISNI:0000 0004 0467 2314)