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Phylogenetic Relationship Among Brackishwater Vibrio Species
Vibriosis is regarded as an important disease of penaeid shrimps affecting larvae in hatcheries. Among the Vibrio species, Vibrio parahaemolyticus, Vibrio vulnificus, Vibrio furnissii, Vibrio campbellii, Vibrio harveyi, Vibrio alginolyticus, and Vibrio anguillarum are often associated with diseases...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
SAGE Publications
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7065438/ https://www.ncbi.nlm.nih.gov/pubmed/32214789 http://dx.doi.org/10.1177/1176934320903288 |
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author | Ashok Kumar, J Vinaya Kumar, K Avunje, S Akhil, V Ashok, S Kumar, Sujeet Sivamani, B Grover, Monendra Rai, Anil Alavandi, SV Vijayan, KK |
author_facet | Ashok Kumar, J Vinaya Kumar, K Avunje, S Akhil, V Ashok, S Kumar, Sujeet Sivamani, B Grover, Monendra Rai, Anil Alavandi, SV Vijayan, KK |
author_sort | Ashok Kumar, J |
collection | PubMed |
description | Vibriosis is regarded as an important disease of penaeid shrimps affecting larvae in hatcheries. Among the Vibrio species, Vibrio parahaemolyticus, Vibrio vulnificus, Vibrio furnissii, Vibrio campbellii, Vibrio harveyi, Vibrio alginolyticus, and Vibrio anguillarum are often associated with diseases in finfish and shellfish of brackishwater ecosystem. Accurate species differentiating methods for the organisms present in an ecosystem are required for precise classification of the species and to take steps for their management. Conventional methods like 16s rRNA phylogeny and multilocus sequence typing (MLST) have often failed to correctly identify Vibrio species. This has necessitated a comprehensive investigation on methodologies available to distinguish Vibrio species associated with brackishwater aquaculture system. To achieve this, 35 whole genomes belonging to 7 Vibrio species were subjected to phylogenetic analysis based on 16s rRNA gene, MLST genes, single-copy orthologous genes, and single-nucleotide polymorphisms. In addition, genome-based similarity indices like average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) were computed as confirmatory tests to verify the phylogenetic relations. There were some misclassifications occurred regarding phylogenetic relations based on 16s rRNA genes and MLST genes, while phylogeny with single-copy orthologous genes produced accurate species-level clustering. Study reveals that the species identification based on whole genome-based estimates or genome-wide variants are more precise than the ones done with single or subset of genes. |
format | Online Article Text |
id | pubmed-7065438 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | SAGE Publications |
record_format | MEDLINE/PubMed |
spelling | pubmed-70654382020-03-25 Phylogenetic Relationship Among Brackishwater Vibrio Species Ashok Kumar, J Vinaya Kumar, K Avunje, S Akhil, V Ashok, S Kumar, Sujeet Sivamani, B Grover, Monendra Rai, Anil Alavandi, SV Vijayan, KK Evol Bioinform Online Original Research Vibriosis is regarded as an important disease of penaeid shrimps affecting larvae in hatcheries. Among the Vibrio species, Vibrio parahaemolyticus, Vibrio vulnificus, Vibrio furnissii, Vibrio campbellii, Vibrio harveyi, Vibrio alginolyticus, and Vibrio anguillarum are often associated with diseases in finfish and shellfish of brackishwater ecosystem. Accurate species differentiating methods for the organisms present in an ecosystem are required for precise classification of the species and to take steps for their management. Conventional methods like 16s rRNA phylogeny and multilocus sequence typing (MLST) have often failed to correctly identify Vibrio species. This has necessitated a comprehensive investigation on methodologies available to distinguish Vibrio species associated with brackishwater aquaculture system. To achieve this, 35 whole genomes belonging to 7 Vibrio species were subjected to phylogenetic analysis based on 16s rRNA gene, MLST genes, single-copy orthologous genes, and single-nucleotide polymorphisms. In addition, genome-based similarity indices like average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) were computed as confirmatory tests to verify the phylogenetic relations. There were some misclassifications occurred regarding phylogenetic relations based on 16s rRNA genes and MLST genes, while phylogeny with single-copy orthologous genes produced accurate species-level clustering. Study reveals that the species identification based on whole genome-based estimates or genome-wide variants are more precise than the ones done with single or subset of genes. SAGE Publications 2020-03-06 /pmc/articles/PMC7065438/ /pubmed/32214789 http://dx.doi.org/10.1177/1176934320903288 Text en © The Author(s) 2020 https://creativecommons.org/licenses/by-nc/4.0/ This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (https://creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage). |
spellingShingle | Original Research Ashok Kumar, J Vinaya Kumar, K Avunje, S Akhil, V Ashok, S Kumar, Sujeet Sivamani, B Grover, Monendra Rai, Anil Alavandi, SV Vijayan, KK Phylogenetic Relationship Among Brackishwater Vibrio Species |
title | Phylogenetic Relationship Among Brackishwater Vibrio
Species |
title_full | Phylogenetic Relationship Among Brackishwater Vibrio
Species |
title_fullStr | Phylogenetic Relationship Among Brackishwater Vibrio
Species |
title_full_unstemmed | Phylogenetic Relationship Among Brackishwater Vibrio
Species |
title_short | Phylogenetic Relationship Among Brackishwater Vibrio
Species |
title_sort | phylogenetic relationship among brackishwater vibrio
species |
topic | Original Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7065438/ https://www.ncbi.nlm.nih.gov/pubmed/32214789 http://dx.doi.org/10.1177/1176934320903288 |
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