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Assessment of databases to determine the validity of β- and γ-carbonic anhydrase sequences from vertebrates

BACKGROUND: The inaccuracy of DNA sequence data is becoming a serious problem, as the amount of molecular data is multiplying rapidly and expectations are high for big data to revolutionize life sciences and health care. In this study, we investigated the accuracy of DNA sequence data from commonly...

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Autores principales: Zolfaghari Emameh, Reza, Kuuslahti, Marianne, Nosrati, Hassan, Lohi, Hannes, Parkkila, Seppo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216627/
https://www.ncbi.nlm.nih.gov/pubmed/32393172
http://dx.doi.org/10.1186/s12864-020-6762-2
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author Zolfaghari Emameh, Reza
Kuuslahti, Marianne
Nosrati, Hassan
Lohi, Hannes
Parkkila, Seppo
author_facet Zolfaghari Emameh, Reza
Kuuslahti, Marianne
Nosrati, Hassan
Lohi, Hannes
Parkkila, Seppo
author_sort Zolfaghari Emameh, Reza
collection PubMed
description BACKGROUND: The inaccuracy of DNA sequence data is becoming a serious problem, as the amount of molecular data is multiplying rapidly and expectations are high for big data to revolutionize life sciences and health care. In this study, we investigated the accuracy of DNA sequence data from commonly used databases using carbonic anhydrase (CA) gene sequences as generic targets. CAs are ancient metalloenzymes that are present in all unicellular and multicellular living organisms. Among the eight distinct families of CAs, including α, β, γ, δ, ζ, η, θ, and ι, only α-CAs have been reported in vertebrates. RESULTS: By an in silico analysis performed on the NCBI and Ensembl databases, we identified several β- and γ-CA sequences in vertebrates, including Homo sapiens, Mus musculus, Felis catus, Lipotes vexillifer, Pantholops hodgsonii, Hippocampus comes, Hucho hucho, Oncorhynchus tshawytscha, Xenopus tropicalis, and Rhinolophus sinicus. Polymerase chain reaction (PCR) analysis of genomic DNA persistently failed to amplify positive β- or γ-CA gene sequences when Mus musculus and Felis catus DNA samples were used as templates. Further BLAST homology searches of the database-derived “vertebrate” β- and γ-CA sequences revealed that the identified sequences were presumably derived from gut microbiota, environmental microbiomes, or grassland ecosystems. CONCLUSIONS: Our results highlight the need for more accurate and fast curation systems for DNA databases. The mined data must be carefully reconciled with our best knowledge of sequences to improve the accuracy of DNA data for publication.
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spelling pubmed-72166272020-05-18 Assessment of databases to determine the validity of β- and γ-carbonic anhydrase sequences from vertebrates Zolfaghari Emameh, Reza Kuuslahti, Marianne Nosrati, Hassan Lohi, Hannes Parkkila, Seppo BMC Genomics Research Article BACKGROUND: The inaccuracy of DNA sequence data is becoming a serious problem, as the amount of molecular data is multiplying rapidly and expectations are high for big data to revolutionize life sciences and health care. In this study, we investigated the accuracy of DNA sequence data from commonly used databases using carbonic anhydrase (CA) gene sequences as generic targets. CAs are ancient metalloenzymes that are present in all unicellular and multicellular living organisms. Among the eight distinct families of CAs, including α, β, γ, δ, ζ, η, θ, and ι, only α-CAs have been reported in vertebrates. RESULTS: By an in silico analysis performed on the NCBI and Ensembl databases, we identified several β- and γ-CA sequences in vertebrates, including Homo sapiens, Mus musculus, Felis catus, Lipotes vexillifer, Pantholops hodgsonii, Hippocampus comes, Hucho hucho, Oncorhynchus tshawytscha, Xenopus tropicalis, and Rhinolophus sinicus. Polymerase chain reaction (PCR) analysis of genomic DNA persistently failed to amplify positive β- or γ-CA gene sequences when Mus musculus and Felis catus DNA samples were used as templates. Further BLAST homology searches of the database-derived “vertebrate” β- and γ-CA sequences revealed that the identified sequences were presumably derived from gut microbiota, environmental microbiomes, or grassland ecosystems. CONCLUSIONS: Our results highlight the need for more accurate and fast curation systems for DNA databases. The mined data must be carefully reconciled with our best knowledge of sequences to improve the accuracy of DNA data for publication. BioMed Central 2020-05-11 /pmc/articles/PMC7216627/ /pubmed/32393172 http://dx.doi.org/10.1186/s12864-020-6762-2 Text en © The Author(s). 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Zolfaghari Emameh, Reza
Kuuslahti, Marianne
Nosrati, Hassan
Lohi, Hannes
Parkkila, Seppo
Assessment of databases to determine the validity of β- and γ-carbonic anhydrase sequences from vertebrates
title Assessment of databases to determine the validity of β- and γ-carbonic anhydrase sequences from vertebrates
title_full Assessment of databases to determine the validity of β- and γ-carbonic anhydrase sequences from vertebrates
title_fullStr Assessment of databases to determine the validity of β- and γ-carbonic anhydrase sequences from vertebrates
title_full_unstemmed Assessment of databases to determine the validity of β- and γ-carbonic anhydrase sequences from vertebrates
title_short Assessment of databases to determine the validity of β- and γ-carbonic anhydrase sequences from vertebrates
title_sort assessment of databases to determine the validity of β- and γ-carbonic anhydrase sequences from vertebrates
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216627/
https://www.ncbi.nlm.nih.gov/pubmed/32393172
http://dx.doi.org/10.1186/s12864-020-6762-2
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