Assessment of databases to determine the validity of beta- and gamma-carbonic anhydrase sequences from vertebrates

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http://hdl.handle.net/10138/316122

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Emameh , R Z , Kuuslahti , M , Nosrati , H , Lohi , H & Parkkila , S 2020 , ' Assessment of databases to determine the validity of beta- and gamma-carbonic anhydrase sequences from vertebrates ' , BMC Genomics , vol. 21 , no. 1 , 352 . https://doi.org/10.1186/s12864-020-6762-2

Title: Assessment of databases to determine the validity of beta- and gamma-carbonic anhydrase sequences from vertebrates
Author: Emameh, Reza Zolfaghari; Kuuslahti, Marianne; Nosrati, Hassan; Lohi, Hannes; Parkkila, Seppo
Contributor: University of Helsinki, Helsinki One Health (HOH)
Date: 2020-05-11
Language: eng
Number of pages: 8
Belongs to series: BMC Genomics
ISSN: 1471-2164
URI: http://hdl.handle.net/10138/316122
Abstract: BackgroundThe 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 alpha, beta, gamma, delta, zeta, eta, theta, and iota, only alpha -CAs have been reported in vertebrates.ResultsBy an in silico analysis performed on the NCBI and Ensembl databases, we identified several beta- and gamma -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 beta- or gamma -CA gene sequences when Mus musculus and Felis catus DNA samples were used as templates. Further BLAST homology searches of the database-derived "vertebrate" beta- and gamma -CA sequences revealed that the identified sequences were presumably derived from gut microbiota, environmental microbiomes, or grassland ecosystems.ConclusionsOur 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.
Subject: Carbonic anhydrase
Contamination
Curation
Database
DNA
Sequencing
MICROBIOTA
GENOME
3111 Biomedicine
1184 Genetics, developmental biology, physiology
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