Complete Mitochondrial Genomes of the Cherskii's Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome.
The complete mitochondrial (mt) genome is sequenced in 2 individuals of the Cherskii's sculpin Cottus czerskii. A surprisingly high level of sequence divergence (10.3%) has been detected between the 2 genomes of C czerskii studied here and the GenBank mt genome of C czerskii (KJ956027). At the...
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ftcdlib:oai:escholarship.org:ark:/13030/qt2n15k8jj 2023-05-15T16:34:58+02:00 Complete Mitochondrial Genomes of the Cherskii's Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome. Balakirev, Evgeniy S Saveliev, Pavel A Ayala, Francisco J 2017-01-01 application/pdf https://escholarship.org/uc/item/2n15k8jj unknown eScholarship, University of California qt2n15k8jj https://escholarship.org/uc/item/2n15k8jj public Amur sculpin Cottus szanaga Cherskii’s sculpin Cottus czerskii GenBank Entry Error Depositary GenBank entry errors monitoring Siberian taimen Hucho taimen erroneous taxonomic identification introgression recombinant mitochondrial genome Cherskii's sculpin Cottus czerskii Biotechnology Human Genome Genetics Environmental Science and Management Biochemistry and Cell Biology Computation Theory and Mathematics Bioinformatics article 2017 ftcdlib 2022-07-25T17:31:29Z The complete mitochondrial (mt) genome is sequenced in 2 individuals of the Cherskii's sculpin Cottus czerskii. A surprisingly high level of sequence divergence (10.3%) has been detected between the 2 genomes of C czerskii studied here and the GenBank mt genome of C czerskii (KJ956027). At the same time, a surprisingly low level of divergence (1.4%) has been detected between the GenBank C czerskii (KJ956027) and the Amur sculpin Cottus szanaga (KX762049, KX762050). We argue that the observed discrepancies are due to incorrect taxonomic identification so that the GenBank accession number KJ956027 represents actually the mt genome of C szanaga erroneously identified as C czerskii. Our results are of consequence concerning the GenBank database quality, highlighting the potential negative consequences of entry errors, which once they are introduced tend to be propagated among databases and subsequent publications. We illustrate the premise with the data on recombinant mt genome of the Siberian taimen Hucho taimen (NCBI Reference Sequence Database NC_016426.1; GenBank accession number HQ897271.1), bearing 2 introgressed fragments (≈0.9 kb [kilobase]) from 2 lenok subspecies, Brachymystax lenok and Brachymystax lenok tsinlingensis, submitted to GenBank on June 12, 2011. Since the time of submission, the H taimen recombinant mt genome leading to incorrect phylogenetic inferences was propagated in multiple subsequent publications despite the fact that nonrecombinant H taimen genomes were also available (submitted to GenBank on August 2, 2014; KJ711549, KJ711550). Other examples of recombinant sequences persisting in GenBank are also considered. A GenBank Entry Error Depositary is urgently needed to monitor and avoid a progressive accumulation of wrong biological information. Article in Journal/Newspaper Hucho taimen Siberian taimen University of California: eScholarship |
institution |
Open Polar |
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University of California: eScholarship |
op_collection_id |
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topic |
Amur sculpin Cottus szanaga Cherskii’s sculpin Cottus czerskii GenBank Entry Error Depositary GenBank entry errors monitoring Siberian taimen Hucho taimen erroneous taxonomic identification introgression recombinant mitochondrial genome Cherskii's sculpin Cottus czerskii Biotechnology Human Genome Genetics Environmental Science and Management Biochemistry and Cell Biology Computation Theory and Mathematics Bioinformatics |
spellingShingle |
Amur sculpin Cottus szanaga Cherskii’s sculpin Cottus czerskii GenBank Entry Error Depositary GenBank entry errors monitoring Siberian taimen Hucho taimen erroneous taxonomic identification introgression recombinant mitochondrial genome Cherskii's sculpin Cottus czerskii Biotechnology Human Genome Genetics Environmental Science and Management Biochemistry and Cell Biology Computation Theory and Mathematics Bioinformatics Balakirev, Evgeniy S Saveliev, Pavel A Ayala, Francisco J Complete Mitochondrial Genomes of the Cherskii's Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome. |
topic_facet |
Amur sculpin Cottus szanaga Cherskii’s sculpin Cottus czerskii GenBank Entry Error Depositary GenBank entry errors monitoring Siberian taimen Hucho taimen erroneous taxonomic identification introgression recombinant mitochondrial genome Cherskii's sculpin Cottus czerskii Biotechnology Human Genome Genetics Environmental Science and Management Biochemistry and Cell Biology Computation Theory and Mathematics Bioinformatics |
description |
The complete mitochondrial (mt) genome is sequenced in 2 individuals of the Cherskii's sculpin Cottus czerskii. A surprisingly high level of sequence divergence (10.3%) has been detected between the 2 genomes of C czerskii studied here and the GenBank mt genome of C czerskii (KJ956027). At the same time, a surprisingly low level of divergence (1.4%) has been detected between the GenBank C czerskii (KJ956027) and the Amur sculpin Cottus szanaga (KX762049, KX762050). We argue that the observed discrepancies are due to incorrect taxonomic identification so that the GenBank accession number KJ956027 represents actually the mt genome of C szanaga erroneously identified as C czerskii. Our results are of consequence concerning the GenBank database quality, highlighting the potential negative consequences of entry errors, which once they are introduced tend to be propagated among databases and subsequent publications. We illustrate the premise with the data on recombinant mt genome of the Siberian taimen Hucho taimen (NCBI Reference Sequence Database NC_016426.1; GenBank accession number HQ897271.1), bearing 2 introgressed fragments (≈0.9 kb [kilobase]) from 2 lenok subspecies, Brachymystax lenok and Brachymystax lenok tsinlingensis, submitted to GenBank on June 12, 2011. Since the time of submission, the H taimen recombinant mt genome leading to incorrect phylogenetic inferences was propagated in multiple subsequent publications despite the fact that nonrecombinant H taimen genomes were also available (submitted to GenBank on August 2, 2014; KJ711549, KJ711550). Other examples of recombinant sequences persisting in GenBank are also considered. A GenBank Entry Error Depositary is urgently needed to monitor and avoid a progressive accumulation of wrong biological information. |
format |
Article in Journal/Newspaper |
author |
Balakirev, Evgeniy S Saveliev, Pavel A Ayala, Francisco J |
author_facet |
Balakirev, Evgeniy S Saveliev, Pavel A Ayala, Francisco J |
author_sort |
Balakirev, Evgeniy S |
title |
Complete Mitochondrial Genomes of the Cherskii's Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome. |
title_short |
Complete Mitochondrial Genomes of the Cherskii's Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome. |
title_full |
Complete Mitochondrial Genomes of the Cherskii's Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome. |
title_fullStr |
Complete Mitochondrial Genomes of the Cherskii's Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome. |
title_full_unstemmed |
Complete Mitochondrial Genomes of the Cherskii's Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome. |
title_sort |
complete mitochondrial genomes of the cherskii's sculpin cottus czerskii and siberian taimen hucho taimen reveal genbank entry errors: incorrect species identification and recombinant mitochondrial genome. |
publisher |
eScholarship, University of California |
publishDate |
2017 |
url |
https://escholarship.org/uc/item/2n15k8jj |
genre |
Hucho taimen Siberian taimen |
genre_facet |
Hucho taimen Siberian taimen |
op_relation |
qt2n15k8jj https://escholarship.org/uc/item/2n15k8jj |
op_rights |
public |
_version_ |
1766025080971722752 |