Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies
Abstract Background Based on an initial collecting of database sequences from the gap junction protein gene family (also called connexin genes) in a few teleosts, the naming of these sequences appeared variable. The reasons could be (i) that the structure in this family is variable across teleosts,...
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ftdoajarticles:oai:doaj.org/article:55e1362829864b1abe37a9afd21dbd17 2023-05-15T15:27:49+02:00 Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies Svein-Ole Mikalsen Marni Tausen Sunnvør í Kongsstovu 2020-03-01T00:00:00Z https://doi.org/10.1186/s12864-020-6620-2 https://doaj.org/article/55e1362829864b1abe37a9afd21dbd17 EN eng BMC http://link.springer.com/article/10.1186/s12864-020-6620-2 https://doaj.org/toc/1471-2164 doi:10.1186/s12864-020-6620-2 1471-2164 https://doaj.org/article/55e1362829864b1abe37a9afd21dbd17 BMC Genomics, Vol 21, Iss 1, Pp 1-19 (2020) Connexins Genome duplication Mammals Nomenclature Ohnologs Orthologs Biotechnology TP248.13-248.65 Genetics QH426-470 article 2020 ftdoajarticles https://doi.org/10.1186/s12864-020-6620-2 2022-12-31T01:10:25Z Abstract Background Based on an initial collecting of database sequences from the gap junction protein gene family (also called connexin genes) in a few teleosts, the naming of these sequences appeared variable. The reasons could be (i) that the structure in this family is variable across teleosts, or (ii) unfortunate naming. Rather clear rules for the naming of genes in fish and mammals have been outlined by nomenclature committees, including the naming of orthologous and ohnologous genes. We therefore analyzed the connexin gene family in teleosts in more detail. We covered the range of divergence times in teleosts (eel, Atlantic herring, zebrafish, Atlantic cod, three-spined stickleback, Japanese pufferfish and spotted pufferfish; listed from early divergence to late divergence). Results The gene family pattern of connexin genes is similar across the analyzed teleosts. However, (i) several nomenclature systems are used, (ii) specific orthologous groups contain genes that are named differently in different species, (iii) several distinct genes have the same name in a species, and (iv) some genes have incorrect names. The latter includes a human connexin pseudogene, claimed as GJA4P, but which in reality is Cx39.2P (a delta subfamily gene often called GJD2like). We point out the ohnologous pairs of genes in teleosts, and we suggest a more consistent nomenclature following the outlined rules from the nomenclature committees. We further show that connexin sequences can indicate some errors in two high-quality chromosome assemblies that became available very recently. Conclusions Minimal consistency exists in the present practice of naming teleost connexin genes. A consistent and unified nomenclature would be an advantage for future automatic annotations and would make various types of subsequent genetic analyses easier. Additionally, roughly 5% of the connexin sequences point out misassemblies in the new high-quality chromosome assemblies from herring and cod. Article in Journal/Newspaper atlantic cod Directory of Open Access Journals: DOAJ Articles BMC Genomics 21 1 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Connexins Genome duplication Mammals Nomenclature Ohnologs Orthologs Biotechnology TP248.13-248.65 Genetics QH426-470 |
spellingShingle |
Connexins Genome duplication Mammals Nomenclature Ohnologs Orthologs Biotechnology TP248.13-248.65 Genetics QH426-470 Svein-Ole Mikalsen Marni Tausen Sunnvør í Kongsstovu Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies |
topic_facet |
Connexins Genome duplication Mammals Nomenclature Ohnologs Orthologs Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
Abstract Background Based on an initial collecting of database sequences from the gap junction protein gene family (also called connexin genes) in a few teleosts, the naming of these sequences appeared variable. The reasons could be (i) that the structure in this family is variable across teleosts, or (ii) unfortunate naming. Rather clear rules for the naming of genes in fish and mammals have been outlined by nomenclature committees, including the naming of orthologous and ohnologous genes. We therefore analyzed the connexin gene family in teleosts in more detail. We covered the range of divergence times in teleosts (eel, Atlantic herring, zebrafish, Atlantic cod, three-spined stickleback, Japanese pufferfish and spotted pufferfish; listed from early divergence to late divergence). Results The gene family pattern of connexin genes is similar across the analyzed teleosts. However, (i) several nomenclature systems are used, (ii) specific orthologous groups contain genes that are named differently in different species, (iii) several distinct genes have the same name in a species, and (iv) some genes have incorrect names. The latter includes a human connexin pseudogene, claimed as GJA4P, but which in reality is Cx39.2P (a delta subfamily gene often called GJD2like). We point out the ohnologous pairs of genes in teleosts, and we suggest a more consistent nomenclature following the outlined rules from the nomenclature committees. We further show that connexin sequences can indicate some errors in two high-quality chromosome assemblies that became available very recently. Conclusions Minimal consistency exists in the present practice of naming teleost connexin genes. A consistent and unified nomenclature would be an advantage for future automatic annotations and would make various types of subsequent genetic analyses easier. Additionally, roughly 5% of the connexin sequences point out misassemblies in the new high-quality chromosome assemblies from herring and cod. |
format |
Article in Journal/Newspaper |
author |
Svein-Ole Mikalsen Marni Tausen Sunnvør í Kongsstovu |
author_facet |
Svein-Ole Mikalsen Marni Tausen Sunnvør í Kongsstovu |
author_sort |
Svein-Ole Mikalsen |
title |
Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies |
title_short |
Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies |
title_full |
Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies |
title_fullStr |
Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies |
title_full_unstemmed |
Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies |
title_sort |
phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies |
publisher |
BMC |
publishDate |
2020 |
url |
https://doi.org/10.1186/s12864-020-6620-2 https://doaj.org/article/55e1362829864b1abe37a9afd21dbd17 |
genre |
atlantic cod |
genre_facet |
atlantic cod |
op_source |
BMC Genomics, Vol 21, Iss 1, Pp 1-19 (2020) |
op_relation |
http://link.springer.com/article/10.1186/s12864-020-6620-2 https://doaj.org/toc/1471-2164 doi:10.1186/s12864-020-6620-2 1471-2164 https://doaj.org/article/55e1362829864b1abe37a9afd21dbd17 |
op_doi |
https://doi.org/10.1186/s12864-020-6620-2 |
container_title |
BMC Genomics |
container_volume |
21 |
container_issue |
1 |
_version_ |
1766358223234793472 |