Abstract
BackgroundBased 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).ResultsThe 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.ConclusionsMinimal 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.
Highlights
Based on an initial collecting of database sequences from the gap junction protein gene family in a few teleosts, the naming of these sequences appeared variable
By using many different phylogenetic models, we could classify the teleost sequences that had a dichotomous relationship with the corresponding mammalian sequences, and thereby point out the sequences that should have the same name as their mammalian orthologous counterpart
If there was no mammalian counterpart they should have a unique name. It was further settled which of the teleost sequences that existed in ohnologous pairs, and thereby should have their names followed by “a” or “b”
Summary
Based on an initial collecting of database sequences from the gap junction protein gene family ( called connexin genes) in a few teleosts, the naming of these sequences appeared variable. 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. The Zebrafish Nomenclature Conventions states that “genes should be named after the mammalian ortholog whenever possible” [5]. All the other genes in a gene family are paralogs, whether intraspecies or interspecies. Note that in this context, the functional relationship or expression pattern is irrelevant A pseudogene in one species can be an ortholog of a functional gene in another species, even if the pseudogene has no known function or is not expressed
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