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Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies
BMC Genomics ( IF 4.4 ) Pub Date : 2020-03-11 , DOI: 10.1186/s12864-020-6620-2
Svein-Ole Mikalsen , Marni Tausen , Sunnvør í Kongsstovu

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). 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. 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.

中文翻译:

硬骨连接蛋白的系统发育研究表明,在最近的硬骨染色体组装中,种内和种间使用的命名法和组装不完全一致

基于最初从几个硬骨鱼中的间隙连接蛋白基因家族(也称为连接蛋白基因)收集数据库序列的结果,这些序列的命名似乎是可变的。原因可能是(i)该家族的结构在硬骨鱼之间是可变的,或者(ii)不幸的命名。命名委员会已经概述了鱼类和哺乳动物基因命名的明确规则,包括直系同源和同源基因的命名。因此,我们更详细地分析了硬骨鱼中的连接蛋白基因家族。我们讨论了硬骨鱼的发散时间范围(鳗鱼,大西洋鲱鱼,斑马鱼,大西洋鳕鱼,三梭stick,日本河豚和斑点河豚;从早期发散到晚期发散列出)。连接蛋白基因的基因家族模式在整个硬骨鱼中相似。但是,(i)使用了几种命名系统,(ii)特定直系同源基团包含在不同物种中命名不同的基因,(iii)在一个物种中多个不同的基因具有相同的名称,并且(iv)一些基因的名称不正确。后者包括一个人连接蛋白假基因,称其为GJA4P,但实际上是Cx39.2P(一种δ亚家族基因,通常称为GJD2like)。我们指出硬骨鱼类中的同源基因对,并根据命名法委员会提出的规则建议更一致的命名法。我们进一步表明,连接蛋白序列可以指示两个高质量染色体组件中的一些错误,这些组件最近才可用。在命名硬骨连接蛋白基因的当前实践中存在最小的一致性。一致和统一的命名法对于将来的自动注释将是一个优势,并将使各种类型的后续遗传分析更加容易。另外,大约有5%的连接蛋白序列指出鲱鱼和鳕鱼中新的高质量染色体装配中的装配错误。
更新日期:2020-03-12
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