School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China.
Genes (Basel). 2021 Nov 19;12(11):1819. doi: 10.3390/genes12111819.
Origination of new genes are of inherent interest of evolutionary geneticists for decades, but few studies have addressed the general pattern in a fish lineage. Using our recent released whole genome data of flatfishes, which evolved one of the most specialized body plans in vertebrates, we identified 1541 (6.9% of the starry flounder genes) flatfish-lineage-specific genes. The origination pattern of these flatfish new genes is largely similar to those observed in other vertebrates, as shown by the proportion of DNA-mediated duplication (1317; 85.5%), RNA-mediated duplication (retrogenes; 96; 6.2%), and de novo-origination (128; 8.3%). The emergence rate of species-specific genes is 32.1 per Mya and the whole average level rate for the flatfish-lineage-specific genes is 20.9 per Mya. A large proportion (31.4%) of these new genes have been subjected to selection, in contrast to the 4.0% in primates, while the old genes remain quite similar (66.4% vs. 65.0%). In addition, most of these new genes (70.8%) are found to be expressed, indicating their functionality. This study not only presents one example of systematic new gene identification in a teleost taxon based on comprehensive phylogenomic data, but also shows that new genes may play roles in body planning.
新基因的起源是进化遗传学家几十年来一直感兴趣的问题，但很少有研究涉及鱼类谱系中的一般模式。利用我们最近发布的平鳍鱼类全基因组数据，这些鱼类进化出了脊椎动物中最具特化的身体结构之一，我们鉴定了 1541 个（星鲽基因的 6.9%）平鳍鱼类谱系特异性基因。这些平鳍鱼类新基因的起源模式与在其他脊椎动物中观察到的模式大致相似，这可以从 DNA 介导的复制（1317 个；85.5%）、RNA 介导的复制（反转录基因；96 个；6.2%）和从头起源（128 个；8.3%）的比例看出。物种特异性基因的出现率为 32.1 个/Mya，平鳍鱼类谱系特异性基因的整体平均水平率为 20.9 个/Mya。很大一部分（31.4%）的这些新基因受到了选择，而灵长类动物只有 4.0%，而旧基因则非常相似（66.4%对 65.0%）。此外，这些新基因中的大多数（70.8%）被发现表达，表明它们具有功能。这项研究不仅提供了一个基于全面系统基因组数据的硬骨鱼类新基因系统鉴定的例子，还表明新基因可能在身体规划中发挥作用。
