Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, including amplification and pseudogenization, in multiple species. A large proportion of these events occurred in phyla for which scarce genomic data were available. However, recent large-scale genomics projects have added a wealth of information on those phyla. Using this input, we annotated perforin-1 homologs in more than eighty species including mammals, reptiles, birds, amphibians and fishes. We have annotated more than 400 perforin genes in all groups studied. Most mammalian species only have one perforin locus, which may contain a related pseudogene. However, we found four independent small expansions in unrelated members of this class. We could reconstruct the full-length coding sequences of only a few avian perforin genes, although we found incomplete and truncated forms of these gene in other birds. In the rest of reptilia, perforin-like genes can be found in at least three different loci containing up to twelve copies. Notably, mammals, non-avian reptiles, amphibians, and possibly teleosts share at least one perforin-1 locus as assessed by flanking genes. Finally, fish genomes contain multiple perforin loci with varying copy numbers and diverse exon/intron patterns. We have also found evidence for shorter genes with high similarity to the C2 domain of perforin in several teleosts. A preliminary analysis suggests that these genes arose at least twice during evolution from perforin-1 homologs. The assisted annotation of new genomic assemblies shows complex patterns of birth-and-death events in the evolution of perforin. These events include duplication/pseudogenization in mammals, multiple amplifications and losses in reptiles and fishes and at least one case of partial duplication with a novel start codon in fishes.

中文翻译：

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perforin-1 进化过程中频繁发生的出生和死亡事件


穿孔素 1 具有打开细胞膜孔的能力，在免疫系统中发挥着关键作用。与这一作用一致，编码穿孔素的基因显示出多个物种中复杂进化事件的特征，包括扩增和假基因化。这些事件大部分发生在基因组数据稀缺的门中。然而，最近的大规模基因组学项目增加了有关这些门的大量信息。利用这一输入，我们注释了 80 多个物种中的穿孔素-1 同源物，包括哺乳动物、爬行动物、鸟类、两栖动物和鱼类。我们对所有研究组中的 400 多个穿孔素基因进行了注释。大多数哺乳动物物种只有一个穿孔素基因座，该基因座可能包含相关的假基因。然而，我们在该类的不相关成员中发现了四个独立的小扩展。尽管我们在其他鸟类中发现了这些基因的不完整和截短形式，但我们只能重建少数鸟类穿孔素基因的全长编码序列。在其他爬行动物中，至少在三个不同的基因座中发现了穿孔素样基因，其中包含多达十二个拷贝。值得注意的是，根据侧翼基因的评估，哺乳动物、非鸟类爬行动物、两栖动物和可能的硬骨鱼共享至少一个穿孔素 1 位点。最后，鱼类基因组包含多个穿孔素基因座，具有不同的拷贝数和不同的外显子/内含子模式。我们还在几种硬骨鱼中发现了与穿孔素 C2 结构域高度相似的较短基因的证据。初步分析表明，这些基因在穿孔素 1 同源物的进化过程中至少出现两次。新基因组组装的辅助注释显示了穿孔素进化过程中出生和死亡事件的复杂模式。 这些事件包括哺乳动物中的复制/假化、爬行动物和鱼类中的多重扩增和丢失以及鱼类中至少一例新起始密码子的部分复制。