Data from: Novel and divergent genes in the evolution of placental mammals

Analysis of genome sequences within a phylogenetic context can give insight into the mode and tempo of gene and protein evolution, including inference of gene ages. This can reveal whether new genes arose on particular evolutionary lineages and were recruited for new functional roles. Here, we apply MCL clustering with all-vs-all reciprocal BLASTP to identify and phylogenetically date ‘Homology Groups’ amongst vertebrate proteins. Homology Groups include new genes and highly divergent duplicate genes. Focussing on the origin of the placental mammals within the Eutheria, we identify 357 novel Homology Groups that arose on the stem lineage of Placentalia, 87 of which are deduced to play core roles in mammalian biology as judged by extensive retention in evolution. We find the human homologues of novel eutherian genes are enriched for expression in preimplantation embryo, brain, and testes, and enriched for functions in keratinization, reproductive development, and the immune system.

在系统发育（phylogenetic）背景下分析基因组序列，可揭示基因与蛋白质进化的模式与速率，包括基因起源时间的推断。该分析能够明确新基因是否在特定进化谱系中诞生，并被招募以承担全新的功能角色。本研究采用结合全对全双向最佳比对BLASTP（all-vs-all reciprocal BLASTP）的MCL聚类方法，对脊椎动物蛋白质中的同源组（Homology Groups）进行识别与系统发育定年。同源组涵盖新基因与高度分化的重复基因。本研究聚焦真兽亚纲（Eutheria）内胎盘哺乳动物的起源，成功识别出在胎盘类（Placentalia）干群谱系中诞生的357个新型同源组；其中87个经进化过程中的广泛保留，被推断为哺乳动物生物学的核心功能基因。研究发现，新型真兽类基因的人类同源物在植入前胚胎、大脑与睾丸中显著富集表达，且在角质化、生殖发育与免疫系统相关功能中显著富集。