背景:海洋哺乳动物,它们已经独立进化成三个不同的谱系,具有共同的生理特征,有助于它们适应海洋环境。
目的:使用来自三个分类顺序的可用基因组数据来鉴定正选择的基因(PSGs)以适应海洋环境:鲸目动物,针脚,和Sirenians。
方法:基于每组偶蹄动物的基因组,食肉和Afrotheria,我们使用CODEML中的分支位点模型进行选择分析.
结果:基于分支站点模型,对鲸目动物进行了460、614和359PSG的预测,针脚,和Sirenians,分别。功能富集分析表明,与止血相关的基因在海洋哺乳动物的所有谱系中均被阳性选择。我们观察到止血和凝血相关基因纤溶酶原激活剂的阳性选择信号,尿激酶(PLAU),多聚蛋白1(MMRN1),γ-谷氨酰羧化酶(GGCX),和血小板内皮聚集受体1(PEAR1)。此外,我们发现钠电压门控通道α亚基9(SCN9A),丝氨酸/精氨酸重复矩阵4(SRRM4),和Ki-ras诱导的肌动蛋白相互作用蛋白(KRAP)处于正选择压力下,并与认知相关,神经突生长,和IP3介导的Ca2+释放,分别。
结论:这项研究将有助于我们对海洋哺乳动物的适应性进化的理解,通过提供一组候选基因的信息,这些基因被预测会影响对水生环境的适应性,以及它们的功能特征。
BACKGROUND: Marine mammals, which have evolved independently into three distinct lineages, share common physiological features that contribute to their adaptation to the marine environment.
OBJECTIVE: To identify positively selected genes (PSGs) for adaptation to the marine environment using available genomic data from three taxonomic orders: cetaceans, pinnipeds, and sirenians.
METHODS: Based on the genomes within each group of Artiodactyla,
Carnivora and Afrotheria, we performed selection analysis using the branch-site model in CODEML.
RESULTS: Based on the branch-site model, 460, 614, and 359 PSGs were predicted for the cetaceans, pinnipeds, and sirenians, respectively. Functional enrichment analysis indicated that genes associated with hemostasis were positively selected across all lineages of marine mammals. We observed positive selection signals for the hemostasis and coagulation-related genes plasminogen activator, urokinase (PLAU), multimerin 1 (MMRN1), gamma-glutamyl carboxylase (GGCX), and platelet endothelial aggregation receptor 1 (PEAR1). Additionally, we found out that the sodium voltage-gated channel alpha subunit 9 (SCN9A), serine/arginine repetitive matrix 4 (SRRM4), and Ki-ras-induced actin-interacting protein (KRAP) are under positive selection pressure and are associated with cognition, neurite outgrowth, and IP3-mediated Ca2 + release, respectively.
CONCLUSIONS: This study will contribute to our understanding of the adaptive evolution of marine mammals by providing information on a group of candidate genes that are predicted to influence adaptation to aquatic environments, as well as their functional characteristics.