Data from: Evolution of toll-like receptors in the context of terrestrial ungulates and cetaceans diversification

Background: Toll-like receptors (TLRs) are the frontline actors in the innate immune response to various pathogens and are expected to be targets of natural selection in species adapted to habitats with contrasting pathogen burdens. The recent publication of genome sequences of giraffe and okapi together afforded the opportunity to examine the evolution of selected TLRs in broad range of terrestrial ungulates and cetaceans during their complex habitat diversification. Through direct sequence comparisons and standard evolutionary approaches, the extent of nucleotide and protein sequence diversity in seven Toll-like receptors (TLR2, TLR3, TLR4, TLR5, TLR7, TLR9 and TLR10) between giraffe and closely related species was determined. In addition, comparison of the patterning of key TLR motifs and domains between giraffe and related species was performed. The quantification of selection pressure and divergence on TLRs among terrestrial ungulates and cetaceans was also performed. Results: Sequence analysis shows that giraffe has 94-99% nucleotide identity with okapi and cattle for all TLRs analyzed. Variations in the number of Leucine-rich repeats were observed in some of TLRs between giraffe, okapi and cattle. Patterning of key TLR domains did not reveal any significant differences in the domain architecture among giraffe, okapi and cattle. Molecular evolutionary analysis for selection pressure identifies positive selection on key sites for all TLRs examined suggesting that pervasive evolutionary pressure has taken place during the evolution of terrestrial ungulates and cetaceans. Analysis of positively selected sites showed some site to be part of Leucine-rich motifs suggesting functional relevance in species-specific recognition of pathogen associated molecular patterns. Notably, clade analysis reveals significant selection divergence between terrestrial ungulates and cetaceans in viral sensing TLR3. Mapping of giraffe TLR3 key substitutions to the structure of the receptor indicates that at least one of giraffe altered sites coincides with TLR3 residue known to play a critical role in receptor signaling activity. Conclusion: There is overall structural conservation in TLRs among giraffe, okapi and cattle indicating that the mechanism for innate immune response utilizing TLR pathways may not have changed very much during the evolution of these species. However, a broader phylogenetic analysis revealed signatures of adaptive evolution among terrestrial ungulates and cetaceans, including the observed selection divergence in TLR3. This suggests that long term ecological dynamics has led to species-specific innovation and functional variation in the mechanisms mediating innate immunity in terrestrial ungulates and cetaceans.背景：Toll样受体（Toll-like receptors, TLRs）是固有免疫应答对抗各类病原体的核心前线效应分子，在适应不同病原体负荷生境的物种中，被认为是自然选择的靶标。近期长颈鹿与霍加狓的基因组序列发表，为探究广泛的陆生有蹄类与鲸类在复杂栖息地分化过程中部分TLRs的演化提供了契机。本研究通过直接序列比对与标准演化分析方法，明确了长颈鹿与近缘物种间7种Toll样受体（TLR2、TLR3、TLR4、TLR5、TLR7、TLR9及TLR10）的核苷酸与蛋白质序列多样性程度。此外，还对比了长颈鹿与近缘物种间关键TLR基序与结构域的分布模式，同时量化分析了陆生有蹄类与鲸类类群中TLRs所受的选择压力与演化分歧。 结果：序列分析显示，在所有被检测的TLRs中，长颈鹿与霍加狓、牛的核苷酸序列一致性达94%-99%。在长颈鹿、霍加狓与牛的部分TLRs中，观察到亮氨酸重复序列数量存在差异。关键TLR结构域的分布模式未在三者间展现出显著的结构架构差异。针对选择压力的分子演化分析表明，所有被检测的TLRs均存在关键位点的正选择，提示陆生有蹄类与鲸类的演化过程中普遍存在演化选择压力。对正选择位点的分析发现，部分位点属于亮氨酸基序的组成部分，这表明这些位点在物种特异性识别病原体相关分子模式（pathogen associated molecular patterns, PAMPs）中具有功能相关性。值得注意的是，进化枝分析揭示，在感知病毒的TLR3中，陆生有蹄类与鲸类间存在显著的选择分歧。将长颈鹿TLR3的关键替换位点映射至受体结构后发现，至少有一处长颈鹿的变异位点与已知对受体信号活性至关重要的TLR3残基重合。 结论：长颈鹿、霍加狓与牛的TLRs整体结构保守，表明利用TLR通路的固有免疫应答机制在这些物种的演化过程中并未发生显著改变。然而，更广泛的系统发育分析揭示了陆生有蹄类与鲸类间存在适应性演化的特征，包括前述TLR3中观察到的选择分歧。这意味着长期的生态动态变化推动了陆生有蹄类与鲸类介导固有免疫的机制产生物种特异性的创新与功能变异。