Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia.
Faculty of Science and Arts, University of Kırıkkale, Kırıkkale, Turkey.
Mol Biol Rep. 2020 Apr;47(4):2975-2984. doi: 10.1007/s11033-020-05382-x. Epub 2020 Mar 31.
Toll-like receptors (TLRs) are transmembrane proteins of the innate immune system, composed of the ectodomain involved in pathogen recognition and the intracellular Toll/interleukin-1 receptor (TIR) domain important for downstream signal transduction. Here, we analyze the genetic variability of TIR nucleotide and amino-acid sequences of the TLR2 gene in 243 brown hares from Europe and the Middle East and tested for the presence of selection signals and spatial structuring. TLR2 TIR domain sequences were PCR amplified and sequenced, while genotyping was performed by phasing. Genetic diversity indices were calculated in DnaSP and Arlequin, while presence of selection signals was tested using MEGA and the Datamonkey web server. The presence of spatial patterns in TIR sequence distribution was tested by spatial Principal Component Analysis (sPCA) in adegenet. A total of 13 haplotypes were revealed with haplotype diversity of 0.424, and nucleotide diversity (π) of 0.00138. Two spatial clusters were revealed: "Anatolia/Middle East" and "Europe". In Anatolia the two most prevalent amino-acid variants, A and B (the latter being the most ancestral) were maintained at similar frequencies; but in Europe a shift in genotype frequencies was observed as well as a higher number of nonsynonymous substitutions giving rise to novel amino-acid protein variants originating from the evolutionarily younger protein variant. Molecular diversity (haplotype and nucleotide diversity) indices were significantly higher in the "Anatolia/Middle East" cluster. A signal of purifying selection was detected acting on the TIR sequences.
Toll 样受体 (TLRs) 是先天免疫系统的跨膜蛋白，由参与病原体识别的胞外结构域和对下游信号转导至关重要的 Toll/白细胞介素-1 受体 (TIR) 结构域组成。在这里，我们分析了来自欧洲和中东的 243 只棕色野兔 TLR2 基因的 TIR 核苷酸和氨基酸序列的遗传变异性，并测试了选择信号和空间结构的存在。TLR2 TIR 结构域序列通过 PCR 扩增和测序进行扩增和测序，而通过相位检测进行基因分型。遗传多样性指数在 DnaSP 和 Arlequin 中计算，而选择信号的存在通过 MEGA 和 Datamonkey 网络服务器进行测试。通过 adegenet 中的空间主成分分析 (sPCA) 测试 TIR 序列分布的空间模式的存在。共揭示了 13 种单倍型，单倍型多样性为 0.424，核苷酸多样性 (π) 为 0.00138。揭示了两个空间聚类：“安纳托利亚/中东”和“欧洲”。在安纳托利亚，两种最常见的氨基酸变体 A 和 B（后者是最原始的）保持相似的频率；但在欧洲，观察到基因型频率发生了变化，并且出现了更多的非同义取代，从而产生了源自进化较年轻的蛋白质变体的新型氨基酸蛋白质变体。“安纳托利亚/中东”聚类中的分子多样性（单倍型和核苷酸多样性）指数显著更高。检测到针对 TIR 序列的纯化选择信号。
