Department of Biological Sciences, Oakland University, Rochester, MI, USA.
Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.
Sci Rep. 2018 Jan 10;8(1):335. doi: 10.1038/s41598-017-18695-y.
Low complexity regions (LCRs) are a common feature shared by many genomes, but their evolutionary and functional significance remains mostly unknown. At the core of the uncertainty is a poor understanding of the mechanisms that regulate their retention in genomes, whether driven by natural selection or neutral evolution. Applying a comparative approach of LCRs to multiple strains and species is a powerful approach to identify patterns of conservation in these regions. Using this method, we investigate the evolutionary history of LCRs in the genus Plasmodium based on orthologous protein coding genes shared by 11 species and strains from primate and rodent-infecting pathogens. We find multiple lines of evidence in support of natural selection as a major evolutionary force shaping the composition and conservation of LCRs through time and signatures that their evolutionary paths are species specific. Our findings add a comparative analysis perspective to the debate on the evolution of LCRs and harness the power of sequence comparisons to identify potential functionally important LCR candidates.
低复杂度区域（LCRs）是许多基因组共有的一个常见特征，但它们的进化和功能意义在很大程度上仍然未知。在这种不确定性的核心是对调节它们在基因组中保留的机制的理解不足，无论是由自然选择还是中性进化驱动的。将 LCRs 的比较方法应用于多个菌株和物种是识别这些区域保守模式的有力方法。使用这种方法，我们基于来自灵长类动物和啮齿动物感染病原体的 11 个物种和菌株共享的直系蛋白编码基因，研究了疟原虫属中 LCRs 的进化历史。我们发现了多种证据支持自然选择是塑造 LCRs 组成和保守性的主要进化力量，并且它们的进化路径是物种特异性的。我们的研究结果为关于 LCRs 进化的争论增加了一个比较分析的视角，并利用序列比较的力量来识别潜在的功能重要的 LCR 候选者。
