伪基因充当检测 prokaryotic pangenomes 中选择的中立参考
Gavin M Douglas1,2, B Jesse Shapiro3,4,5
1Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada. gavin.douglas@mcgill.ca.
Nature ecology & evolution
|January 4, 2024
概括
伪基因有助于揭示细菌的进化. 完整和非功能性基因的比较表明,细菌泛基体中的许多罕见辅助基因提供了适应性的好处,而不仅仅是中性或有害的影响.
科学领域:
- 微生物基因组学 微生物基因组学
- 进化生物学是进化的生物学.
- 细菌遗传学 细菌遗传学
背景情况:
- 细菌基因组包括辅助基因,但驱动它们分歧的力量 (遗传漂移与选择) 是有争议的.
- 罕见的基因,包括单子基因,构成了庞基因组的很大一部分,其适应性,有害性或中性作用尚不清楚.
- 之前的模型将有效种群大小 (Ne) 与泛基因组大小联系起来,已经通过中性和适应性镜头进行了解释.
研究的目的:
- 区分细菌泛基因组进化的中性和适应性模型.
- 为了研究塑造细菌罕见辅助基因含量的进化力量.
- 建立一种方法来推断罕见基因的适应性效应,使用伪基因作为中立参考.
主要方法:
- 利用伪基因作为一个中立的进化标志物来评估罕见基因的作用.
- 在细菌基因组中分析了基因家族伪基因和完整的基因拷贝数.
- 定义并计算了668种 prokaryotic 中单个完整基因与单个伪基因 (si/sp) 的比例.
主要成果:
- 大多数功能类别显示,当基因家族中只有一个完整的副本存在时,罕见的伪基因被耗尽.
- 可转移的元素被增添了伪基因,表明中性或有害的角色.
- 单体完整与单体伪基因比率 (si/sp) 表明了多种不同 prokaryotes 的许多罕见辅助基因的适应性值.
结论:
- 伪基因分析提供了一种强大的方法来推断细菌基因组中的进化力.
- 罕见的辅助基因不仅是中性的或有害的;许多基因赋予了适应性的优势.
- 这项研究完善了我们对细菌基因组演化的理解,以及辅助基因含量的重要性.
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