在Saccharomycotina亚族中,基因组因素影响了编码子的使用
Bryan Zavala1, Lauren Dineen1, Kaitlin J Fisher2,3
1Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis, NC 28081, USA.
G3 (Bethesda, Md.)
|August 30, 2024
概括
在酵母物种之间,真菌密码的使用偏差有很大差异,受基因组特征和tRNA可用性的影响. 在Saccharomycodales极端偏差表明独特的进化压力对密码体选择.
科学领域:
- 基因组学就是基因组学.
- 分子进化分子进化
- 生物信息学是一种生物信息学.
背景情况:
- 代码的使用偏差,同义代码的不统一使用,影响基因表达,并由各种力量塑造.
- 了解真菌,特别是Saccharomycotina亚族中的子使用模式,对于破译进化机制和细胞功能至关重要.
研究的目的:
- 从1,051个Saccharomycotina物种中对1,154个菌株进行编码子使用偏差的表征.
- 研究导致这些偏见的分子机制,进化驱动因素和基因组特征.
- 探索转化选择的影响,并确定谱系特定的编码子使用模式.
主要方法:
- 在各种真菌物种中对子使用模式的比较基因组分析.
- 机器学习算法用于基于codon使用偏差对酵母序列进行分类.
- 分析基因表达,tRNA库和基因组特征 (GC含量,基因组长度,BUSCO计数).
主要成果:
- 观察到对A/T结尾的编码子的一般偏好,与GC含量和tRNA-ome大小相关.
- 的使用偏差允许酵母序列的准确分类>90%.
- 在Saccharomycodales中极端的密码体使用偏差与解码CGN密码体的阿尔金因tRNA缺乏有关.
结论:
- 在Saccharomycotina中的Codon使用偏差是由基因组特征和GC内容以及翻译选择所塑造的.
- 萨卡罗米科达类表现出独特的编码子使用模式,这是由阿尔金因tRNA功能下降所驱动的.
- 超出已知的因素的额外进化力量有助于酵母系中特定的编码子偏好和避免.
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