在Saccharomycotina亚族中,基因组因素影响了编码子的使用
bioRxiv : the preprint server for biology
|June 3, 2024
概括
在Saccharomycotina酵母中,代使用偏差显示出对A/T结尾的代的偏好,并受到基因组特征的影响. 在Saccharomycodales中极端偏差与缺乏阿尔金因tRNAs有关.
科学领域:
- * 基因组学和分子生物学:研究菌中子使用模式及其进化驱动因素.
- *生物信息学和机器学习:应用计算方法来根据编码子偏差对酵母序列进行分类.
背景情况:
- * 代码使用偏差,即同义代码的不均选择,影响细胞功能,如翻译和转录稳定性.
- *Saccharomycotina亚属,包括像Saccharomyces cerevisiae和Candida albicans这样的酵母,可以作为研究这些偏差的模型.
- *先前的研究表明,代的使用是由转化选择和中性进化力量塑造的.
研究的目的:
- 调查子使用模式,它们的潜在分子机制,进化驱动因素和Saccharomycotina亚科的基因组相关性.
- 为了确定转化选择在这个真菌群体内对代使用偏差的影响程度.
- 为了确定特定的血统与不寻常的代码子使用,并探索这些模式背后的原因.
主要方法:
- 分析了来自Saccharomycotina 1,051个物种的1,154个菌株的子使用情况.
- 采用机器学习来根据子使用模式对酵母序列进行分类.
- 检查了编码子使用偏差,GC含量,tRNA-ome大小和各种基因组组装指标之间的相关性.
- 研究了基因表达,tRNA序列和Saccharomycodales序列中的密码体进化.
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.
- 的使用模式允许以>90%的准确度对酵母类别进行分类.
- 翻译选择对代码使用偏差的影响受到基因组特征的影响,例如编码序列数和基因组长度.
- 萨卡罗米科达类 (Saccharomycodales) 序列表现出极端的编码器使用偏差,与预测的CGN基因编码器的tRNA缺乏有关,只有AGN编码器可用.
结论:
- *在Saccharomycotina中,Codon使用偏差是由基因组特征和GC偏差所塑造的,这与之前的真菌研究一致.
- * 特定的酵母系表现出极端的代偏好和避免,表明独特的进化压力.
- * 在Saccharomycodales中缺乏阿尔金因tRNA与CGN编码子的功能衰退有关.
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