核苷酸取代在分子进化中发挥了重要作用,了解它们的动力学将有助于基因研究。与确定的DNA序列相关的研究持续了几十年,直到全基因组测序出现。紫外线辐射(UVR)可以在短时间内产生碱基变化和其他遗传变异,因此,从基因组角度探索UVR引起的突变更有意义。在这项研究中选择单核核子菌株WT583作为实验材料,因为它可以在PDA平板上自发产生大量的oidia,来自oidia的单核子与它们的母亲单核子具有相同的基因型。暴露于紫外线辐射后,100个随机选择的突变体,用WT583作为参考基因组,被送去进行基因组测序。BWA,samtools,使用GATK软件进行SNP呼叫,和R包CMplot用于可视化SNP在参考基因组的重叠群上的分布。此外,使用基于k-mer的方法检测DNA片段缺失。此外,非同义基因进行了功能注释。分析了总共3707个单碱基取代和228个串联突变。紧邻的碱基对腺嘌呤和胞嘧啶的突变频率显示出不同的影响。对于腺嘌呤,即时5'侧和3'侧碱基的总体效果是T>A>C>G和A>T>G>C,分别;对于胞嘧啶,即时5'侧和3'侧碱基的总体效果是T>C>A>G和C>T>A>G,分别。关于串联突变,双跃迁的突变频率,双重转换,3\'侧过渡,和5'侧过渡分别为131、8、72和17。具有高突变频率的3'侧过渡具有共同的特征,他们在A→T或T→A的5'侧进行颠换,没有共价键变化,这表明串联基序的序列背景可能与其突变频率有关。总的来说,3707个突变位点非随机分布在参考基因组的重叠群上。此外,腺嘌呤3'侧的嘧啶促进了其颠换频率,UVR在enoki基因组中以低频率产生超过200bp的DNA片段缺失。具有非同义突变的基因的功能注释表明UVR可以在短时间内产生丰富的突变。
Nucleotide substitutions have played an important role in molecular evolution, and understanding their dynamics would contribute to genetic studies. Related research with defined DNA sequences lasted for decades until whole-genome sequencing arose. UV radiation (UVR) can generate base changes and other genetic variations in a short period of time, so it would be more meaningful to explore mutations caused by UVR from a genomic perspective. The monokaryon enoki strain WT583 was selected as the experimental material in this study because it can spontaneously produce large amounts of oidia on PDA plates, and the monokaryons originating from oidia have the same genotype as their mother monokaryon. After exposure to UV radiation, 100 randomly selected mutants, with WT583 as the reference genome, were sent for genome sequencing. BWA, samtools, and GATK software were employed for SNP calling, and the R package CMplot was used to visualize the distribution of the SNPs on the contigs of the reference genome. Furthermore, a k-mer-based method was used to detect DNA fragment deletion. Moreover, the non-synonymous genes were functionally annotated. A total of 3707 single-base substitutions and 228 tandem mutations were analyzed. The immediate adjacent bases showed different effects on the mutation frequencies of adenine and cytosine. For adenine, the overall effects of the immediate 5\'-side and 3\'-side bases were T > A > C > G and A > T > G > C, respectively; for cytosine, the overall effects of the immediate 5\'-side and 3\'-side bases were T > C > A > G and C > T > A > G, respectively. Regarding tandem mutations, the mutation frequencies of double-transition, double-transversion, 3\'-side transition, and 5\'-side transition were 131, 8, 72, and 17, respectively. Transitions at the 3\'-side with a high mutation frequency shared a common feature, where they held transversions at the 5\'-side of A→T or T→A without covalent bond changes, suggesting that the sequence context of tandem motifs might be related to their mutation frequency. In total, 3707 mutation sites were non-randomly distributed on the contigs of the reference genome. In addition, pyrimidines at the 3\'-side of adenine promoted its transversion frequency, and UVR generated DNA fragment deletions over 200 bp with a low frequency in the enoki genome. The functional annotation of the genes with non-synonymous mutation indicated that UVR could produce abundant mutations in a short period of time.