The speciation and fast global domestication of bread wheat have made a great impact on three subgenomes of bread wheat. DNA base composition is an essential genome feature, which follows the individual-strand base equality rule and [AT]-increase pattern at the genome, chromosome, and polymorphic site levels among thousands of species. Systematic analyses on base compositions of bread wheat and its wild progenitors could facilitate further understanding of the evolutionary pattern of genome/subgenome-wide base composition of allopolyploid species and its potential causes. Genome/subgenome-wide base-composition patterns were investigated by using the data of polymorphic site in 93 accessions from worldwide populations of bread wheat, its diploid and tetraploid progenitors, and their corresponding reference genome sequences. Individual-strand base equality rule and [AT]-increase pattern remain in recently formed hexaploid species bread wheat at the genome, subgenome, chromosome, and polymorphic site levels. However, D subgenome showed the fastest [AT]-increase across polymorphic site from Aegilops tauschii to bread wheat than that on A and B subgenomes from wild emmer to bread wheat. The fastest [AT]-increase could be detected almost all chromosome windows on D subgenome, suggesting different mechanisms between D and other two subgenomes. Interestingly, the [AT]-increase is mainly contributed by intergenic regions at non-selective sweeps, especially the fastest [AT]-increase of D subgenome. Further transition frequency and sequence context analysis indicated that three subgenomes shared same mutation type, but D subgenome owns the highest mutation rate on high-frequency mutation type. The highest mutation rate on D subgenome was further confirmed by using a bread-wheat-private SNP set. The exploration of loci/genes related to the [AT] value of D subgenome suggests the fastest [AT]-increase of D subgenome could be involved in DNA repair systems distributed on three subgenomes of bread wheat. The highest mutation rate is detected on D subgenome of bread wheat during domestication after allopolyploidization, leading to the fastest [AT]-increase pattern of D subgenome. The phenomenon may come from the joint action of multiple repair systems inherited from its wild progenitors.

中文翻译：

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面包小麦三个亚基因组之间的不同核苷酸模式及其异源多倍化后驯化过程中的潜在起源


面包小麦的物种形成和全球快速驯化对面包小麦的三个亚基因组产生了巨大影响。 DNA碱基组成是一个重要的基因组特征，在数千个物种的基因组、染色体和多态性位点水平上遵循单链碱基平等规则和[AT]增加模式。对面包小麦及其野生祖先的碱基组成进行系统分析有助于进一步了解异源多倍体物种的基因组/亚基因组碱基组成的进化模式及其潜在原因。利用来自全球面包小麦群体、其二倍体和四倍体祖先的 93 个种质的多态性位点数据及其相应的参考基因组序列，研究了基因组/亚基因组范围内的碱基组成模式。最近形成的六倍体物种面包小麦在基因组、亚基因组、染色体和多态性位点水平上仍然保留着单链碱基平等规则和[AT]增加模式。然而，从节节山羊草到面包小麦的多态性位点上，D 亚基因组的 [AT] 增加最快，而 A 和 B 亚基因组从野生二粒小麦到面包小麦的多态性位点增加最快。 D 亚基因组上的几乎所有染色体窗口都可以检测到最快的 [AT] 增加，这表明 D 亚基因组和其他两个亚基因组之间存在不同的机制。有趣的是，[AT]增加主要是由非选择性扫描时的基因间区域贡献的，尤其是D亚基因组中最快的[AT]增加。进一步的转换频率和序列上下文分析表明，三个亚基因组具有相同的突变类型，但D亚基因组在高频突变类型上的突变率最高。 通过使用面包小麦专用 SNP 集进一步证实了 D 亚基因组的最高突变率。对与 D 亚基因组 [AT] 值相关的基因座/基因的探索表明，D 亚基因组 [AT] 增加最快可能涉及分布在面包小麦三个亚基因组上的 DNA 修复系统。异源多倍体驯化过程中，面包小麦D亚基因组突变率最高，导致D亚基因组[AT]增加最快。这种现象可能来自于其野生祖先遗传的多个修复系统的联合作用。