Triticum and Aegilops diploid species have morphological and genetic diversity and are crucial genetic resources for wheat breeding. According to the chromosomal pairing-affinity of these species, their genome nomenclatures have been defined. However, evaluations of genome differentiation based on genome-wide nucleotide variations are still limited, especially in the three genomes of the genus Aegilops: Ae. caudata L. (CC genome), Ae. comosa Sibth. et Sm. (MM genome), and Ae. uniaristata Vis. (NN genome). To reveal the genome differentiation of these diploid species, we first performed RNA-seq-based polymorphic analyses for C, M, and N genomes, and then expanded the analysis to include the 12 diploid species of Triticum and Aegilops. Genetic divergence of the exon regions throughout the entire chromosomes in the M and N genomes was larger than that between A- and Am-genomes. Ae. caudata had the second highest genetic diversity following Ae. speltoides, the putative B genome donor of common wheat. In the phylogenetic trees derived from the nuclear and chloroplast genome-wide polymorphism data, the C, D, M, N, U, and S genome species were connected with short internal branches, suggesting that these diploid species emerged during a relatively short period in the evolutionary process. The highly consistent nuclear and chloroplast phylogenetic topologies indicated that nuclear and chloroplast genomes of the diploid Triticum and Aegilops species coevolved after their diversification into each genome, accounting for most of the genome differentiation among the diploid species. RNA-sequencing-based analyses successfully evaluated genome differentiation among the diploid Triticum and Aegilops species and supported the chromosome-pairing-based genome nomenclature system, except for the position of Ae. speltoides. Phylogenomic and epigenetic analyses of intergenic and centromeric regions could be essential for clarifying the mechanisms behind this inconsistency.

中文翻译：

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在整个同源基因座通过全基因组多态性的RNA基于测序的调查赋予二倍体基因组分化小麦和山羊草

小麦和埃格勒克二倍体物种具有形态和遗传多样性，是小麦育种的重要遗传资源。根据这些物种的染色体配对亲和力，已经定义了它们的基因组命名法。但是，基于全基因组核苷酸变异的基因组分化的评估仍然有限，特别是在埃及埃格勒菌属（Aegilops）：Ae的三个基因组中。caudata L.（CC基因组），ae。科摩萨·锡伯斯。等。（MM基因组）和Ae。Uniaristata Vis。（NN基因组）。为了揭示这些二倍体物种的基因组分化，我们首先对C，M和N基因组进行了基于RNA-seq的多态性分析，然后将分析范围扩大到包括Triticum和Aegilops的12个二倍体物种。在M和N基因组的整个染色体上，外显子区域的遗传差异大于A基因组和Am基因组之间的差异。e caudata具有仅次于Ae的第二高的遗传多样性。speltoides，普通小麦的推定B基因组供体。在从核和叶绿体全基因组多态性数据获得的系统发育树中，C，D，M，N，U和S基因组物种与较短的内部分支相关，这表明这些二倍体物种在相对较短的时间内出现。进化过程。高度一致的核和叶绿体系统发生拓扑学表明，二倍体小麦和埃吉洛普斯物种的核和叶绿体基因组在多样化进入每个基因组后共同进化，这解释了二倍体物种之间的大多数基因组分化。基于RNA测序的分析成功地评估了二倍体小麦和埃科植物的基因组分化，并支持基于染色体配对的基因组命名系统，但Ae的位置除外。speltoides。基因间和着丝粒区域的系统遗传学和表观遗传学分析对于阐明这种不一致背后的机制可能至关重要。