Dramatic changes occasionally occur in intergenic regions leading to genomic alterations during speciation and will consequently obscure the ancestral species that have contributed to the formation of allopolyploid organisms. The S genome of five species of section Sitopsis of genus Aegilops is considered to be an origin of B-genome in cultivated tetraploid and hexaploid wheat species, although its actual donor is still unclear. Here, we attempted to elucidate phylogenetic relationship among Sitopsis species by performing RNA sequencing of the coding regions of each chromosome. Thus, genome-wide polymorphisms were extensively analyzed in 19 accessions of the Sitopsis species in reference to the tetraploid and hexaploid wheat B genome sequences and consequently were efficiently anchored to the B-genome chromosomes. The results of our genome-wide exon sequencing and resultant phylogenetic analysis indicate that Ae. speltoides is likely to be the direct donor of all chromosomes of the wheat B genome. Our results also indicate that the genome differentiation during wheat allopolyploidization from S to B proceeds at different speeds over the chromosomes rather than at constant rate and recombination could be a factor determining the speed. This observation is potentially generalized to genome differentiation during plant allopolyploid evolution.

中文翻译：

---

通过对山羊草科 Sitopsis 种叶转录物的 RNA 测序分析推断小麦 B 基因组染色体的起源。

基因间区域偶尔会发生巨大的变化，导致物种形成过程中的基因组改变，从而掩盖有助于异源多倍体生物形成的祖先物种。山羊草属的五个种的S基因组被认为是栽培四倍体和六倍体小麦物种中B基因组的起源，尽管其实际供体仍不清楚。在这里，我们试图通过对每条染色体的编码区进行 RNA 测序来阐明 Sitopsis 物种之间的系统发育关系。因此，参考四倍体和六倍体小麦 B 基因组序列，对 19 个 Sitopsis 物种的全基因组多态性进行了广泛分析，并因此有效地锚定到 B 基因组染色体上。我们的全基因组外显子测序和由此产生的系统发育分析的结果表明，Ae。speltoides 很可能是小麦 B 基因组所有染色体的直接供体。我们的结果还表明，小麦异源多倍化过程中从 S 到 B 的基因组分化在染色体上以不同的速度进行，而不是以恒定的速度进行，重组可能是决定速度的一个因素。这一观察结果可能推广到植物异源多倍体进化过程中的基因组分化。