If two related plant species hybridize, their genomes may be combined and duplicated within a single nucleus, thereby forming an allotetraploid. How the emerging plant balances two co‐evolved genomes is still a matter of ongoing research. Here, we focus on satellite DNA (satDNA), the fastest turn‐over sequence class in eukaryotes, aiming to trace its emergence, amplification, and loss during plant speciation and allopolyploidization. As a model, we used Chenopodium quinoa Willd. (quinoa), an allopolyploid crop with 2n  = 4x  = 36 chromosomes. Quinoa originated by hybridization of an unknown female American Chenopodium diploid (AA genome) with an unknown male Old World diploid species (BB genome), dating back 3.3–6.3 million years. Applying short read clustering to quinoa (AABB), C. pallidicaule (AA), and C. suecicum (BB) whole genome shotgun sequences, we classified their repetitive fractions, and identified and characterized seven satDNA families, together with the 5S rDNA model repeat. We show unequal satDNA amplification (two families) and exclusive occurrence (four families) in the AA and BB diploids by read mapping as well as Southern, genomic, and fluorescent in situ hybridization. Whereas the satDNA distributions support C. suecicum as possible parental species, we were able to exclude C. pallidicaule as progenitor due to unique repeat profiles. Using quinoa long reads and scaffolds, we detected only limited evidence of intergenomic homogenization of satDNA after allopolyploidization, but were able to exclude dispersal of 5S rRNA genes between subgenomes. Our results exemplify the complex route of tandem repeat evolution through Chenopodium speciation and allopolyploidization, and may provide sequence targets for the identification of quinoa's progenitors.

中文翻译：

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藜麦（Chenopodium quinoa）的异源四倍体化后的卫星DNA风景揭示了独特的A和B亚基因组。

如果两个相关的植物物种杂交，它们的基因组可以合并并在单个细胞核中复制，从而形成异源四倍体。新兴植物如何平衡两个共同进化的基因组仍在进行中。在这里，我们重点研究卫星DNA（satDNA），这是真核生物中最快的周转序列类别，旨在追踪其在植物物种形成和同种多倍体化过程中的出现，扩增和损失。作为模型，我们使用了藜藜藜。（藜），一种具有2 n  = 4 x  = 36个染色体的同种多倍体作物。藜麦起源于一个未知的女性美国藜的杂交二倍体（AA基因组）和未知的雄性旧世界二倍体物种（BB基因组），距今3.3-630万年。将短读聚类应用于奎奴亚藜（AABB），苍白梭菌（AA）和小穗梭菌（BB）全基因组shot弹枪序列，我们对它们的重复部分进行分类，并鉴定和鉴定了七个satDNA家族，以及5S rDNA模型重复序列。我们通过阅读图谱以及Southern，基因组和荧光原位杂交显示了AA和BB二倍体中不相等的satDNA扩增（两个家族）和唯一出现（四个家族）。尽管satDNA分布可能支持小球藻（C. suecicum）作为可能的亲本物种，但我们能够排除苍白球菌（C. pallidicaule）作为祖细胞，由于独特的重复序列。使用藜麦长读和支架，我们只检测到了异源多倍体化后satDNA基因组同质化的有限证据，但能够排除5S rRNA基因在亚基因组之间的分散。我们的结果例证了通过藜属物种形成和同种多倍体化的串联重复进化的复杂途径，并可能为鉴定藜麦祖细胞提供序列靶标。