Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
Institute of Biology, Martin-Luther-Universität Halle-Wittenberg, 06120, Halle (Saale), Germany.
Plant J. 2020 Jul;103(1):32-52. doi: 10.1111/tpj.14705. Epub 2020 Mar 23.
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.
如果两个相关的植物物种杂交，它们的基因组可能在单个细胞核内组合和复制，从而形成异源四倍体。新形成的植物如何平衡两个共同进化的基因组仍然是一个正在进行的研究课题。在这里，我们专注于卫星 DNA（satDNA），这是真核生物中周转最快的序列类别，旨在追踪其在植物物种形成和异源多倍体形成过程中的出现、扩增和丢失。作为一个模型，我们使用了 Chenopodium quinoa Willd.（藜麦），一种异源多倍体作物，其染色体数为 2n = 4x = 36。藜麦起源于一个未知的美洲二倍体 Chenopodium 种（AA 基因组）与一个未知的旧世界二倍体种（BB 基因组）的杂交，距今已有 330-630 万年。我们应用短读聚类方法对藜麦（AABB）、C. pallidicaule（AA）和 C. suecicum（BB）的全基因组鸟枪法序列进行分类，鉴定并描述了七个 satDNA 家族，以及 5S rDNA 模型重复序列。通过读映射以及 Southern、基因组和荧光原位杂交，我们显示了在 AA 和 BB 二倍体中 satDNA 的不均匀扩增（两个家族）和特有发生（四个家族）。虽然 satDNA 的分布支持 C. suecicum 作为可能的亲本物种，但由于独特的重复图谱，我们能够排除 C. pallidicaule 作为祖先物种。使用藜麦的长读和支架，我们在异源多倍体化后仅检测到 satDNA 种间同质化的有限证据，但能够排除 5S rRNA 基因在亚基因组之间的扩散。我们的结果例证了串联重复通过 Chenopodium 物种形成和异源多倍体化的复杂进化途径，并可能为鉴定藜麦的祖先提供序列靶标。
