Polyploidy, especially allopolyploidy, which entails merging divergent genomes via hybridization and whole-genome duplication (WGD), is a major route to speciation in plants. The duplication among the parental genomes (subgenomes) often leads to one subgenome becoming dominant over the other(s), resulting in subgenome asymmetry in gene content and expression. Polyploid wheats are allopolyploids with most genes present in two (tetraploid) or three (hexaploid) functional copies, which commonly show subgenome expression asymmetry. It is unknown whether a similar subgenome asymmetry exists during translation. We aim to address this key biological question and explore the major contributing factors to subgenome translation asymmetry. Here, we obtain the first tetraploid wheat translatome and reveal that subgenome expression asymmetry exists at the translational level. We further perform in vivo RNA structure profiling to obtain the wheat RNA structure landscape and find that mRNA structure has a strong impact on translation, independent of GC content. We discover a previously uncharacterized contribution of RNA structure in subgenome translation asymmetry. We identify 3564 single-nucleotide variations (SNVs) across the transcriptomes between the two tetraploid wheat subgenomes, which induce large RNA structure disparities. These SNVs are highly conserved within durum wheat cultivars but are divergent in both domesticated and wild emmer wheat. We successfully determine both the translatome and in vivo RNA structurome in tetraploid wheat. We reveal that RNA structure serves as an important modulator of translational subgenome expression asymmetry in polyploids. Our work provides a new perspective for molecular breeding of major polyploid crops.

中文翻译：

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小麦体内RNA结构景观揭示了RNA结构在调节翻译亚基因组表达不对称性中的普遍作用


多倍体，特别是异源多倍体，需要通过杂交和全基因组复制（WGD）合并不同的基因组，是植物物种形成的主要途径。亲本基因组（亚基因组）之间的重复通常会导致一个亚基因组相对于其他亚基因组占主导地位，从而导致基因内容和表达的亚基因组不对称。多倍体小麦是异源多倍体，大多数基因以两个（四倍体）或三个（六倍体）功能拷贝存在，通常表现出亚基因组表达不对称。目前尚不清楚翻译过程中是否存在类似的亚基因组不对称性。我们的目标是解决这个关键的生物学问题，并探索亚基因组翻译不对称的主要影响因素。在这里，我们获得了第一个四倍体小麦翻译组，并揭示了翻译水平上存在亚基因组表达不对称性。我们进一步进行体内 RNA 结构分析，以获得小麦 RNA 结构景观，并发现 mRNA 结构对翻译有很大影响，与 GC 含量无关。我们发现了 RNA 结构在亚基因组翻译不对称性中的一个先前未表征的贡献。我们在两个四倍体小麦亚基因组之间的转录组中发现了 3564 个单核苷酸变异 (SNV)，这些变异导致了巨大的 RNA 结构差异。这些 SNV 在硬粒小麦品种中高度保守，但在驯化和野生二粒小麦中存在差异。我们成功确定了四倍体小麦的翻译组和体内 RNA 结构组。我们揭示了 RNA 结构是多倍体中翻译亚基因组表达不对称性的重要调节剂。我们的工作为主要多倍体作物的分子育种提供了新的视角。