Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China.
Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
Genome Biol. 2021 Nov 30;22(1):326. doi: 10.1186/s13059-021-02549-y.
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.
多倍体，尤其是异源多倍体，通过杂交和全基因组加倍（WGD）融合不同的基因组，是植物物种形成的主要途径。亲本基因组（亚基因组）之间的复制常常导致一个亚基因组相对于其他亚基因组（多个）占优势，从而导致基因含量和表达的亚基因组不对称。多倍体小麦是异源多倍体，大多数基因存在两个（四倍体）或三个（六倍体）功能副本，通常表现出亚基因组表达的不对称性。目前尚不清楚在翻译过程中是否存在类似的亚基因组不对称。我们旨在解决这个关键的生物学问题，并探讨导致亚基因组翻译不对称的主要因素。
在这里，我们获得了第一个四倍体小麦翻译组，并揭示了亚基因组表达的不对称性存在于翻译水平。我们进一步进行体内 RNA 结构分析，获得了小麦 RNA 结构图谱，并发现 mRNA 结构对翻译有很强的影响，独立于 GC 含量。我们发现了 RNA 结构在亚基因组翻译不对称性中以前未被描述的贡献。我们在两个四倍体小麦亚基因组的转录本中发现了 3564 个单核苷酸变异（SNVs），这些变异导致了大量的 RNA 结构差异。这些 SNVs在硬粒小麦品种内高度保守，但在栽培和野生二粒小麦中则存在差异。
我们成功地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的重要调节因子。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。
