State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
Institute for Advanced Studies, Wuhan University, Wuhan, China.
Nat Genet. 2024 Sep;56(9):1953-1963. doi: 10.1038/s41588-024-01877-6. Epub 2024 Aug 15.
Assembly of complete genomes can reveal functional genetic elements missing from draft sequences. Here we present the near-complete telomere-to-telomere and contiguous genome of the cotton species Gossypium raimondii. Our assembly identified gaps and misoriented or misassembled regions in previous assemblies and produced 13 centromeres, with 25 chromosomal ends having telomeres. In contrast to satellite-rich Arabidopsis and rice centromeres, cotton centromeres lack phased CENH3 nucleosome positioning patterns and probably evolved by invasion from long terminal repeat retrotransposons. In-depth expression profiling of transposable elements revealed a previously unannotated DNA transposon (MuTC01) that interacts with miR2947 to produce trans-acting small interfering RNAs (siRNAs), one of which targets the newly evolved LEC2 (LEC2b) to produce phased siRNAs. Systematic genome editing experiments revealed that this tripartite module, miR2947-MuTC01-LEC2b, controls the morphogenesis of complex folded embryos characteristic of Gossypium and its close relatives in the cotton tribe. Our study reveals a trans-acting siRNA-based tripartite regulatory pathway for embryo development in higher plants.
组装完整的基因组可以揭示从草案序列中缺失的功能遗传元件。在这里，我们呈现了棉花物种陆地棉近乎完整的端粒到端粒和连续的基因组。我们的组装确定了之前组装中的缺口和错位或组装错误的区域，并生成了 13 个着丝粒，其中 25 个染色体末端具有端粒。与富含卫星的拟南芥和水稻着丝粒不同，棉花着丝粒缺乏相分离的 CENH3 核小体定位模式，可能是由长末端重复逆转录转座子的入侵而进化而来的。对转座元件的深入表达谱分析揭示了一个以前未注释的 DNA 转座子（MuTC01），它与 miR2947 相互作用产生反式作用的小干扰 RNA（siRNA），其中一个靶向新进化的 LEC2（LEC2b）产生相分离的 siRNA。系统的基因组编辑实验表明，这个三分体模块 miR2947-MuTC01-LEC2b 控制了棉花及其棉族近缘种复杂折叠胚胎形态发生。我们的研究揭示了一种基于反式作用 siRNA 的高等植物胚胎发育的三分体调控途径。
