北京大学朱玉贤等研究人员合作发现，端粒到端粒的棉花基因组组装揭示着丝粒演化以及与Mutator转座子相关的胚胎发育调控模块。2024年8月15日，国际知名学术期刊《自然—遗传学》在线发表了这一成果。

研究人员展示了近乎完整的端粒到端粒的棉花种Gossypium raimondii基因组。该组装识别了先前组装中的缺口以及方向错误或组装错误的区域，产生了13个着丝粒，并在25个染色体末端发现了端粒。与富含卫星DNA的拟南芥和水稻着丝粒不同，棉花着丝粒缺乏阶段性CENH3核小体定位模式，可能是由长末端重复逆转录转座子侵入进化而来的。

对转座元件的深入表达分析揭示了一种以前未注释的DNA转座子（MuTC01），它与miR2947相互作用，产生反式小干扰RNA（siRNA），其中一个siRNA靶向新演化的LEC2（LEC2b），以产生阶段性siRNA。系统的基因组编辑实验表明，这个由miR2947–MuTC01–LEC2b组成的三方模块控制了棉花及其近亲棉族植物中特有的复杂折叠胚胎的形态发生。该研究揭示了高等植物中基于反式siRNA的三方调控通路对胚胎发育的控制机制。

据了解，完整基因组的组装可以揭示草图序列中缺失的功能性遗传元件。

附：英文原文

Title: A telomere-to-telomere cotton genome assembly reveals centromere evolution and a Mutator transposon-linked module regulating embryo development

Author: Huang, Gai, Bao, Zhigui, Feng, Li, Zhai, Jixian, Wendel, Jonathan F., Cao, Xiaofeng, Zhu, Yuxian

Issue&Volume: 2024-08-15

Abstract: 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.

DOI: 10.1038/s41588-024-01877-6

Source: https://www.nature.com/articles/s41588-024-01877-6