高分辨率基因组组装揭示黑麦中逆转录转座子介导的着丝粒动力学

IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Congyang Yi, Qian Liu, Congle Zhu, Chang Liu, Chen Zhou, Wanna He, Chunhui Wang, Jing Yuan, Yang Liu, Fangpu Han
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引用次数: 0

摘要

黑麦(Secale cereale)基因组的特点是具有较大的重复区域,包括亚端粒异染色质和反转录转座子优势的着丝粒,这与大多数特征植物基因组中基于卫星重复的着丝粒形成对比。本研究旨在通过高分辨率基因组组装解码这些难以捉摸的区域的结构和进化,重点关注着丝粒动力学和染色质调控。使用PacBio HiFi和纳米孔测序,我们产生了一个染色体尺度的组装,包括三个完整的着丝粒和亚端粒异染色质。我们确定末端串联重复序列阵列是建立与反转录转座子沉积相关的特殊染色质环境的关键决定因素。值得注意的是,黑麦着丝粒表现出一种非常规的表观遗传特征,缺乏传统的激活和抑制标记,但显示出独特的DNA低甲基化模式。这种富含反转录转座子的景观既促进了年轻LTR反转录转座子的整合,也促进了CENH3的募集。跨物种的CENH3 ChIP-seq分析显示,在栽培和野生黑麦世系中,大脑反转录转座子与增强的CENH3负载相关,特别是通过其保守的蛋白酶和整合酶结构域,这表明着丝粒进化存在潜在的正反馈循环。我们的研究结果确立了逆转录转座子作为着丝粒染色质和身份的自主组织者,挑战了卫星依赖着丝粒规范的范式。反转录转座子在维持CENH3招募和促进基因组创新方面的双重作用为着丝粒可塑性提供了机制基础。本研究推进了小麦科作物的功能基因组学研究,为着丝粒工程控制作物减数分裂稳定性和染色体传递开辟了新的途径。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
High-resolution genome assembly reveals retrotransposon-mediated centromere dynamics in rye
The genome of rye, Secale cereale, is distinguished by large repetitive regions including subtelomeric heterochromatin and retrotransposon-dominant centromeres, which contrast with the satellite-repeat-based centromeres in most characterized plant genome assemblies. This study aims to decode the architecture and evolution of these elusive regions through high-resolution genome assembly, with a focus on centromere dynamics and chromatin regulation. Using PacBio HiFi and Nanopore sequencing, we generate a chromosome-scale assembly encompassing three complete centromeres and resolving subtelomeric heterochromatin. We identify terminal tandem repeat arrays as key determinants in establishing specialized chromatin environments linked to retrotransposon deposition. Notably, rye centromeres exhibit an unconventional epigenetic signature depleted of conventional activation and repression marks but displaying unique DNA hypomethylation patterns. This retrotransposon-enriched landscape promotes both the integration of young LTR retrotransposons and the recruitment of CENH3. Cross-species CENH3 ChIP-seq analyses reveal that Cereba retrotransposons are associated with enhanced CENH3 loading in cultivated and wild rye lineages, particularly through their conserved protease and integrase domains, suggesting a potential positive feedback loop for centromere evolution. Our findings establish retrotransposons as autonomous organizers of centromere chromatin and identity in rye, challenging the paradigm of satellite-dependent centromere specification. The dual role of retrotransposons in maintaining CENH3 recruitment while facilitating genomic innovation provides a mechanistic basis for centromere plasticity. This work advances functional genomics of Triticeae crops and opens new avenues for centromere engineering to manipulate meiotic stability and chromosome transmission in crop breeding.
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来源期刊
Genome Biology
Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍: Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.
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