杨树的超级泛基因组揭示了广泛分布的林木适应和多样化的基因组面貌。

IF 17.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Molecular Plant Pub Date : 2024-05-06 Epub Date: 2024-03-13 DOI:10.1016/j.molp.2024.03.009
Tingting Shi, Xinxin Zhang, Yukang Hou, Changfu Jia, Xuming Dan, Yulin Zhang, Yuanzhong Jiang, Qiang Lai, Jiajun Feng, Jianju Feng, Tao Ma, Jiali Wu, Shuyu Liu, Lei Zhang, Zhiqin Long, Liyang Chen, Nathaniel R Street, Pär K Ingvarsson, Jianquan Liu, Tongming Yin, Jing Wang
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引用次数: 0

摘要

了解基因组进化和适应性创新之间的内在机制和联系是进化研究的一个关键目标。杨树是世界上分布最广、栽培最多的树种之一,表现出广泛的表型多样性和环境适应性。在这项研究中,我们提出了一个由 19 个杨树基因组组成的属级超级泛基因组,揭示了私有基因在促进当地环境和气候适应方面可能发挥的关键作用。通过整合泛基因组与转录组、甲基组和染色质可及性图谱,我们揭示了泛基因和重复基因的进化轨迹与调控和表观遗传结构的局部基因组景观密切相关,特别是基因体区域的CG甲基化。通过进一步的比较基因组分析,我们发现了跨物种的 142,202 个结构变异(SVs),这些变异与大量基因相交,并对表型和适应性差异做出了重大贡献。我们通过实验验证了一个影响 CUC2 基因表达的 ∼180 bp 存在/不存在变异,该基因对叶片锯齿的形成至关重要。最后,我们开发了一个用户友好型网络工具,其中包含与杨树超级泛基因组相关的多组学资源 (http://www.populus-superpangenome.com/)。总之,目前开创性的林木超级泛基因组资源不仅有助于推进这一全球重要树属的育种工作,而且还为了解林木生物学的潜在途径提供了宝贵的见解。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees.

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.

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来源期刊
Molecular Plant
Molecular Plant 植物科学-生化与分子生物学
CiteScore
37.60
自引率
2.20%
发文量
1784
审稿时长
1 months
期刊介绍: Molecular Plant is dedicated to serving the plant science community by publishing novel and exciting findings with high significance in plant biology. The journal focuses broadly on cellular biology, physiology, biochemistry, molecular biology, genetics, development, plant-microbe interaction, genomics, bioinformatics, and molecular evolution. Molecular Plant publishes original research articles, reviews, Correspondence, and Spotlights on the most important developments in plant biology.
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