The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees

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外文摘要：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 culti-vated 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 encompass-ing 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 valu-able insights into potential avenues for comprehending tree biology.

外文关键词：

Populuspangenomeswhole-genome duplicationstructural variationgenome evolution

作者：

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、P?r K.Ingvarsson、Jianquan Liu、Tongming Yin、Jing Wang

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作者单位：

Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education,College of Life Sciences,Sichuan University,Chengdu,Sichuan,China

College of Horticulture and Forestry,Tarim University,Alar 843300,China

Umeå Plant Science Centre,Department of Plant Physiology,Umeå University,Umeå,Västerbotten,Sweden

Linnean Centre for Plant Biology,Department of Plant Biology,Uppsala BioCenter,Swedish University of Agricultural Sciences,Uppsala,Sweden

The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China,Nanjing Forestry University,Nanjing,Jiangsu,China

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基金：

National Key Research and Development Program of ChinaNational Key Research and Development Program of ChinaNational Natural Science Foundation of ChinaNational Natural Science Foundation of ChinaFundamental Research Funds for the Central UniversitiesFundamental Research Funds for the Central Universities

项目编号：

2022YFD22012002021YFD220020232371695319715672023SCUNL105SCU2022D003

出版年：

2024

DOI：

10.1016/j.molp.2024.03.009

分子植物(英文版)

中科院上海生命科学研究院植物生理生态所　中国植物生理学会

分子植物(英文版)

CSTPCD

影响因子：0.659

ISSN：1674-2052

年,卷(期)：2024.17(5)