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

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 Par K.Ingvarsson Jianquan Liu Tongming Yin Jing Wang 

机构地区：[1]Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education,College of Life Sciences,Sichuan University,Chengdu,Sichuan,China [2]College of Horticulture and Forestry,Tarim University,Alar 843300,China [3]Umea Plant Science Centre,Department of Plant Physiology,Umea University,Umea,Vasterbotten,Sweden [4]Linnean Centre for Plant Biology,Department of Plant Biology,Uppsala BioCenter,Swedish University of Agricultural Sciences,Uppsala,Sweden [5]The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China,Nanjing Forestry University,Nanjing,Jiangsu,China

出　　处：《Molecular Plant》2024年第5期725-746,共22页分子植物（英文版）

基　　金：supported by the National Key Research and Development Program of China(2022YFD2201200 to J.W.and 2021YFD2200202 to T.Y.and J.L.);National Natural Science Foundation of China(32371695 and 31971567 to J.W.);Fundamental Research Funds for the Central Universities(2023SCUNL105 and SCU2022D003 to J.W.).

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 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 142202 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.

关 键 词：POPULUS pangenomes whole-genome duplication structural variation genome evolution 

分 类 号：Q94[生物学—植物学]