The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees. Shi, T., Zhang, X., Hou, Y., Jia, C., Dan, X., Zhang, Y., Jiang, Y., Lai, Q., Feng, J., Feng, J., Ma, T., Wu, J., Liu, S., Zhang, L., Long, Z., Chen, L., Street, N. R., Ingvarsson, P. K., Liu, J., Yin, T., & Wang, J. Molecular Plant, 17(5):725–746, May, 2024. Publisher: Elsevier![The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex \textlessh2\textgreaterAbstract\textless/h2\textgreater\textlessp\textgreaterUnderstanding 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.\textless/p\textgreater
@article{shi_super-pangenome_2024,
title = {The super-pangenome of {Populus} unveils genomic facets for its adaptation and diversification in widespread forest trees},
volume = {17},
issn = {1674-2052},
url = {https://www.cell.com/molecular-plant/abstract/S1674-2052(24)00082-0},
doi = {10.1016/j.molp.2024.03.009},
abstract = {{\textless}h2{\textgreater}Abstract{\textless}/h2{\textgreater}{\textless}p{\textgreater}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 \textit{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 \textit{CUC2} gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the \textit{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.{\textless}/p{\textgreater}},
language = {English},
number = {5},
urldate = {2024-05-10},
journal = {Molecular Plant},
author = {Shi, Tingting and Zhang, Xinxin and Hou, Yukang and Jia, Changfu and Dan, Xuming and Zhang, Yulin and Jiang, Yuanzhong and Lai, Qiang and Feng, Jiajun and Feng, Jianju and Ma, Tao and Wu, Jiali and Liu, Shuyu and Zhang, Lei and Long, Zhiqin and Chen, Liyang and Street, Nathaniel R. and Ingvarsson, Pär K. and Liu, Jianquan and Yin, Tongming and Wang, Jing},
month = may,
year = {2024},
pmid = {38486452},
note = {Publisher: Elsevier},
keywords = {genome evolution, pan-genomes, structural variation, whole genome duplication},
pages = {725--746},
}
Downloads: 0
{"_id":"FcFQFe5P2sxSXrED6","bibbaseid":"shi-zhang-hou-jia-dan-zhang-jiang-lai-etal-thesuperpangenomeofpopulusunveilsgenomicfacetsforitsadaptationanddiversificationinwidespreadforesttrees-2024","author_short":["Shi, T.","Zhang, X.","Hou, Y.","Jia, C.","Dan, X.","Zhang, Y.","Jiang, Y.","Lai, Q.","Feng, J.","Feng, J.","Ma, T.","Wu, J.","Liu, S.","Zhang, L.","Long, Z.","Chen, L.","Street, N. R.","Ingvarsson, P. K.","Liu, J.","Yin, T.","Wang, J."],"bibdata":{"bibtype":"article","type":"article","title":"The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees","volume":"17","issn":"1674-2052","url":"https://www.cell.com/molecular-plant/abstract/S1674-2052(24)00082-0","doi":"10.1016/j.molp.2024.03.009","abstract":"\\textlessh2\\textgreaterAbstract\\textless/h2\\textgreater\\textlessp\\textgreaterUnderstanding 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 <i>Populus</i> 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 <i>CUC2</i> gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the <i>Populus</i> 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.\\textless/p\\textgreater","language":"English","number":"5","urldate":"2024-05-10","journal":"Molecular Plant","author":[{"propositions":[],"lastnames":["Shi"],"firstnames":["Tingting"],"suffixes":[]},{"propositions":[],"lastnames":["Zhang"],"firstnames":["Xinxin"],"suffixes":[]},{"propositions":[],"lastnames":["Hou"],"firstnames":["Yukang"],"suffixes":[]},{"propositions":[],"lastnames":["Jia"],"firstnames":["Changfu"],"suffixes":[]},{"propositions":[],"lastnames":["Dan"],"firstnames":["Xuming"],"suffixes":[]},{"propositions":[],"lastnames":["Zhang"],"firstnames":["Yulin"],"suffixes":[]},{"propositions":[],"lastnames":["Jiang"],"firstnames":["Yuanzhong"],"suffixes":[]},{"propositions":[],"lastnames":["Lai"],"firstnames":["Qiang"],"suffixes":[]},{"propositions":[],"lastnames":["Feng"],"firstnames":["Jiajun"],"suffixes":[]},{"propositions":[],"lastnames":["Feng"],"firstnames":["Jianju"],"suffixes":[]},{"propositions":[],"lastnames":["Ma"],"firstnames":["Tao"],"suffixes":[]},{"propositions":[],"lastnames":["Wu"],"firstnames":["Jiali"],"suffixes":[]},{"propositions":[],"lastnames":["Liu"],"firstnames":["Shuyu"],"suffixes":[]},{"propositions":[],"lastnames":["Zhang"],"firstnames":["Lei"],"suffixes":[]},{"propositions":[],"lastnames":["Long"],"firstnames":["Zhiqin"],"suffixes":[]},{"propositions":[],"lastnames":["Chen"],"firstnames":["Liyang"],"suffixes":[]},{"propositions":[],"lastnames":["Street"],"firstnames":["Nathaniel","R."],"suffixes":[]},{"propositions":[],"lastnames":["Ingvarsson"],"firstnames":["Pär","K."],"suffixes":[]},{"propositions":[],"lastnames":["Liu"],"firstnames":["Jianquan"],"suffixes":[]},{"propositions":[],"lastnames":["Yin"],"firstnames":["Tongming"],"suffixes":[]},{"propositions":[],"lastnames":["Wang"],"firstnames":["Jing"],"suffixes":[]}],"month":"May","year":"2024","pmid":"38486452","note":"Publisher: Elsevier","keywords":"genome evolution, pan-genomes, structural variation, whole genome duplication","pages":"725–746","bibtex":"@article{shi_super-pangenome_2024,\n\ttitle = {The super-pangenome of {Populus} unveils genomic facets for its adaptation and diversification in widespread forest trees},\n\tvolume = {17},\n\tissn = {1674-2052},\n\turl = {https://www.cell.com/molecular-plant/abstract/S1674-2052(24)00082-0},\n\tdoi = {10.1016/j.molp.2024.03.009},\n\tabstract = {{\\textless}h2{\\textgreater}Abstract{\\textless}/h2{\\textgreater}{\\textless}p{\\textgreater}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 \\textit{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 \\textit{CUC2} gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the \\textit{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.{\\textless}/p{\\textgreater}},\n\tlanguage = {English},\n\tnumber = {5},\n\turldate = {2024-05-10},\n\tjournal = {Molecular Plant},\n\tauthor = {Shi, Tingting and Zhang, Xinxin and Hou, Yukang and Jia, Changfu and Dan, Xuming and Zhang, Yulin and Jiang, Yuanzhong and Lai, Qiang and Feng, Jiajun and Feng, Jianju and Ma, Tao and Wu, Jiali and Liu, Shuyu and Zhang, Lei and Long, Zhiqin and Chen, Liyang and Street, Nathaniel R. and Ingvarsson, Pär K. and Liu, Jianquan and Yin, Tongming and Wang, Jing},\n\tmonth = may,\n\tyear = {2024},\n\tpmid = {38486452},\n\tnote = {Publisher: Elsevier},\n\tkeywords = {genome evolution, pan-genomes, structural variation, whole genome duplication},\n\tpages = {725--746},\n}\n\n\n\n\n\n\n\n","author_short":["Shi, T.","Zhang, X.","Hou, Y.","Jia, C.","Dan, X.","Zhang, Y.","Jiang, Y.","Lai, Q.","Feng, J.","Feng, J.","Ma, T.","Wu, J.","Liu, S.","Zhang, L.","Long, Z.","Chen, L.","Street, N. R.","Ingvarsson, P. K.","Liu, J.","Yin, T.","Wang, J."],"key":"shi_super-pangenome_2024","id":"shi_super-pangenome_2024","bibbaseid":"shi-zhang-hou-jia-dan-zhang-jiang-lai-etal-thesuperpangenomeofpopulusunveilsgenomicfacetsforitsadaptationanddiversificationinwidespreadforesttrees-2024","role":"author","urls":{"Paper":"https://www.cell.com/molecular-plant/abstract/S1674-2052(24)00082-0"},"keyword":["genome evolution","pan-genomes","structural variation","whole genome duplication"],"metadata":{"authorlinks":{}}},"bibtype":"article","biburl":"https://bibbase.org/zotero/upscpub","dataSources":["9cGcv2t8pRzC92kzs"],"keywords":["genome evolution","pan-genomes","structural variation","whole genome duplication"],"search_terms":["super","pangenome","populus","unveils","genomic","facets","adaptation","diversification","widespread","forest","trees","shi","zhang","hou","jia","dan","zhang","jiang","lai","feng","feng","ma","wu","liu","zhang","long","chen","street","ingvarsson","liu","yin","wang"],"title":"The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees","year":2024}