Research article - Peer-reviewed, 2022
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The Chinese pine genome and methylome unveil key features of conifer evolution
Niu, Shihui; Li, Jiang; Bo, Wenhao; Yang, Weifei; Zuccolo, Andrea; Giacomello, Stefania; Chen, Xi; Han, Fangxu; Yang, Junhe; Song, Yitong; Nie, Yumeng; Zhou, Biao; Wang, Peiyi; Zuo, Quan; Zhang, Hui; Ma, Jingjing; Wang, Jun; Wang, Lvji; Zhu, Qianya; Zhao, Huanhuan; Liu, Zhanmin; Zhang, Xuemei; Liu, Tao; Pei, Surui; Li, Zhimin; Hu, Yao; Yang, Yehui; Li, Wenzhao; Zan, Yanjun; Zhou, Linghua; Lin, Jinxing; Yuan, Tongqi; Li, Wei; Li, Yue; Wei, Hairong; Wu, Harry X.Show less authors
Abstract
Conifers dominate the world's forest ecosystems and are the most widely planted tree species. Their giant and complex genomes present great challenges for assembling a complete reference genome for evolutionary and genomic studies. We present a 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) and revealed that its genome size is mostly attributable to huge intergenic regions and long introns with high transposable element (TE) content. Large genes with long introns exhibited higher expressions levels. Despite a lack of recent whole-genome duplication, 91.2% of genes were duplicated through dispersed duplication, and expanded gene families are mainly related to stress responses, which may underpin conifers' adaptation, particularly in cold and/or arid conditions. The reproductive regulation network is distinct compared with angiosperms. Slow removal of TEs with high-level methylation may have contributed to genomic expansion. This study provides insights into conifer evolution and resources for advancing research on conifer adaptation and development.Published in
Cell2022, volume: 185, number: 1, pages: 204-217
Publisher: CELL PRESS
Authors' information
Niu, Shihui
Beijing Forestry University
Li, Jiang
Beijing Forestry University
Bo, Wenhao
Beijing Forestry University
Zuccolo, Andrea
King Abdullah University of Science and Technology
Zuccolo, Andrea
Scuola Superiore Sant'Anna
Giacomello, Stefania
Royal Institute of Technology
Chen, Xi
Beijing Forestry University
Han, Fangxu
Beijing Forestry University
Yang, Junhe
Beijing Forestry University
Song, Yitong
Beijing Forestry University
Nie, Yumeng
Beijing Forestry University
Zhou, Biao
Beijing Forestry University
Wang, Peiyi
Beijing Forestry University
Zuo, Quan
Beijing Forestry University
Zhang, Hui
Beijing Forestry University
Ma, Jingjing
Beijing Forestry University
Wang, Jun
Beijing Forestry University
Wang, Lvji
Beijing Forestry University
Zhu, Qianya
Beijing Forestry University
Zhao, Huanhuan
Beijing Forestry University
Liu, Zhanmin
Qigou State-Owned Forest Farm
Zhang, Xuemei
Annoroad Gene Technology Beijing Co Ltd
Liu, Tao
Annoroad Gene Technology Beijing Co Ltd
Pei, Surui
Annoroad Gene Technology Beijing Co Ltd
Li, Zhimin
Annoroad Gene Technology Beijing Co Ltd
Hu, Yao
Alibaba Group
Yang, Yehui
Alibaba Group
Li, Wenzhao
Alibaba Group
Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology
Zhou, Linghua
Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology
Lin, Jinxing
Beijing Forestry University
Yuan, Tongqi
Beijing Forestry University
Li, Wei
Beijing Forestry University
Li, Yue
Beijing Forestry University
Wei, Hairong
Michigan Technological University
Wu, Harry X.
Umeå University
Wu, Harry X. (Wu, Harry)
Commonwealth Scientific and Industrial Research Organisation (CSIRO)
Wu, Harry X.
Beijing Forestry University
UKÄ Subject classification
Forest Science
Publication Identifiers
DOI: https://doi.org/10.1016/j.cell.2021.12.006
URI (permanent link to this page)
https://res.slu.se/id/publ/115858