Zan, Yanjun
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
Research article2022Peer reviewedOpen access
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.
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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
Cell
2022, volume: 185, number: 1, pages: 204-217
Publisher: CELL PRESS
SLU Authors
Zhou, Linghua
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
Wu, Harry
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)
UKÄ Subject classification
Forest Science
Publication identifier
- DOI: https://doi.org/10.1016/j.cell.2021.12.006
Permanent link to this page (URI)
https://res.slu.se/id/publ/115858