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The Chinese pine genome and methylome unveil key features of conifer evolution

Niu, Shihui and Li, Jiang and Bo, Wenhao and Zuccolo, Andrea and Giacomello, Stefania and Chen, Xi and Han, Fangxu and Yang, Junhe and Song, Yitong and Nie, Yumeng and Zhou, Biao and Wang, Peiyi and Zuo, Quan and Zhang, Hui and Ma, Jingjing and Wang, Jun and Wang, Lvji and Zhu, Qianya and Zhao, Huanhuan and Liu, Zhanmin and Zhang, Xuemei and Liu, Tao and Pei, Surui and Li, Zhimin and Hu, Yao and Yang, Yehui and Li, Wenzhao and Zan, Yanjun and Zhou, Linghua and Lin, Jinxing and Yuan, Tongqi and Li, Wei and Li, Yue and Wei, Hairong and Wu, Harry X. (2022). The Chinese pine genome and methylome unveil key features of conifer evolution. Cell. 185 :1 , 204-217
[Research article]

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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.

Authors/Creators:Niu, Shihui and Li, Jiang and Bo, Wenhao and Zuccolo, Andrea and Giacomello, Stefania and Chen, Xi and Han, Fangxu and Yang, Junhe and Song, Yitong and Nie, Yumeng and Zhou, Biao and Wang, Peiyi and Zuo, Quan and Zhang, Hui and Ma, Jingjing and Wang, Jun and Wang, Lvji and Zhu, Qianya and Zhao, Huanhuan and Liu, Zhanmin and Zhang, Xuemei and Liu, Tao and Pei, Surui and Li, Zhimin and Hu, Yao and Yang, Yehui and Li, Wenzhao and Zan, Yanjun and Zhou, Linghua and Lin, Jinxing and Yuan, Tongqi and Li, Wei and Li, Yue and Wei, Hairong and Wu, Harry X.
Title:The Chinese pine genome and methylome unveil key features of conifer evolution
Series Name/Journal:Cell
Year of publishing :2022
Volume:185
Number:1
Page range:204-217
Number of Pages:14
Publisher:CELL PRESS
ISSN:0092-8674
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution-Noncommercial-No Derivative Works 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Forest Science
URN:NBN:urn:nbn:se:slu:epsilon-p-115858
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-115858
Additional ID:
Type of IDID
DOI10.1016/j.cell.2021.12.006
Web of Science (WoS)000746989500002
ID Code:27181
Faculty:S - Faculty of Forest Sciences
Department:(S) > Dept. of Forest Genetics and Plant Physiology
Deposited By: SLUpub Connector
Deposited On:23 Feb 2022 10:08
Metadata Last Modified:16 May 2022 15:04

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