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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Article

KAUST Department

Biological and Environmental Science and Engineering (BESE) Division

Date

2021-12-28

Online Publication Date

2021-12-28

Print Publication Date

2021-12

Submitted Date

2021-07-27

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http://hdl.handle.net/10754/675069

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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.

Citation

Niu, S., Li, J., Bo, W., Yang, W., Zuccolo, A., Giacomello, S., … Wu, H. X. (2021). The Chinese pine genome and methylome unveil key features of conifer evolution. Cell. doi:10.1016/j.cell.2021.12.006

Sponsors

This work was supported by The National Natural Science Foundation of China (no. 31870651 and 31600535) and The Program of Introducing Talents of Discipline to Universities (111 project, B13007). We would like to thank Dongmei Hu for her help in drawing some diagrams and English editing by Dr. Peter Stevens and Dr. Jennifer Sanders. S.-H.N. J.L. W.-H.B. and W.-F.Y. are joint first authors, and A.Z. and S.G. are joint second authors who contributed to most parts of the work; W.-F.Y. X.-M.Z. T.L. S.-R.P. and Z.-M.L. contributed to the assembly and sequence analysis; A.Z. S.G. Y.-J.Z. and L.-H.Z. contributed to analysis of the repeat sequence and LTR-RT evolution; J.-J.M. F.-X.H. X.C. J.-H.Y. Y.-T.S. Y.-M.N. B.Z. P.-Y.W. Q.Z. and H.Z. contributed to manually annotating all TFs and TRs families; X.C. F.-X.H. J.-H.Y. Y.-T.S. Y.-M.N. B.Z. P.-Y.W. Q.Z. H.Z. Q.-Y.Z. and H.-H.Z. contributed to the pairwise Y2H assay between 12 TFs; and J.W. and L.-J.W. contributed to analyses of the chromosome morphology and genome size. Z.-M.L. selected the elite tree. Y.H. Y.-H.Y. and W.-Z.L. re-engineered the assembler Canu into a Workflow Description Language Canu (WDL-Canu) and quality controlled the assembly. J.-X.L. T.-Q.Y. W.L. and Y.L. contributed to the design and supervision of various parts of the research; H.X.W. conceived this research. H.X.W. and H.-R.W. headed and managed the project; S.-H.N. coordinated the sequencing, assembly, bioinformatics, and writing activities; S.-H.N. H.X.W. and H.-R.W. wrote and edited most of the manuscript. All authors commented on the manuscript. The authors declare no competing interests.

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