Cunninghamia lanceolata genome illuminates the evolutionary dynamics of gymnosperms
5 affiliations
- 1Chinese Fir Engineering Technology Research Center of the State Forestry and Grassland Administration at College of Forestry, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- 2College of Biology and Agriculture, Zunyi Normal University, Zunyi 563006, China
- 3Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- 4Technical Department, Biomarker Technologies Corporation, Beijing 101300, China
- 5PubBio-Tech, Wuhan 430070, China
Abstract
Seed plants comprise angiosperms and gymnosperms. The latter includes gnetophytes, cycads, Ginkgo, and conifers. Conifers are distributed worldwide, with 630 species distributed across eight families and 70 genera. Their distinctiveness has triggered much debate on their origin, evolution, and phylogenetic placement among seed plants. To better understand the evolution of gymnosperms and their relation to other seed plants, we report here a high-quality genome sequence for a tree species, Chinese fir ( Cunninghamia lanceolata ), which has excellent timber quality and high aluminum adaptability and is a member of Cupressaceae with high levels of heterozygosity. We assembled an 11.24 Gb genome with a contig N50 value of 2.15 Mb and anchored the 10.89 Gb sequence to 11 chromosomes. Phylogenomic analyses showed that cycads sister to Ginkgo, which place to sister in all gymnosperm lineages, and Gnetales within conifers sister to Pinaceae. Whole-genome duplication (WGD) analysis showed that the ancestor of seed plants has differentiated into angiosperms and gymnosperms after having experienced a WGD event. The ancestor of extant gymnosperm has experienced a gymnosperm-specific WGD event and the extant angiosperms do not share a common WGD before their most recent common ancestor diverged into existing angiosperms lineages. Analysis of the MADS-box gene family of C. lanceolata revealed the developmental mechanism of the reproductive organs in C. lanceolata , which supported the (A)B(C) model of the development of gymnosperms reproductive organs. In addition, astringent seeds and shedding of whole branches (with withered leaves) might be a strategy of C. lanceolata that evolved during long-term adaptation to an aluminum-rich environment. The findings also reveal the molecular regulation mechanism of shade tolerance in C. lanceolata seedlings. Our results improve the resolution of ancestral genomic features within seed plants and the knowledge of genome evolution and diversification of gymnosperms.
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BibTeX
@article{lin2026cunninghamia,
title = {{Cunninghamia lanceolata genome illuminates the evolutionary dynamics of gymnosperms}},
author = {Si-Zu Lin and Yuehua Chen and Chao Wu and Wei-Hong Sun and Z Y Li and Hengchi Chen and Jie-Yu Wang and Chang-Mian Ji and Shu-Bin Li and Zhi-Wen Wang and Wen‐Chieh Tsai and Xiang-Qing Ma and Si-Ren Lan and Fei-Ping Zhang and Ya-Cong Xie and Lei Yao and Yan Zhang and Meng-Meng Lü and Jia-Jun Zhang and Diyang Zhang and Yi-Quan Ye and Xia Yu and Shan-Shan Xu and Zhi-Hui Ma and Guo-Chang DING and Guangqiu Cao and Zong-Ming He and Pengfei Wu and Kai-Min Lin and Ai-Qin Liu and Yanqing Lin and Shaoning Ruan and Bao Liu and Shi-Jiang Cao and Lili Zhou and Ming Li and Peng Shuai and Xiaolong Hou and Yi-Han Wu and Nuo Li and Sheng Xiong and Yang Hao and Zhuang Zhou and Xuedie Liu and Dan-Dan Zuo and Jia Li and Pei Wang and Jian Zhang and Ding‐Kun Liu and Gui-Zhen Chen and Jie Huang and Ming‐Zhong Huang and YJ Li and Qin-Yao Zheng and Xue-Wei Zhao and Xiang Zhao and Wen-Ying Zhong and Xuewen Zhang and Zheng-Bao Xia and Ying Yu},
journal = {Cell Reports},
year = {2026},
month = jun,
doi = {10.1016/j.celrep.2026.117566},
url = {https://doi.org/10.1016/j.celrep.2026.117566},
note = {CC BY},
}
RIS
TY - JOUR
TI - Cunninghamia lanceolata genome illuminates the evolutionary dynamics of gymnosperms
AU - Si-Zu Lin
AU - Yuehua Chen
AU - Chao Wu
AU - Wei-Hong Sun
AU - Z Y Li
AU - Hengchi Chen
AU - Jie-Yu Wang
AU - Chang-Mian Ji
AU - Shu-Bin Li
AU - Zhi-Wen Wang
AU - Wen‐Chieh Tsai
AU - Xiang-Qing Ma
AU - Si-Ren Lan
AU - Fei-Ping Zhang
AU - Ya-Cong Xie
AU - Lei Yao
AU - Yan Zhang
AU - Meng-Meng Lü
AU - Jia-Jun Zhang
AU - Diyang Zhang
AU - Yi-Quan Ye
AU - Xia Yu
AU - Shan-Shan Xu
AU - Zhi-Hui Ma
AU - Guo-Chang DING
AU - Guangqiu Cao
AU - Zong-Ming He
AU - Pengfei Wu
AU - Kai-Min Lin
AU - Ai-Qin Liu
AU - Yanqing Lin
AU - Shaoning Ruan
AU - Bao Liu
AU - Shi-Jiang Cao
AU - Lili Zhou
AU - Ming Li
AU - Peng Shuai
AU - Xiaolong Hou
AU - Yi-Han Wu
AU - Nuo Li
AU - Sheng Xiong
AU - Yang Hao
AU - Zhuang Zhou
AU - Xuedie Liu
AU - Dan-Dan Zuo
AU - Jia Li
AU - Pei Wang
AU - Jian Zhang
AU - Ding‐Kun Liu
AU - Gui-Zhen Chen
AU - Jie Huang
AU - Ming‐Zhong Huang
AU - YJ Li
AU - Qin-Yao Zheng
AU - Xue-Wei Zhao
AU - Xiang Zhao
AU - Wen-Ying Zhong
AU - Xuewen Zhang
AU - Zheng-Bao Xia
AU - Ying Yu
PY - 2026
DA - 2026/06/18
JO - Cell Reports
DO - 10.1016/j.celrep.2026.117566
UR - https://doi.org/10.1016/j.celrep.2026.117566
AB - Seed plants comprise angiosperms and gymnosperms. The latter includes gnetophytes, cycads, Ginkgo, and conifers. Conifers are distributed worldwide, with 630 species distributed across eight families and 70 genera. Their distinctiveness has triggered much debate on their origin, evolution, and phylogenetic placement among seed plants. To better understand the evolution of gymnosperms and their relation to other seed plants, we report here a high-quality genome sequence for a tree species, Chinese fir ( Cunninghamia lanceolata ), which has excellent timber quality and high aluminum adaptability and is a member of Cupressaceae with high levels of heterozygosity. We assembled an 11.24 Gb genome with a contig N50 value of 2.15 Mb and anchored the 10.89 Gb sequence to 11 chromosomes. Phylogenomic analyses showed that cycads sister to Ginkgo, which place to sister in all gymnosperm lineages, and Gnetales within conifers sister to Pinaceae. Whole-genome duplication (WGD) analysis showed that the ancestor of seed plants has differentiated into angiosperms and gymnosperms after having experienced a WGD event. The ancestor of extant gymnosperm has experienced a gymnosperm-specific WGD event and the extant angiosperms do not share a common WGD before their most recent common ancestor diverged into existing angiosperms lineages. Analysis of the MADS-box gene family of C. lanceolata revealed the developmental mechanism of the reproductive organs in C. lanceolata , which supported the (A)B(C) model of the development of gymnosperms reproductive organs. In addition, astringent seeds and shedding of whole branches (with withered leaves) might be a strategy of C. lanceolata that evolved during long-term adaptation to an aluminum-rich environment. The findings also reveal the molecular regulation mechanism of shade tolerance in C. lanceolata seedlings. Our results improve the resolution of ancestral genomic features within seed plants and the knowledge of genome evolution and diversification of gymnosperms.
SN - 2211-1247
SN - 2639-1856
ER -