@article{5ca788d797e141a1b0a9e28b8fb1b8a2,
title = "The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence",
abstract = "To date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation of synteny, despite resulting from an ancient whole-genome duplication over 100 million years ago, is unprecedented in plants and probably speaks to the uniqueness of tree ferns. Our detailed investigations into stem anatomy and lignin biosynthesis shed new light on the evolution of stem formation in tree ferns. We identified a phenolic compound, alsophilin, that is abundant in xylem, and we provided the molecular basis for its biosynthesis. Finally, analysis of demographic history revealed two genetic bottlenecks, resulting in rapid demographic declines of A. spinulosa. The A. spinulosa genome fills a crucial gap in the plant genomic landscape and helps elucidate many unique aspects of tree fern biology.",
author = "Xiong Huang and Wenling Wang and Ting Gong and David Wickell and Kuo, {Li Yaung} and Xingtan Zhang and Jialong Wen and Hoon Kim and Fachuang Lu and Hansheng Zhao and Song Chen and Hui Li and Wenqi Wu and Changjiang Yu and Su Chen and Wei Fan and Shuai Chen and Xiuqi Bao and Li Li and Dan Zhang and Longyu Jiang and Xiaojing Yan and Zhenyang Liao and Gongke Zhou and Yalong Guo and John Ralph and Sederoff, {Ronald R.} and Hairong Wei and Ping Zhu and Li, {Fay Wei} and Ray Ming and Quanzi Li",
note = "Funding Information: This work was supported by the Fundamental Research Funds of Chinese Academy of Forestry (grant no. CAFYBB2017ZY001 to Q.L.); the National Natural Science Foundation of China (grant no. 32071787 to Q.L.); start-up funding for polyploid poplar research from the Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University (to H.W.); CAMS Innovation Fund for Medical Sciences (grant no. CIFMS2021-I2M-1-029 to P.Z. and T.G.); PUMC Disciplinary Development of Synthetic Biology (grant no. 201920100801 to P.Z.); and the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science, grant no. DE-SC0018409 to J.R.). We acknowledge the research team of X. Chen and Q. Hou, Department of Pharmacology of our Institute, for the cytotoxic and anti-inflammation bioassays. We thank Y. Fang for providing the gene annotations in A. capillus-veneris. We also thank H. Liu, K. Dipak and S. Shi for helping in resequencing the sample collections, and Y. Cao (State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry) and H. Zhang (the Core Facilities of Life Sciences at Peking University) for assistance with the microscopic observations. Funding Information: This work was supported by the Fundamental Research Funds of Chinese Academy of Forestry (grant no. CAFYBB2017ZY001 to Q.L.); the National Natural Science Foundation of China (grant no. 32071787 to Q.L.); start-up funding for polyploid poplar research from the Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University (to H.W.); CAMS Innovation Fund for Medical Sciences (grant no. CIFMS2021-I2M-1-029 to P.Z. and T.G.); PUMC Disciplinary Development of Synthetic Biology (grant no. 201920100801 to P.Z.); and the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science, grant no. DE-SC0018409 to J.R.). We acknowledge the research team of X. Chen and Q. Hou, Department of Pharmacology of our Institute, for the cytotoxic and anti-inflammation bioassays. We thank Y. Fang for providing the gene annotations in A. capillus-veneris. We also thank H. Liu, K. Dipak and S. Shi for helping in resequencing the sample collections, and Y. Cao (State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry) and H. Zhang (the Core Facilities of Life Sciences at Peking University) for assistance with the microscopic observations. Publisher Copyright: {\textcopyright} 2022, The Author(s).",
year = "2022",
month = may,
doi = "10.1038/s41477-022-01146-6",
language = "English (US)",
volume = "8",
pages = "500--512",
journal = "Nature Plants",
issn = "2055-026X",
publisher = "Palgrave Macmillan",
number = "5",
}