ArticleNature plants2022
The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence.
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Article in Nature plants, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 62 papers.
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62 citing papers in PubMed, 103 citations in OpenAlex.
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- Genomics is modifying our concepts of evolution in homosporous and heterosporous vascular plants.American journal of botany · 2026Review
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- Genome-wide characterization of the LAC gene family in five fern species reveals evolutionary diversification and putative roles in lignin biosynthesis in Alsophila spinulosa.BMC plant biology · 2026Article
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- Decoding the genome of Brainea insignis reveals insights into fern evolution and conservation.Nature communications · 2025Article
- Exploring fern pathosystems and immune receptors to bridge gaps in plant immunity.BMC biology · 2025Article
- Resolving the Stasis-Dynamism Paradox: Genome Evolution in Tree Ferns.Molecular biology and evolution · 2025Article
- The genome of the vining fernProceedings of the National Academy of Sciences of the United States of America · 2025Article
- The genome assembly of the duckweed fern, Azolla caroliniana.The Journal of heredity · 2025Article
- The pan genome analysis ofHorticulture research · 2025Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
33 authors at 14 institutions in 4 countries.
Xiong Huang *State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.
Wenling Wang *Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Ting Gong *State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.ORCID http://orcid.org/0000-0001-8877-9482
David Wickell *Thompson Institute, Ithaca, NY, USA.
Li-Yaung KuoInstitute of Molecular & Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan.
Xingtan ZhangShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Jialong WenBeijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing, China.
Hoon KimDepartment of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA.ORCID http://orcid.org/0000-0001-7425-7464
Fachuang LuDepartment of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA.ORCID http://orcid.org/0000-0002-8230-9129
Hansheng ZhaoState Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China.ORCID http://orcid.org/0000-0002-5405-0375
Song ChenState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.ORCID http://orcid.org/0000-0003-2896-8235
Hui LiState Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.
Wenqi WuBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.
Changjiang YuCollege of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China.
Su ChenState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.
Wei FanState Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.
Shuai ChenShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Xiuqi BaoState Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
Li LiState Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.ORCID http://orcid.org/0000-0002-9496-2280
Dan ZhangState Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
Longyu JiangState Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
Dipak KhadkaGoldenGate International College, Tribhuvan University, Battisputali, Kathmandu, Nepal.
Xiaojing YanState Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.
Zhenyang LiaoShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Gongke ZhouCollege of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China.
Yalong GuoState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, China.ORCID http://orcid.org/0000-0002-4643-4889
John RalphDepartment of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA.ORCID http://orcid.org/0000-0002-6093-4521
Ronald R SederoffForest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA.
Hairong WeiCollege of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA. hairong@mtu.edu.ORCID http://orcid.org/0000-0002-3551-4998
Ping ZhuState Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. zhuping@imm.ac.cn.ORCID http://orcid.org/0000-0001-8537-2169
Fay-Wei LiThompson Institute, Ithaca, NY, USA. fl329@cornell.edu.ORCID http://orcid.org/0000-0002-0076-0152
Ray MingDepartment of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. rayming@illinois.edu.ORCID http://orcid.org/0000-0002-9417-5789
Quanzi LiState Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China. liqz@caf.ac.cn.ORCID http://orcid.org/0000-0002-7405-4402
Agricultural Genomics Institute at Shenzhen · CNChinese Academy of Medical Sciences & Peking Union Medical College · CNChinese Academy of Forestry · CNUniversity of Wisconsin–Madison · USBeijing Forestry University · CNCornell University · USQingdao Agricultural University · CNInstitute of Botany · CNInternational Bamboo and Rattan Organization · CNMichigan Technological University · USNational Tsing Hua University · TWNorth Carolina State University · USTribhuvan University · NPUniversity of Illinois Urbana-Champaign · US
Funding
No grant is acknowledged in the PubMed record.
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.
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AtelinaeFernsSpidersAnimalsGenome, PlantPhylogeny
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