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Li FW, Nishiyama T, Waller M, Frangedakis E, Keller J, Li Z, Fernandez-Pozo N, Barker MS, Bennett T, Blázquez MA, Cheng S, Cuming AC, de Vries J, de Vries S, Delaux PM, Diop IS, Harrison CJ, Hauser D, Hernández-García J, Kirbis A, Meeks JC, Monte I, Mutte SK, Neubauer A, Quandt D, Robison T, Shimamura M, Rensing SA, Villarreal JC, Weijers D, Wicke S, Wong GKS, Sakakibara K, Szövényi P. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts. Nat Plants 2020; 6:259-272. [PMID: 32170292 PMCID: PMC8075897 DOI: 10.1038/s41477-020-0618-2] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/11/2020] [Indexed: 05/12/2023]
Abstract
Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.
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Affiliation(s)
- Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA.
- Plant Biology Section, Cornell University, Ithaca, NY, USA.
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Ishikawa, Japan
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | | | - Jean Keller
- LRSV, Université de Toulouse, CNRS, UPS Castanet-Tolosan, Toulouse, France
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Tom Bennett
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, Valencia, Spain
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Jan de Vries
- Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Georg-August University Göttingen, Göttingen, Germany
| | - Sophie de Vries
- Institute of Population Genetics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Pierre-Marc Delaux
- LRSV, Université de Toulouse, CNRS, UPS Castanet-Tolosan, Toulouse, France
| | - Issa S Diop
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Jorge Hernández-García
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, Valencia, Spain
| | - Alexander Kirbis
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - John C Meeks
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, USA
| | - Isabel Monte
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Sumanth K Mutte
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Anna Neubauer
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
| | - Tanner Robison
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Masaki Shimamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Stefan A Rensing
- Faculty of Biology, Philipps University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, Germany
| | - Juan Carlos Villarreal
- Department of Biology, Laval University, Quebec City, Quebec, Canada
- Smithsonian Tropical Research Institute, Balboa, Panamá
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Münster, Germany
| | - Gane K-S Wong
- Department of Biological Sciences, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
- BGI-Shenzhen, Shenzhen, China
| | | | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland.
- Zurich-Basel Plant Science Center, Zurich, Switzerland.
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