John L. Bowman, Monash University, Australia
Takayuki Kohchi, Kyoto University, Japan
Katsuyuki T. Yamato, Kindai University, Japan
Jerry Jenkins, US Department of Energy
Shengqiang Shu, US Department of Energy
Kimitsune Ishizaki, Kobe University, Japan
Shohei Yamaoka, Kyoto University, Japan
Ryuichi Nishihama, Kyoto University, Japan
Yasukazu Nakamura, National Institute of Genetics, Japan
Frédéric Berger, Austrian Academy of Sciences, Austria
Catherine Adam, US Department of Energy
Shiori Sugamata Aki, Nara Institute of Science and Technology, Japan
Felix Althoff, University of Osnabrück, Germany
Takashi Araki, Kyoto University, Japan
Mario A. Arteaga-Vazquez, Universidad Veracruzana, Mexico
Sureshkumar Balasubrmanian, Monash University, Australia
Kerrie Barry, US Department of Energy
Diane Bauer, US Department of Energy
Christian R. Boehm, University of Cambridge, UK
Liam Briginshaw, Monash University, Australia
Juan Caballero-Perez, National Laboratory of Genomics for Biodiversity, Mexico
Bruno Catarino, University of Oxford, UK
Feng Chen, University of Tennessee - Knoxville
Shota Chiyoda, Kyoto University, Japan
Mansi Chovatia, US Department of Energy
Kevin M. Davies, The New Zealand Institute for Plant & Food Research Limited, New Zealand
Mihails Delmans, University of Cambridge, UK
Taku Demura, Nara Institute of Science and Technology, Japan
Tom Dierschke, Monash University, Australia
Liam Dolan, University of Oxford, UK
Tomokazu Kawashima, University of KentuckyFollow


The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant.

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Notes/Citation Information

Published in Cell, v. 171, issue 2, p. 287-304.

© 2017 The Author(s). Published by Elsevier Inc.

This is an open access article under the CC BY-NC-ND license (

Due to the large number of authors, only the first 30 and the authors affiliated with the University of Kentucky are listed in the author section above. For the complete list of authors, please download this article or visit:

Digital Object Identifier (DOI)

Funding Information

The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Funding from ARC FF0561326, DP130100177, DP160100892 (J.L.B), MEXT KAKENHI Grant Numbers (15K21758, 16H06279, 25113001, 25113009 [T. Kohchi], 22112514, 24112715, 24510272 [K.T.Y.], 15H04391, 15H01233, 17H06472 [K. Ishizaki], FWF grant P28320-B21 (F.B.), SNF grant 310030B_160336 (U.G.), Gates Cambridge Trust (C.R.B.), Program to Disseminate Tenure Tracking System, MEXT, Japan (Y.I.), the Marsden Fund of New Zealand grant PAF1302 (K.D.), UC MEXUS Collaborative program grant 2011-UCMEXUS-19941-44-OAC7 (M.A.A.-V, X.C., and E.D.L.), Consejo Nacional de Ciencia y Tecnología (CONACYT) grant CB-158550 (M.A.A.-V.), COSEAMX1 JEAI EPIMAIZE, Universidad Veracruzana (M.A.A.-V. and D.G.), CONACYT grant CB-158561 (A.E.D.A.), Newton Fund grant RG79985 (M.A.A.-V. and J.H.), and Universidad Veracruzana - Cuerpo Académico CA-UVER-234, Marie Sklodowska-Curie action (#658900) (D.G.) is acknowledged.

Related Content

Supplemental Information includes four figures and 11 tables and can be found with this article online at

An audio PaperClip is available at

Genomic resources are available from web sites of both JGI (!info?alias=Org_Mpolymorpha_er) and the Marchantia user community (

Raw sequence reads are available at (SRX874572-SRX874573, SRX555320-SRX555475, SRX301553-SRX301560, SRX114614-SRX114615, SRX030759-SRX030787, SRX2268331-SRX2268345).

Additional phylogenetic analyses are available at Mendeley,

figs1.jpg (306 kB)
Figure S1. Evolution of ARF and AUX/IAA families, Related to Figure 5

figs2.jpg (393 kB)
Figure S2. Conservation of AtTIR1/AFBs and COI1 Residues Involved in Signaling Interactions, Related to Figure 5

figs3.jpg (91 kB)
Figure S3. Summary of the Proposed Origins of Components of Auxin Biosynthesis and Signaling Components, Related to Figure 5

figs4.jpg (196 kB)
Figure S4. ABA Signaling Pathway, Related to Figure 5

mmc1.xlsx (3126 kB)
Table S1. Structural Genomics — Gene Content, Related to Figure 1

mmc2.xlsx (17508 kB)
Table S2. Structural Genomics — FPKM Expression Data, Related to Figure 1 (6263 kB)
Table S3. Structural Genomics — Ortholog Analyses, Related to Figure 1

mmc4.xlsx (11303 kB)
Table S4. Structural Genomics — Whole Genome and Gene Duplications, Related to Figure 1

mmc5.xlsx (4059 kB)
Table S5. Structural Genomics — Repetitive DNA, Related to Figure 1

mmc6.xlsx (4448 kB)
Table S6. Structural Genomics — Sex Chromosome Analyses, Related to Figure 2

mmc7.xlsx (966 kB)
Table S7. Phylogenetic Analyses — Nucleus, DNA, RNA, Related to Figure 3

mmc8.xlsx (28591 kB)
Table S8. Phylogenetic Analyses — Hormone Signaling Pathways, Related to Figure 5

mmc9.xlsx (5857 kB)
Table S9. Phylogenetic Analyses — Receptors, Ligands, and Other Signaling Molecules, Related to Figure 6

mmc10.xlsx (35825 kB)
Table S10. Phylogenetic Analyses — Biochemistry, Cell Biology, and Defense, Related to Figure 6

mmc11.xlsx (4643 kB)
Table S11. Structural Genomics — Genome Assembly, Related to STAR Methods

mmc12.mp3 (3015 kB)
Audio PaperClip