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.
Digital Object Identifier (DOI)
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.
Supplemental Information includes four figures and 11 tables and can be found with this article online at https://doi.org/10.1016/j.cell.2017.09.030.
An audio PaperClip is available at https://doi.org/10.1016/j.cell.2017.09.030#mmc12.
Genomic resources are available from web sites of both JGI (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Mpolymorpha_er) and the Marchantia user community (http://marchantia.info/).
Raw sequence reads are available at https://www.ncbi.nlm.nih.gov/sra (SRX874572-SRX874573, SRX555320-SRX555475, SRX301553-SRX301560, SRX114614-SRX114615, SRX030759-SRX030787, SRX2268331-SRX2268345).
Additional phylogenetic analyses are available at Mendeley, https://doi.org/10.17632/zb7hwyj3hp.1.
Bowman, John L.; Kohchi, Takayuki; Yamato, Katsuyuki T.; Jenkins, Jerry; Shu, Shengqiang; Ishizaki, Kimitsune; Yamaoka, Shohei; Nishihama, Ryuichi; Nakamura, Yasukazu; Berger, Frédéric; Adam, Catherine; Aki, Shiori Sugamata; Althoff, Felix; Araki, Takashi; Arteaga-Vazquez, Mario A.; Balasubrmanian, Sureshkumar; Barry, Kerrie; Bauer, Diane; Boehm, Christian R.; Briginshaw, Liam; Caballero-Perez, Juan; Catarino, Bruno; Chen, Feng; Chiyoda, Shota; Chovatia, Mansi; Davies, Kevin M.; Delmans, Mihails; Demura, Taku; Dierschke, Tom; Dolan, Liam; and Kawashima, Tomokazu, "Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome" (2017). Plant and Soil Sciences Faculty Publications. 126.
Figure S1. Evolution of ARF and AUX/IAA families, Related to Figure 5
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Figure S2. Conservation of AtTIR1/AFBs and COI1 Residues Involved in Signaling Interactions, Related to Figure 5
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Figure S3. Summary of the Proposed Origins of Components of Auxin Biosynthesis and Signaling Components, Related to Figure 5
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Figure S4. ABA Signaling Pathway, Related to Figure 5
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Table S1. Structural Genomics — Gene Content, Related to Figure 1
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Table S2. Structural Genomics — FPKM Expression Data, Related to Figure 1
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Table S3. Structural Genomics — Ortholog Analyses, Related to Figure 1
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Table S4. Structural Genomics — Whole Genome and Gene Duplications, Related to Figure 1
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Table S5. Structural Genomics — Repetitive DNA, Related to Figure 1
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Table S6. Structural Genomics — Sex Chromosome Analyses, Related to Figure 2
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Table S7. Phylogenetic Analyses — Nucleus, DNA, RNA, Related to Figure 3
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Table S8. Phylogenetic Analyses — Hormone Signaling Pathways, Related to Figure 5
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Table S9. Phylogenetic Analyses — Receptors, Ligands, and Other Signaling Molecules, Related to Figure 6
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Table S10. Phylogenetic Analyses — Biochemistry, Cell Biology, and Defense, Related to Figure 6
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Table S11. Structural Genomics — Genome Assembly, Related to STAR Methods
mmc12.mp3 (3015 kB)