Auxin signaling is essential for organogenesis but not for cell survival in the liverwort Marchantia polymorpha

R Core Team (2020) R: A Language and Environment for Statistical

Computing. R Foundation for Statistical Computing, Vienna, Austria

Ahlmann-Eltze C (2019). ggsignif: Significance Brackets for ‘ggplot2’. R

package version 0.6.0. https://CRAN.R-project.org/package=ggsignif

(accessed: 30 May 2020)

Althoff F, Kopischke S, Zobell O, Ide K, Ishizaki K, Kohchi T, Zachgo

S (2014) Comparison of the MpEF1α and CaMV35 promoters for ap­

plication in Marchantia polymorpha overexpression studies.

Transgenic Res 23(2): 235–244

Bowman JL, Briginshaw LN, Fisher TJ, Flores-Sandoval E (2019)

Something ancient and something neofunctionalized—evolution of

land plant hormone signaling pathways. Curr Opin Plant Biol 47:

64–72

Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K,

Yamaoka S, Nishihama R, Nakamura Y, Berger F, et al. (2017)

Insights into land plant evolution garnered from the Marchantia

polymorpha genome. Cell 171(2): 287–304.e15

Breuninger H, Thamm A, Streubel S, Sakayama H, Nishiyama T,

Dolan L (2016) Diversification of a transcription factor family led

to the evolution of antagonistically acting genetic regulators of

root hair growth. Curr Biol 26(12): 1622–1628

Chen S, Zhou Y, Chen Y, Gu J (2018) Fastp: an ultra-fast all-in-one

FASTQ preprocessor. Bioinformatics 34(17): i884–i890

Chiyoda S, Ishizaki K, Kataoka H, Yamato KT, Kohchi T (2008) Direct

transformation of the liverwort Marchantia polymorpha L. By par­

ticle bombardment using immature thalli developing from spores.

Plant Cell Rep 27(9): 1467–1473

Conway JR, Lex A, Gehlenborg N (2017) Upsetr: an R package for the

visualization of intersecting sets and their properties. Bioinformatics

33(18): 2938–2940

Delbarre A, Muller P, Imhoff V, Guern J (1996) Comparison of

mechanisms controlling uptake and accumulation of

2,4-dichlorophenoxy acetic acid, naphthalene-1-acetic acid, and

indole-3-acetic acid in suspension-cultured tobacco cells. Planta

198(4): 532–541

Delwiche CF, Cooper ED (2015) The evolutionary origin of a terrestrial

flora. Curr Biol 25(19): R899–R910

Dharmasiri N, Dharmasiri S, Estelle M (2005) The F-box protein TIR1

is an auxin receptor. Nature 435(7041): 441–445

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut

P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal

RNA-seq aligner. Bioinformatics 29(1): 15–21

Eklund DM, Ishizaki K, Flores-Sandoval E, Kikuchi S, Takebayashi Y,

Tsukamoto S, Hirakawa Y, Nonomura M, Kato H, Kouno M, et al.

(2015) Auxin produced by the indole-3-pyruvic acid pathway regu­

lates development and gemmae dormancy in the liverwort

Marchantia polymorpha. Plant Cell 27(6): 1650–1669

Flores-Sandoval E, Eklund DM, Bowman JL (2015) A simple auxin

transcriptional response system regulates multiple morphogenetic

processes in the liverwort Marchantia polymorpha. PLoS Genet

11(5): e1005207

Flores-Sandoval E, Eklund DM, Hong S-F, Alvarez JP, Fisher TJ,

Lampugnani ER, Golz JF, Vázquez-Lobo A, Dierschke T, Lin S-S,

et al. (2018) Class C ARFs evolved before the origin of land plants

and antagonize differentiation and developmental transitions in

Marchantia polymorpha. New Phytol 218(4): 1612–1630

Downloaded from https://academic.oup.com/plcell/article/35/3/1058/6931799 by Kyoto university user on 01 September 2023

Supplemental Figure S6. Responses of NAA-responsive

genes to IAA and 2,4-D.

Supplemental Figure S7. Responses of 2,4-D-responsive

genes to IAA and NAA.

Supplemental Figure S8. GO terms enriched in genes that

responded to NAA in an MpTIR1-independent manner.

Supplemental Figure S9. Growth of Mptir1-1ko mutants.

Supplemental Figure S10. Generation and genotyping of

MpTIR1-locus deletion mutants.

Supplemental Figure S11. Reproducibility of Mptir1 de­

fects in Mptir1ld mutants.

Supplemental Figure S12. Contribution of auxin-responsive

genes to the transcriptional properties of Mptir1-1ko cells.

Supplemental Figure S13. Transcriptional changes of

genes related to auxin biosynthesis and signaling in spores,

sporelings, and thalli.

Supplemental Figure S14. MpTIR1 is expressed before the

establishment of the 3D body axes.

Supplemental Data Set 1. Pairwise comparisons between

auxin- and mock-treated samples in WT or Mptir1-1ko cells.

Supplemental Data Set 2. Pairwise comparisons between

2,4-D- and mock-treated WT thalli.

Supplemental Data Set 3. Genes that responded to NAA

in Mptir1-1ko cells.

Supplemental Data Set 4. GO terms enriched in genes up­

regulated by NAA-treatment in Mptir1-1ko cells.

Supplemental Data Set 5. GO terms enriched in genes

downregulated by NAA-treatment in Mptir1-1ko cells.

Supplemental Data Set 6. Pairwise comparisons between

Mptir1-1ko cells and WT samples.

Supplemental Data Set 7. IDs and names of auxin biosyn­

thesis genes, auxin signaling genes, and transcription factors

(TFs) in M. polymorpha.

Supplemental Data Set 8. Oligos used in this study.

Supplemental Data Set 9. Summary of statistical analyses

Supplemental Data Set 10. Public RNA-seq data used in

this study.

THE PLANT CELL 2023: 35; 1058–1075

1074

| THE PLANT CELL 2023: 35; 1058–1075

Ishizaki K, Nishihama R, Ueda M, Inoue K, Ishida S, Nishimura Y,

Shikanai T, Kohchi T (2015) Development of gateway binary vector

series with four different selection markers for the liverwort

Marchantia polymorpha. PLoS One 10(9): e0138876

Ishizaki K, Nonomura M, Kato H, Yamato KT, Kohchi T (2012)

Visualization of auxin-mediated transcriptional activation using a

common auxin-responsive reporter system in the liverwort

Marchantia polymorpha. J Plant Res 125(5): 643–651

Jones VAS, Dolan L (2017) MpWIP regulates air pore complex develop­

ment in the liverwort Marchantia polymorpha. Development 144(8):

1472–1476

Jurado S, Abraham Z, Manzano C, López-Torrejón G, Pacios LF, Del

Pozo JC (2010) The Arabidopsis cell cycle F-box protein SKP2A binds

to auxin. Plant Cell 22(12): 3891–3904

Kato H, Ishizaki K, Kouno M, Shirakawa M, Bowman JL, Nishihama

R, Kohchi T (2015) Auxin-mediated transcriptional system with a

minimal set of components is critical for morphogenesis through

the life cycle in Marchantia polymorpha. PLoS Genet 11(5): e1005084

Kato H, Kouno M, Takeda M, Suzuki H, Ishizaki K, Nishihama R,

Kohchi T (2017) The roles of the sole activator-type auxin response

factor in pattern formation of Marchantia polymorpha. Plant Cell

Physiol 58(10): 1642–1651

Kato H, Mutte SK, Suzuki H, Crespo I, Das S, Radoeva T, Fontana M,

Yoshitake Y, Hainiwa E, van den Berg W, et al. (2020a) Design prin­

ciples of a minimal auxin response system. Nat Plants 6(5): 473–482

Kato H, Nishihama R, Weijers D, Kohchi T (2018) Evolution of nuclear

auxin signaling: lessons from genetic studies with basal land plants. J

Exp Bot 69(2): 291–301

Kato H, Yasui Y, Ishizaki K (2020b) Gemma cup and gemma develop­

ment in Marchantia polymorpha. New Phytol 228(2): 459–465

Kepinski S, Leyser O (2005) The Arabidopsis F-box protein TIR1 is an

auxin receptor. Nature 435(7041): 446–451

Kim J, Harter K, Theologis A (1997) Protein–protein interactions

among the Aux/IAA proteins. Proc Natl Acad Sci U S A 94(22):

11786–11791

Kohchi T, Yamato KT, Ishizaki K, Yamaoka S, Nishihama R (2021)

Development and molecular genetics of Marchantia polymorpha.

Annu Rev Plant Biol 72(1): 1–26

Koide E, Suetsugu N, Iwano M, Gotoh E, Nomura Y, Stolze SC,

Nakagami H, Kohchi T, Nishihama R (2020) Regulation of

photosynthetic carbohydrate metabolism by a raf-like kinase in

the liverwort Marchantia polymorpha. Plant Cell Physiol 61(3): 631–643

Kubota A, Ishizaki K, Hosaka M, Kohchi T (2013) Efficient

Agrobacterium-mediated transformation of the liverwort

Marchantia polymorpha using regenerating thalli. Biosci Biotechnol

Biochem 77(1): 167–172

Kubota A, Kita S, Ishizaki K, Nishihama R, Yamato KT, Kohchi T

(2014) Co-option of a photoperiodic growth-phase transition system

during land plant evolution. Nat Commun 5(1): 3668

Lavy M, Prigge MJ, Tao S, Shain S, Kuo A, Kirchsteiger K, Estelle M

(2016) Constitutive auxin response in Physcomitrella reveals complex

interactions between Aux/IAA and ARF proteins. eLife 5: e13325

Liao C-Y, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D

(2015) Reporters for sensitive and quantitative measurement of aux­

in response. Nat Methods 12(3): 207–210

Liao Y, Smyth GK, Shi W (2019) The R package Rsubread is easier, fas­

ter, cheaper and better for alignment and quantification of RNA se­

quencing reads. Nucleic Acids Res 47(8): e47

Love MI, Huber W, Anders S (2014) Moderated estimation of fold

change and dispersion for RNA-seq data with DESeq 2. Genome

Biol 15(12): 550

Moody LA (2020) Three-dimensional growth: a developmental innov­

ation that facilitated plant terrestrialization. J Plant Res 133(3):

283–290

Mutte SK, Kato H, Rothfels C, Melkonian M, Wong GK-S, Weijers D

(2018) Origin and evolution of the nuclear auxin response system.

eLife 7: e33399

Downloaded from https://academic.oup.com/plcell/article/35/3/1058/6931799 by Kyoto university user on 01 September 2023

Frank MH, Scanlon MJ (2015) Transcriptomic evidence for the evolu­

tion of shoot meristem function in sporophyte-dominant land plants

through concerted selection of ancestral gametophytic and sporo­

phytic genetic programs. Mol Biol Evol 32(2): 355–367

Friml J, Gallei M, Gelová Z, Johnson A, Mazur E, Monzer A,

Rodriguez L, Roosjen M, Verstraeten I, Živanović BD, et al.

(2022) ABP1-TMK Auxin perception mediates ultrafast global

phosphorylation and auxin canalization. Nature 609(7927):

575–581

Fujisawa M, Hayashi K, Nishio T, Bando T, Okada S, Yamato KT,

Fukuzawa H, Ohyania K (2001) Isolation of X and Y chromosomespecific DNA markers from a liverwort, Marchantia polymorpha, by

representational difference analysis. Genetics 159(3): 981–985

Gaal DJ, Dufresne SJ, Maravolo NC (1982) Transport of

14

C-indoleacetic acid in the hepatic Marchantia polymorpha.

Bryologist 85(4): 410–418

Galvan-Ampudia CS, Cerutti G, Legrand J, Brunoud G,

Martin-Arevalillo R, Azais R, Bayle V, Moussu S, Wenzl C,

Jaillais Y, et al. (2020) Temporal integration of auxin information

for the regulation of patterning. eLife 9: e55832

Gamborg OL, Miller RA, Ojima K (1968) Nutrient requirements of sus­

pension cultures of soybean root cells. Exp Cell Res 50(1): 151–158

Gastwirth JL, Gel YR, Hui WLW, Lyubchich V, Miao W, Noguchi K

(2020). lawstat: Tools for Biostatistics, Public Policy, and Law. R pack­

age version 3.4. https://CRAN.R-project.org/package=lawstat (ac­

cessed: 30 May 2020)

Gehlenborg N (2019). UpSetR: A More Scalable Alternative to Venn

and Euler Diagrams for Visualizing Intersecting Sets. R package ver­

sion 1.4.0. https://CRAN.R-project.org/package=UpSetR (accessed:

30 May 2020)

Gray WM, del Pozo JC, Walker L, Hobbie L, Risseeuw E, Banks T,

Crosby WL, Yang M, Ma H, Estelle M (1999) Identification of an

SCF ubiquitin-ligase complex required for auxin response in

Arabidopsis thaliana. Genes Dev 13(13): 1678–1691

Gray WM, Kepinski S, Rouse D, Leyser O, Estelle M (2001) Auxin reg­

ulates SCFTIR1-dependent degradation of AUX/IAA proteins. Nature

414(6861): 271–276

Guan C, Jiao Y (2020) Interplay between the shoot apical meristem and

lateral organs. Abiotech 1(3): 178–184

Harrison CJ (2017) Development and genetics in the evolution of land

plant body plans. Philos Trans R Soc Lond B Biol Sci 372(1713):

20150490

Herud-Sikimić O, Stiel AC, Kolb M, Shanmugaratnam S, Berendzen

KW, Feldhaus C, Höcker B, Jürgens G (2021) A biosensor for the dir­

ect visualization of auxin. Nature 592(7856): 768–772

Higo A, Niwa M, Yamato KT, Yamada L, Sawada H, Sakamoto T,

Kurata T, Shirakawa M, Endo M, Shigenobu S, et al. (2016)

Transcriptional framework of male gametogenesis in the liverwort

Marchantia polymorpha L. Plant Cell Physiol 57(2): 325–338

Hisanaga T, Okahashi K, Yamaoka S, Kajiwara T, Nishihama R,

Shimamura M, Yamato KT, Bowman JL, Kohchi T, Nakajima K

(2019) A cis-acting bidirectional transcription switch controls sexual

dimorphism in the liverwort. EMBO J 38(6): e100240

Hothorn T, Bretz F, Westfall P (2008) Simultaneous inference in gen­

eral parametric models. Biometrical J 50(3): 346–363

Ishida S, Suzuki H, Iwaki A, Kawamura S, Yamaoka S, Kojima M,

Takebayashi Y, Yamaguchi K, Shigenobu S, Sakakibara H, et al.

(2022) Diminished auxin signaling triggers cellular reprogramming

by inducing a regeneration factor in the liverwort Marchantia poly­

morpha. Plant Cell Physiol 63(3): 384–400

Ishizaki K, Chiyoda S, Yamato KT, Kohchi T (2008)

Agrobacterium-mediated transformation of the haploid liverwort

Marchantia polymorpha L., an emerging model for plant biology.

Plant Cell Physiol 49(7): 1084–1091

Ishizaki K, Johzuka-Hisatomi Y, Ishida S, Iida S, Kohchi T (2013)

Homologous recombination-mediated gene targeting in the liver­

wort Marchantia polymorpha L. Sci Rep 3(1): 1532

Suzuki et al.

TIR1 is essential for plant patterning

| 1075

Solly JE, Cunniffe NJ, Harrison CJ (2017) Regional growth rate differ­

ences specified by apical notch activities regulate liverwort thallus

shape. Curr Biol 27(1): 16–26

Su SH, Gibbs NM, Jancewicz AL, Masson PH (2017) Molecular me­

chanisms of root gravitropism. Curr Biol 27(17): R964–R972

Sugano SS, Nishihama R, Shirakawa M, Takagi J, Matsuda Y, Ishida S,

Shimada T, Hara-Nishimura I, Osakabe K, Kohchi T (2018)

Efficient CRISPR/Cas9-based genome editing and its application to

conditional genetic analysis in Marchantia polymorpha. PLoS One

13(10): 1–22

Suzuki H, Harrison CJ, Shimamura M, Kohchi T, Nishihama R (2020)

Positional cues regulate dorsal organ formation in the liverwort

Marchantia polymorpha. J Plant Res 133(3): 311–321

Szemenyei H, Hannon M, Long JA (2008) TOPLESS Mediates auxindependent transcriptional repression during Arabidopsis embryo­

genesis. Science 319(5868): 1384–1386

Takato S, Kakei Y, Mitsui M, Ishida Y, Suzuki M, Yamazaki C,

Hayashi KI, Ishii T, Nakamura A, Soeno K, et al. (2017) Auxin sig­

naling through SCFTIR1/AFBs mediates feedback regulation of IAA bio­

synthesis. Biosci Biotechnol Biochem 81(7): 1320–1326

Tan X, Calderon-Villalobos LIA, Sharon M, Zheng C, Robinson CV,

Estelle M, Zheng N (2007) Mechanism of auxin perception by the

TIR1 ubiquitin ligase. Nature 446(7136): 640–645

Thelander M, Landberg K, Sundberg E (2019) Minimal auxin sensing

levels in vegetative moss stem cells revealed by a ratiometric report­

er. New Phytol 224(2): 775–788

Tiwari SB, Hagen G, Guilfoyle T (2003) The roles of auxin response fac­

tor domains in auxin-responsive transcription. Plant Cell 15(2):

533–543

Ulmasov T, Hagen G, Guilfoyle TJ (1997) ARF1, a transcription factor

that binds to auxin response elements. Science 276(5320):

1865–1868

Ulmasov T, Hagen G, Guilfoyle TJ (1999) Dimerization and DNA bind­

ing of auxin response factors. Plant J 19(3): 309–319

Verma S, Attuluri VPS, Robert HS (2021) An essential function for

auxin in embryo development. Cold Spring Harb Perspect Biol

13(4): a039966

Wickham H (2016) ggplot2: Elegant Graphics for Data Analysis.

Springer-Verlag, New York

Yasui Y, Tsukamoto S, Sugaya T, Nishihama R, Wang Q, Kato H,

Yamato KT, Fukaki H, Mimura T, Kubo H, et al. (2019) GEMMA

CUP-ASSOCIATED MYB1, an ortholog of axillary meristem regula­

tors, is essential in vegetative reproduction in Marchantia polymor­

pha. Curr Biol 29(23): 3987–3995.e5

Yoshida S, BarbierdeReuille P, Lane B, Bassel GW, Prusinkiewicz P,

Smith RS, Weijers D (2014) Genetic control of plant development

by overriding a geometric division rule. Dev Cell 29(1): 75–87

Downloaded from https://academic.oup.com/plcell/article/35/3/1058/6931799 by Kyoto university user on 01 September 2023

Nishihama R, Ishida S, Urawa H, Kamei Y, Kohchi T (2016)

Conditional gene expression/deletion systems for Marchantia poly­

morpha using its own heat-shock promoter and Cre/loxP-mediated

site-specific recombination. Plant Cell Physiol 57(2): 271–280

Nishihama R, Ishizaki K, Hosaka M, Matsuda Y, Kubota A, Kohchi T

(2015) Phytochrome-mediated regulation of cell division and growth

during regeneration and sporeling development in the liverwort

Marchantia polymorpha. J Plant Res 128(3): 407–421

Okada S, Fujisawa M, Sone T, Nakayama S, Nishiyama R, Takenaka

M, Yamaoka S, Sakaida M, Kono K, Takahama M, et al. (2000)

Construction of male and female PAC genomic libraries suitable

for identification of Y-chromosome-specific clones from the liver­

wort, Marchantia polymorpha. Plant J 24(3): 421–428

Paponov IA, Friz T, Budnyk V, Teale W, Wüst F, Paponov M,

Al-Babili S, Palme K (2019) Natural auxin does not inhibit

Brefeldin A induced PIN1 and PIN2 internalization in root cells.

Front Plant Sci 10: 1–7

Pfaffl MW (2001) A new mathematical model for relative quantifica­

tion in real-time RT-PCR. Nucleic Acids Res 29(9): e45

Prigge MJ, Lavy M, Ashton NW, Estelle M (2010) Physcomitrella pa­

tens auxin-resistant mutants affect conserved elements of an auxinsignaling pathway. Curr Biol 20(21): 1907–1912

Prigge MJ, Platre M, Kadakia N, Zhang Y, Greenham K, Szutu W,

Pandey BK, Bhosale RA, Bennett MJ, Busch W, et al. (2020)

Genetic analysis of the Arabidopsis TIR1/AFB auxin receptors reveals

both overlapping and specialized functions. eLife 9: e54740

Proust H, Honkanen S, Jones VAS, Morieri G, Prescott H, Kelly S,

Ishizaki K, Kohchi T, Dolan L (2016) RSL Class I genes controlled

the development of epidermal structures in the common ancestor

of land plants. Curr Biol 26(1): 93–99

Qi L, Kwiatkowski M, Chen H, Hoermayer L, Sinclair S, Zou M, del

Genio CI, Kubeš MF, Napier R, Jaworski K, et al. (2022)

Adenylate cyclase activity of TIR1/AFB auxin receptors in plants.

Nature 611(7934): 133–138

Rensing SA, Goffinet B, Meyberg R, Wu SZ, Bezanilla M (2020) The

moss physcomitrium (Physcomitrella) patens: a model organism for

non-seed plants. Plant Cell 32(5): 1361–1376

Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M,

Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, et al.

(2012) Fiji: an open-source platform for biological-image analysis.

Nat Methods 9(7): 676–682

Schneider G, Chicken E, Becvarik R (2020). NSM3: Functions and Datasets

to Accompany Hollander, Wolfe, and Chicken-Nonparametric Statistical

Methods, Third Edition. R package version 1.15. https://CRAN.R-project.

org/package=NSM3 (accessed: 22 February 2021)

Shimamura M (2016) Marchantia polymorpha; taxonomy, phylogeny,

and morphology of a model system. Plant Cell Physiol 57(2): 230–256

THE PLANT CELL 2023: 35; 1058–1075

...