Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan's molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth.

Center for Integrative Biological Signalling Studies University of Freiburg 79104 Freiburg Germany

Department of Applied Genetics and Cell Biology University of Natural Resources and Life Sciences Vienna Muthgasse 18 1190 Vienna Austria

Department of Forest Genetics and Plant Physiology Umeå Plant Science Centre Swedish University of Agricultural Sciences SE 901 87 Umeå Sweden

Department of Plant and Environmental Sciences University of Copenhagen Thorvaldsensvej 40 DK 1871 Frederiksberg C Denmark

Faculty of Biology Department of Molecular Plant Physiology University of Freiburg 79104 Freiburg Germany

Institut Jean Pierre Bourgin Institut National de la Recherche Agronomique AgroParisTech CNRS Université Paris Saclay RD10 CEDEX 78026 Versailles France

Institute of Science and Technology Austria 3400 Klosterneuburg Austria

Laboratory of Growth Regulators Faculty of Science Palacký University and Institute of Experimental Botany The Czech Academy of Sciences Šlechtitelů 27 78371 Olomouc Czech Republic

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Sauer M., Robert S., Kleine-Vehn J. Auxin: Simply complicated. J. Exp. Bot. 2013;64:2565–2577. doi: 10.1093/jxb/ert139. PubMed DOI

Rosquete M.R., Barbez E., Kleine-Vehn J. Cellular auxin homeostasis: Gatekeeping is housekeeping. Mol. Plant. 2012;5:772–786. doi: 10.1093/mp/ssr109. PubMed DOI

Sauer M., Kleine-Vehn J. PIN-FORMED and PIN-LIKES auxin transport facilitators. Development. 2019;146:dev168088. doi: 10.1242/dev.168088. PubMed DOI

Gallei M., Luschnig C., Friml J. Auxin signalling in growth: Schrödinger’s cat out of the bag. Curr. Opin. Plant Biol. 2020;53:43–49. doi: 10.1016/j.pbi.2019.10.003. PubMed DOI

Barbez E., Kubeš M., Rolčík J., Béziat C., Pěnčík A., Wang B., Rosquete M.R., Zhu J., Dobrev P.I., Lee Y. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. 2012;485:119–122. doi: 10.1038/nature11001. PubMed DOI

Béziat C., Barbez E., Feraru M.I., Lucyshyn D., Kleine-Vehn J. Light triggers PILS-dependent reduction in nuclear auxin signalling for growth transition. Nat. Plants. 2017;3:17105. doi: 10.1038/nplants.2017.105. PubMed DOI PMC

Calderón Villalobos L.I.A., Lee S., De Oliveira C., Ivetac A., Brandt W., Armitage L., Sheard L.B., Tan X., Parry G., Mao H., et al. A combinatorial TIR1/AFB–Aux/IAA co-receptor system for differential sensing of auxin. Nat. Chem. Biol. 2012;8:477–485. doi: 10.1038/nchembio.926. PubMed DOI PMC

Dharmasiri N., Dharmasiri S., Weijers D., Lechner E., Yamada M., Hobbie L., Ehrismann J.S., Jürgens G., Estelle M. Plant development is regulated by a family of auxin receptor F box proteins. Dev. Cell. 2005;9:109–119. doi: 10.1016/j.devcel.2005.05.014. PubMed DOI

Fendrych M., Leung J., Friml J. TIR1/AFB-Aux/IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. Elife. 2016;5:e19048. doi: 10.7554/eLife.19048. PubMed DOI PMC

Fendrych M., Akhmanova M., Merrin J., Glanc M., Hagihara S., Takahashi K., Uchida N., Torii K.U., Friml J. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nat. Plants. 2018;4:453. doi: 10.1038/s41477-018-0190-1. PubMed DOI PMC

Cao M., Chen R., Li P., Yu Y., Zheng R., Ge D., Zheng W., Wang X., Gu Y., Gelová Z. TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. 2019;568:240–243. doi: 10.1038/s41586-019-1069-7. PubMed DOI

Dai N., Wang W., Patterson S.E., Bleecker A.B. The TMK subfamily of receptor-like kinases in Arabidopsis display an essential role in growth and a reduced sensitivity to auxin. PLoS ONE. 2013;8:e60990. doi: 10.1371/journal.pone.0060990. PubMed DOI PMC

Majda M., Robert S. The role of auxin in cell wall expansion. Int. J. Mol. Sci. 2018;19:951. doi: 10.3390/ijms19040951. PubMed DOI PMC

Lampugnani E.R., Khan G.A., Somssich M., Persson S. Building a plant cell wall at a glance. J. Cell Sci. 2018;131:jcs207373. doi: 10.1242/jcs.207373. PubMed DOI

Pauly M., Keegstra K. Biosynthesis of Plant Cell wall matrix polysaccharide xyloglucan. Annu. Rev. Plant Biol. 2016;67:235–259. doi: 10.1146/annurev-arplant-043015-112222. PubMed DOI

Schultink A., Liu L., Zhu L., Pauly M. Structural diversity and function of xyloglucan sidechain substituents. Plants. 2014;3:526–542. doi: 10.3390/plants3040526. PubMed DOI PMC

Hager A., Menzel H., Krauss A. Experiments and hypothesis concerning the primary action of auxin in elongation growth. Planta. 1971;100:47–75. doi: 10.1007/BF00386886. PubMed DOI

Dünser K., Kleine-Vehn J. Differential growth regulation in plants—the acid growth balloon theory. Curr. Opin. Plant Biol. 2015;28:55–59. doi: 10.1016/j.pbi.2015.08.009. PubMed DOI

Cosgrove D.J. Re-constructing our models of cellulose and primary cell wall assembly. Curr. Opin. Plant Biol. 2014;22:122–131. doi: 10.1016/j.pbi.2014.11.001. PubMed DOI PMC

Barbez E., Dünser K., Gaidora A., Lendl T., Busch W. Auxin steers root cell expansion via apoplastic pH regulation in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA. 2017;114:E4884–E4893. doi: 10.1073/pnas.1613499114. PubMed DOI PMC

Aryal B., Jonsson K., Baral A., Sancho-Andres G., Routier- Kierzkowska A.-L., Kierzkowski D., Bhalerao R.P. Interplay between Cell Wall and Auxin Mediates the Control of Differential Cell Elongation during Apical Hook Development. Curr. Biol. 2020;30:1733–1739. doi: 10.1016/j.cub.2020.02.055. PubMed DOI

Abel S., Oeller P.W., Theologis A. Early auxin-induced genes encode short-lived nuclear proteins. Proc. Natl. Acad. Sci. USA. 1994;91:326–330. doi: 10.1073/pnas.91.1.326. PubMed DOI PMC

Catalá C., Rose J.K., Bennett A.B. Auxin regulation and spatial localization of an endo-1, 4-β-d-glucanase and a xyloglucan endotransglycosylase in expanding tomato hypocotyls. Plant J. 1997;12:417–426. doi: 10.1046/j.1365-313X.1997.12020417.x. PubMed DOI

Catalá C., Rose J.K., York W.S., Albersheim P., Darvill A.G., Bennett A.B. Characterization of a tomato xyloglucan endotransglycosylase gene that is down-regulated by auxin in etiolated hypocotyls. Plant Physiol. 2001;127:1180–1192. doi: 10.1104/pp.010481. PubMed DOI PMC

Osato Y., Yokoyama R., Nishitani K. A principal role for AtXTH18 in Arabidopsis thaliana root growth: A functional analysis using RNAi plants. J. Plant Res. 2006;119:153–162. doi: 10.1007/s10265-006-0262-6. PubMed DOI

Sánchez M., Gianzo C., Sampedro J., Revilla G., Zarra I. Changes in α-xylosidase during intact and auxin-induced growth of pine hypocotyls. Plant Cell Physiol. 2003;44:132–138. doi: 10.1093/pcp/pcg016. PubMed DOI

Talbott L.D., Ray P.M. Changes in Molecular Size of Previously Deposited and Newly Synthesized Pea Cell Wall Matrix Polysaccharides. Eff. Auxin Turgor. 1992;98:369–379. doi: 10.1104/pp.98.1.369. PubMed DOI PMC

Vissenberg K., Oyama M., Osato Y., Yokoyama R., Verbelen J.-P., Nishitani K. Differential expression of AtXTH17, AtXTH18, AtXTH19 and AtXTH20 genes in Arabidopsis roots. Physiological roles in specification in cell wall construction. Plant Cell Physiol. 2005;46:192–200. doi: 10.1093/pcp/pci013. PubMed DOI

Xu W., Purugganan M.M., Polisensky D.H., Antosiewicz D.M., Fry S.C., Braam J. Arabidopsis TCH4, regulated by hormones and the environment, encodes a xyloglucan endotransglycosylase. Plant Cell. 1995;7:1555–1567. PubMed PMC

York W.S., Darvill A.G., Albersheim P. Inhibition of 2, 4-dichlorophenoxyacetic acid-stimulated elongation of pea stem segments by a xyloglucan oligosaccharide. Plant Physiol. 1984;75:295–297. doi: 10.1104/pp.75.2.295. PubMed DOI PMC

Rakusová H., Gallego-Bartolomé J., Vanstraelen M., Robert H.S., Alabadí D., Blázquez M.A., Benková E., Friml J. Polarization of PIN3-dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana. Plant J. 2011;67:817–826. doi: 10.1111/j.1365-313X.2011.04636.x. PubMed DOI

Moller I., Sørensen I., Bernal A.J., Blaukopf C., Lee K., Øbro J., Pettolino F., Roberts A., Mikkelsen J.D., Knox J.P. High-throughput mapping of cell-wall polymers within and between plants using novel microarrays. Plant J. 2007;50:1118–1128. doi: 10.1111/j.1365-313X.2007.03114.x. PubMed DOI

Kračun S.K., Fangel J.U., Rydahl M.G., Pedersen H.L., Vidal-Melgosa S., Willats W.G.T. High-Throughput Glycomics and Glycoproteomics. Springer; Berlin/Heidelberg, Germany: 2017. Carbohydrate microarray technology applied to high-throughput mapping of plant cell wall glycans using comprehensive microarray polymer profiling (CoMPP) pp. 147–165. PubMed

Rydahl M.G., Hansen A.R., Kračun S.K., Mravec J. Report on the current inventory of the toolbox for plant cell wall analysis: Proteinaceous and small molecular probes. Front. Plant Sci. 2018;9:581. doi: 10.3389/fpls.2018.00581. PubMed DOI PMC

Ruprecht C., Bartetzko M.P., Senf D., Dallabernadina P., Boos I., Andersen M.C., Kotake T., Knox J.P., Hahn M.G., Clausen M.H. A synthetic glycan microarray enables epitope mapping of plant cell wall glycan-directed antibodies. Plant Physiol. 2017;175:1094–1104. doi: 10.1104/pp.17.00737. PubMed DOI PMC

Labavitch J.M., Ray P.M. Turnover of cell wall polysaccharides in elongating pea stem segments. Plant Physiol. 1974;53:669–673. doi: 10.1104/pp.53.5.669. PubMed DOI PMC

Nishitani K., Masuda Y. Auxin-induced changes in the cell wall xyloglucans: Effects of auxin on the two different subtractions of xyloglucans in the epicotyl cell wall of Vigna angularis. Plant Cell Physiol. 1983;24:345–355.

Feraru E., Feraru M.I., Barbez E., Waidmann S., Sun L., Gaidora A., Kleine-Vehn J. PILS6 is a temperature-sensitive regulator of nuclear auxin input and organ growth in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA. 2019;116:3893–3898. doi: 10.1073/pnas.1814015116. PubMed DOI PMC

Sun L., Feraru E., Feraru M.I., Waidmann S., Wang W., Passaia G., Wang Z.-Y., Wabnik K., Kleine-Vehn J. PIN-LIKES coordinate brassinosteroid signaling with nuclear auxin input in Arabidopsis thaliana. Curr. Biol. 2020;30:1579–1588. doi: 10.1016/j.cub.2020.02.002. PubMed DOI PMC

Nguema-Ona E., Andème-Onzighi C., Aboughe-Angone S., Bardor M., Ishii T., Lerouge P., Driouich A. The reb1-1 Mutation of Arabidopsis. Effect on the Structure and Localization of Galactose-Containing Cell Wall Polysaccharides. Plant Physiol. 2006;140:1406–1417. doi: 10.1104/pp.105.074997. PubMed DOI PMC

Lerouxel O., Choo T.S., Séveno M., Usadel B., Faye L.C., Lerouge P., Pauly M. Rapid structural phenotyping of plant cell wall mutants by enzymatic oligosaccharide fingerprinting. Plant Physiol. 2002;130:1754–1763. doi: 10.1104/pp.011965. PubMed DOI PMC

Cavalier D.M., Lerouxel O., Neumetzler L., Yamauchi K., Reinecke A., Freshour G., Zabotina O.A., Hahn M.G., Burgert I., Pauly M., et al. Disrupting Two Arabidopsis thaliana Xylosyltransferase Genes Results in Plants Deficient in Xyloglucan, a Major Primary Cell Wall Component. Plant Cell. 2008;20:1519–1537. doi: 10.1105/tpc.108.059873. PubMed DOI PMC

Kong Y., Peña M.J., Renna L., Avci U., Pattathil S., Tuomivaara S.T., Li X., Reiter W.-D., Brandizzi F., Hahn M.G., et al. Galactose-Depleted Xyloglucan Is Dysfunctional and Leads to Dwarfism in Arabidopsis. Plant Physiol. 2015;167:1296–1306. doi: 10.1104/pp.114.255943. PubMed DOI PMC

Peaucelle A., Wightman R., Höfte H. The Control of Growth Symmetry Breaking in the Arabidopsis Hypocotyl. Curr. Biol. 2015;25:1746–1752. doi: 10.1016/j.cub.2015.05.022. PubMed DOI

Peaucelle A., Braybrook S.A., Le Guillou L., Bron E., Kuhlemeier C., Höfte H. Pectin-induced changes in cell wall mechanics underlie organ initiation in Arabidopsis. Curr. Biol. 2011;21:1720–1726. doi: 10.1016/j.cub.2011.08.057. PubMed DOI

Hurný A., Cuesta C., Cavallari N., Ötvös K., Duclercq J., Dokládal L., Montesinos J.C., Gallemí M., Semerádová H., Rauter T. SYNERGISTIC ON AUXIN AND CYTOKININ 1 positively regulates growth and attenuates soil pathogen resistance. Nat. Commun. 2020;11:2170. doi: 10.1038/s41467-020-15895-5. PubMed DOI PMC

Takahashi K., Hayashi K.-I., Kinoshita T. Auxin activates the plasma membrane H+-ATPase by phosphorylation during hypocotyl elongation in Arabidopsis. Plant Physiol. 2012;159:632–641. doi: 10.1104/pp.112.196428. PubMed DOI PMC

Cheng Y., Dai X., Zhao Y. Auxin biosynthesis by the YUCCA flavin monooxygenases controls the formation of floral organs and vascular tissues in Arabidopsis. Genes Dev. 2006;20:1790–1799. doi: 10.1101/gad.1415106. PubMed DOI PMC

Staswick P.E., Serban B., Rowe M., Tiryaki I., Maldonado M.T., Maldonado M.C., Suza W. Characterization of an Arabidopsis enzyme family that conjugates amino acids to indole-3-acetic acid. Plant Cell. 2005;17:616–627. doi: 10.1105/tpc.104.026690. PubMed DOI PMC

Bastien R., Legland D., Martin M., Fregosi L., Peaucelle A., Douady S., Moulia B., Höfte H. KymoRod: A method for automated kinematic analysis of rod-shaped plant organs. Plant J. 2016;88:468–475. doi: 10.1111/tpj.13255. PubMed DOI

Gendreau E., Traas J., Desnos T., Grandjean O., Caboche M., Hofte H. Cellular basis of hypocotyl growth in Arabidopsis thaliana. Plant Physiol. 1997;114:295–305. doi: 10.1104/pp.114.1.295. PubMed DOI PMC

Speicher T.L., Li P.Z., Wallace I.S. Phosphoregulation of Plant Cellulose Synthase Complex and Cellulose Synthase-Like Proteins. Plants. 2018;7:52. doi: 10.3390/plants7030052. PubMed DOI PMC

Chen S., Ehrhardt D.W., Somerville C.R. Mutations of cellulose synthase (CESA1) phosphorylation sites modulate anisotropic cell expansion and bidirectional mobility of cellulose synthase. Proc. Natl. Acad. Sci. USA. 2010;107:17188–17193. doi: 10.1073/pnas.1012348107. PubMed DOI PMC

Han H., Verstraeten I., Roosjen M., Mazur E., Rýdza N., Hajný J., Ötvös K., Weijers D., Friml J. Rapid auxin-mediated phosphorylation of Myosin regulates trafficking and polarity in Arabidopsis. bioRxiv. 2021 doi: 10.1101/2021.04.13.439603. DOI

Vaahtera L., Schulz J., Hamann T. Cell wall integrity maintenance during plant development and interaction with the environment. Nat. Plants. 2019;5:924–932. doi: 10.1038/s41477-019-0502-0. PubMed DOI

Serre N.B.C., Kralík D., Yun P., Slouka Z., Shabala S., Fendrych M. AFB1 controls rapid auxin signalling through membrane depolarization in Arabidopsis thaliana root. Nat. Plants. 2021 doi: 10.1038/s41477-021-00969-z. PubMed DOI PMC

Zhao F., Chen W.-Q., Sechet J., Martin M., Bovio S., Lionnet C., Long Y., Battu V., Mouille G., Monéger F. Xyloglucans and microtubules synergistically maintain meristem geometry and phyllotaxis. Plant Physiol. 2019;181:1191–1206. doi: 10.1104/pp.19.00608. PubMed DOI PMC

Peña M.J., Ryden P., Madson M., Smith A.C., Carpita N.C. The galactose residues of xyloglucan are essential to maintain mechanical strength of the primary cell walls in Arabidopsis during growth. Plant Physiol. 2004;134:443–451. doi: 10.1104/pp.103.027508. PubMed DOI PMC

Zhang T., Tang H., Vavylonis D., Cosgrove D.J. Disentangling loosening from softening: Insights into primary cell wall structure. Plant J. 2019;100:1101–1117. doi: 10.1111/tpj.14519. PubMed DOI

Cosgrove D.J. Plant cell wall extensibility: Connecting plant cell growth with cell wall structure, mechanics, and the action of wall-modifying enzymes. J. Exp. Bot. 2015;67:463–476. doi: 10.1093/jxb/erv511. PubMed DOI

Lima D.U., Loh W., Buckeridge M.S. Xyloglucan–cellulose interaction depends on the sidechains and molecular weight of xyloglucan. Plant Physiol. Biochem. 2004;42:389–394. doi: 10.1016/j.plaphy.2004.03.003. PubMed DOI

Park Y.B., Cosgrove D.J. Changes in cell wall biomechanical properties in the xyloglucan-deficient xxt1/xxt2 mutant of Arabidopsis. Plant Physiol. 2012;158:465–475. doi: 10.1104/pp.111.189779. PubMed DOI PMC

Kim S.-J., Chandrasekar B., Rea A.C., Danhof L., Zemelis-Durfee S., Thrower N., Shepard Z.S., Pauly M., Brandizzi F., Keegstra K. The synthesis of xyloglucan, an abundant plant cell wall polysaccharide, requires CSLC function. Proc. Natl. Acad. Sci. USA. 2020;117:20316–20324. doi: 10.1073/pnas.2007245117. PubMed DOI PMC

Jensen J.K., Schultink A., Keegstra K., Wilkerson C.G., Pauly M. RNA-Seq Analysis of Developing Nasturtium Seeds (Tropaeolum majus): Identification and Characterization of an Additional Galactosyltransferase Involved in Xyloglucan Biosynthesis. Mol. Plant. 2012;5:984–992. doi: 10.1093/mp/sss032. PubMed DOI PMC

Zhong R., Cui D., Phillips D.R., Richardson E.A., Ye Z.-H. A Group of O-Acetyltransferases Catalyze Xyloglucan Backbone Acetylation and Can Alter Xyloglucan Xylosylation Pattern and Plant Growth When Expressed in Arabidopsis. Plant Cell Physiol. 2020;61:1064–1079. doi: 10.1093/pcp/pcaa031. PubMed DOI PMC

Liu L., Hsia M.M., Dama M., Vogel J., Pauly M. A xyloglucan backbone 6-O-acetyltransferase from Brachypodium distachyon modulates xyloglucan xylosylation. Mol. Plant. 2016;9:615–617. doi: 10.1016/j.molp.2015.11.004. PubMed DOI

Vanzin G.F., Madson M., Carpita N.C., Raikhel N.V., Keegstra K., Reiter W.-D. The mur2 mutant of Arabidopsis thaliana lacks fucosylated xyloglucan because of a lesion in fucosyltransferase AtFUT1. Proc. Natl. Acad. Sci. USA. 2002;99:3340–3345. doi: 10.1073/pnas.052450699. PubMed DOI PMC

Günl M., Neumetzler L., Kraemer F., de Souza A., Schultink A., Pena M., York W.S., Pauly M. AXY8 encodes an α-fucosidase, underscoring the importance of apoplastic metabolism on the fine structure of Arabidopsis cell wall polysaccharides. Plant Cell. 2011;23:4025–4040. doi: 10.1105/tpc.111.089193. PubMed DOI PMC

Sampedro J., Gianzo C., Iglesias N., Guitián E., Revilla G., Zarra I. AtBGAL10 is the main xyloglucan β-galactosidase in Arabidopsis, and its absence results in unusual xyloglucan subunits and growth defects. Plant Physiol. 2012;158:1146–1157. doi: 10.1104/pp.111.192195. PubMed DOI PMC

Ferrero L.V., Gastaldi V., Ariel F.D., Viola I.L., Gonzalez D.H. Class I TCP proteins TCP14 and TCP15 are required for elongation and gene expression responses to auxin. Plant Mol. Biol. 2021;105:147–159. doi: 10.1007/s11103-020-01075-y. PubMed DOI

Zhu J., Geisler M. Keeping it all together: Auxin–actin crosstalk in plant development. J. Exp. Bot. 2015;66:4983–4998. doi: 10.1093/jxb/erv308. PubMed DOI

Lampropoulos A., Sutikovic Z., Wenzl C., Maegele I., Lohmann J.U., Forner J. GreenGate-A novel, versatile, and efficient cloning system for plant transgenesis. PLoS ONE. 2013;8:e83043. doi: 10.1371/journal.pone.0083043. PubMed DOI PMC

Schindelin J., Arganda-Carreras I., Frise E., Kaynig V., Longair M., Pietzsch T., Preibisch S., Rueden C., Saalfeld S., Schmid B. Fiji: An open-source platform for biological-image analysis. Nat. Methods. 2012;9:676–682. doi: 10.1038/nmeth.2019. PubMed DOI PMC

Grabov A., Ashley M., Rigas S., Hatzopoulos P., Dolan L., Vicente-Agullo F. Morphometric analysis of root shape. New Phytol. 2005;165:641–652. doi: 10.1111/j.1469-8137.2004.01258.x. PubMed DOI

Mashiguchi K., Tanaka K., Sakai T., Sugawara S., Kawaide H., Natsume M., Hanada A., Yaeno T., Shirasu K., Yao H. The main auxin biosynthesis pathway in Arabidopsis. Proc. Natl. Acad. Sci. USA. 2011;108:18512–18517. doi: 10.1073/pnas.1108434108. PubMed DOI PMC

Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv. 20131303.3997

Quinlan A.R., Hall I.M. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–842. doi: 10.1093/bioinformatics/btq033. PubMed DOI PMC

Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 2011;17:10–12. doi: 10.14806/ej.17.1.200. DOI

Patro R., Duggal G., Love M.I., Irizarry R.A., Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods. 2017;14:417. doi: 10.1038/nmeth.4197. PubMed DOI PMC

Zhang R., Calixto C.P., Marquez Y., Venhuizen P., Tzioutziou N.A., Guo W., Spensley M., Entizne J.C., Lewandowska D., Ten Have S. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Res. 2017;45:5061–5073. doi: 10.1093/nar/gkx267. PubMed DOI PMC

Soneson C., Love M.I., Robinson M.D. Differential analyses for RNA-seq: Transcript-level estimates improve gene-level inferences. F1000Research. 2015;4 doi: 10.12688/f1000research.7563.1. PubMed DOI PMC

Robinson M.D., McCarthy D.J., Smyth G.K. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–140. doi: 10.1093/bioinformatics/btp616. PubMed DOI PMC

Pěnčík A., Casanova-Sáez R., Pilařová V., Žukauskaitė A., Pinto R., Micol J.L., Ljung K., Novák O. Ultra-rapid auxin metabolite profiling for high-throughput mutant screening in Arabidopsis. J. Exp. Bot. 2018;69:2569–2579. doi: 10.1093/jxb/ery084. PubMed DOI PMC

Harholt J., Jensen J.K., Sørensen S.O., Orfila C., Pauly M., Scheller H.V. ARABINAN DEFICIENT 1 is a putative arabinosyltransferase involved in biosynthesis of pectic arabinan in Arabidopsis. Plant Physiol. 2006;140:49–58. doi: 10.1104/pp.105.072744. PubMed DOI PMC

Puhlmann J., Bucheli E., Swain M.J., Dunning N., Albersheim P., Darvill A.G., Hahn M.G. Generation of Monoclonal Antibodies against Plant Cell-Wall Polysaccharides (I. Characterization of a Monoclonal Antibody to a Terminal [alpha]-(1-> 2)-Linked Fucosyl-Containing Epitope. Plant Physiol. 1994;104:699–710. doi: 10.1104/pp.104.2.699. PubMed DOI PMC