skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls

Abstract

Knowledge of plant secondary cell wall (SCW) regulation and deposition is mainly based on the Arabidopsis model of a ‘typical’ lignocellulosic SCW. However, SCWs in other plants can vary from this. The SCW of mature cotton seed fibres is highly cellulosic and lacks lignification whereas xylem SCWs are lignocellulosic. We used cotton as a model to study different SCWs and the expression of the genes involved in their formation via RNA deep sequencing and chemical analysis of stem and seed fibre.

Authors:
; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
University of Wisconsin System, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1618554
Alternate Identifier(s):
OSTI ID: 1393388
Grant/Contract Number:  
FC02-07ER64494
Resource Type:
Published Article
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Name: BMC Genomics Journal Volume: 18 Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer Science + Business Media
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Secondary cell wall; Primary cell wall; Transcription factor; Cotton; Gossypium hirsutum; Cellulose synthase; Lignin; Syringyl; Guaiacyl; p-Hydroxyphenyl

Citation Formats

MacMillan, Colleen P., Birke, Hannah, Chuah, Aaron, Brill, Elizabeth, Tsuji, Yukiko, Ralph, John, Dennis, Elizabeth S., Llewellyn, Danny, and Pettolino, Filomena A. Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls. United Kingdom: N. p., 2017. Web. doi:10.1186/s12864-017-3902-4.
MacMillan, Colleen P., Birke, Hannah, Chuah, Aaron, Brill, Elizabeth, Tsuji, Yukiko, Ralph, John, Dennis, Elizabeth S., Llewellyn, Danny, & Pettolino, Filomena A. Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls. United Kingdom. doi:10.1186/s12864-017-3902-4.
MacMillan, Colleen P., Birke, Hannah, Chuah, Aaron, Brill, Elizabeth, Tsuji, Yukiko, Ralph, John, Dennis, Elizabeth S., Llewellyn, Danny, and Pettolino, Filomena A. Tue . "Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls". United Kingdom. doi:10.1186/s12864-017-3902-4.
@article{osti_1618554,
title = {Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls},
author = {MacMillan, Colleen P. and Birke, Hannah and Chuah, Aaron and Brill, Elizabeth and Tsuji, Yukiko and Ralph, John and Dennis, Elizabeth S. and Llewellyn, Danny and Pettolino, Filomena A.},
abstractNote = {Knowledge of plant secondary cell wall (SCW) regulation and deposition is mainly based on the Arabidopsis model of a ‘typical’ lignocellulosic SCW. However, SCWs in other plants can vary from this. The SCW of mature cotton seed fibres is highly cellulosic and lacks lignification whereas xylem SCWs are lignocellulosic. We used cotton as a model to study different SCWs and the expression of the genes involved in their formation via RNA deep sequencing and chemical analysis of stem and seed fibre.},
doi = {10.1186/s12864-017-3902-4},
journal = {BMC Genomics},
number = 1,
volume = 18,
place = {United Kingdom},
year = {2017},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1186/s12864-017-3902-4

Citation Metrics:
Cited by: 6 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Molecular and Biochemical Evidence for Phenylpropanoid Synthesis and Presence of Wall-linked Phenolics in Cotton Fibers
journal, July 2009


Lignin Biosynthesis
journal, June 2003


VND-INTERACTING2, a NAC Domain Transcription Factor, Negatively Regulates Xylem Vessel Formation in Arabidopsis
journal, April 2010

  • Yamaguchi, Masatoshi; Ohtani, Misato; Mitsuda, Nobutaka
  • The Plant Cell, Vol. 22, Issue 4
  • DOI: 10.1105/tpc.108.064048

MYB83 Is a Direct Target of SND1 and Acts Redundantly with MYB46 in the Regulation of Secondary Cell Wall Biosynthesis in Arabidopsis
journal, October 2009

  • McCarthy, R. L.; Zhong, R.; Ye, Z. -H.
  • Plant and Cell Physiology, Vol. 50, Issue 11
  • DOI: 10.1093/pcp/pcp139

Transcriptional regulation of lignin biosynthesis
journal, November 2009


The Cell Biology of Cellulose Synthesis
journal, April 2014


Hemicelluloses
journal, June 2010


Molecular characterization of EgMYB1, a putative transcriptional repressor of the lignin biosynthetic pathway
journal, November 2007


A Kinesin-Like Protein Is Essential for Oriented Deposition of Cellulose Microfibrils and Cell Wall Strength
journal, December 2002

  • Zhong, Ruiqin; Burk, David H.; Morrison, W. Herbert
  • The Plant Cell, Vol. 14, Issue 12
  • DOI: 10.1105/tpc.005801

Determining the polysaccharide composition of plant cell walls
journal, August 2012

  • Pettolino, Filomena A.; Walsh, Cherie; Fincher, Geoffrey B.
  • Nature Protocols, Vol. 7, Issue 9
  • DOI: 10.1038/nprot.2012.081

g:Profiler—a web server for functional interpretation of gene lists (2011 update)
journal, June 2011

  • Reimand, Jüri; Arak, Tambet; Vilo, Jaak
  • Nucleic Acids Research, Vol. 39, Issue suppl_2
  • DOI: 10.1093/nar/gkr378

Glycoproteome of Elongating Cotton Fiber Cells
journal, September 2013

  • Kumar, Saravanan; Kumar, Krishan; Pandey, Pankaj
  • Molecular & Cellular Proteomics, Vol. 12, Issue 12
  • DOI: 10.1074/mcp.M113.030726

The MYB46 Transcription Factor Is a Direct Target of SND1 and Regulates Secondary Wall Biosynthesis in Arabidopsis
journal, September 2007

  • Zhong, R.; Richardson, E. A.; Ye, Z.-H.
  • The Plant Cell Online, Vol. 19, Issue 9, p. 2776-2792
  • DOI: 10.1105/tpc.107.053678

The MYB46/MYB83-mediated transcriptional regulatory programme is a gatekeeper of secondary wall biosynthesis
journal, July 2014

  • Ko, J. -H.; Jeon, H. -W.; Kim, W. -C.
  • Annals of Botany, Vol. 114, Issue 6
  • DOI: 10.1093/aob/mcu126

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
journal, January 2013


Lignin Deposition in Cotton Cells ? Where is the lignin?
journal, January 2016

  • Macmillan, Colleen P.; Birke, Hannah
  • Journal of Plant Biochemistry & Physiology, Vol. 1, Issue 2
  • DOI: 10.4172/2329-9029.1000e106

Changes in Biochemical Composition of the Cell Wall of the Cotton Fiber During Development
journal, June 1977

  • Meinert, Maureen C.; Delmer, Deborah P.
  • Plant Physiology, Vol. 59, Issue 6
  • DOI: 10.1104/pp.59.6.1088

Transcriptional Profile of the Arabidopsis Root Quiescent Center
journal, June 2005


Transcriptional Activation of Secondary Wall Biosynthesis by Rice and Maize NAC and MYB Transcription Factors
journal, September 2011

  • Zhong, R.; Lee, C.; McCarthy, R. L.
  • Plant and Cell Physiology, Vol. 52, Issue 10
  • DOI: 10.1093/pcp/pcr123

MYB103 is required for FERULATE-5-HYDROXYLASE expression and syringyl lignin biosynthesis in Arabidopsis stems
journal, October 2012

  • Öhman, David; Demedts, Brecht; Kumar, Manoj
  • The Plant Journal, Vol. 73, Issue 1
  • DOI: 10.1111/tpj.12018

Contribution of NAC Transcription Factors to Plant Adaptation to Land
journal, March 2014


A Specialized Outer Layer of the Primary Cell Wall Joins Elongating Cotton Fibers into Tissue-Like Bundles
journal, April 2009

  • Singh, Bir; Avci, Utku; Eichler Inwood, Sarah E.
  • Plant Physiology, Vol. 150, Issue 2
  • DOI: 10.1104/pp.109.135459

Mutation of WRKY transcription factors initiates pith secondary wall formation and increases stem biomass in dicotyledonous plants
journal, December 2010

  • Wang, H.; Avci, U.; Nakashima, J.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 51, p. 22338-22343
  • DOI: 10.1073/pnas.1016436107

A Battery of Transcription Factors Involved in the Regulation of Secondary Cell Wall Biosynthesis in Arabidopsis
journal, October 2008


Functional Characterization of Poplar Wood-Associated NAC Domain Transcription Factors
journal, December 2009

  • Zhong, Ruiqin; Lee, Chanhui; Ye, Zheng-Hua
  • Plant Physiology, Vol. 152, Issue 2
  • DOI: 10.1104/pp.109.148270

An update on the nomenclature for the cellulose synthase genes in Populus
journal, May 2009


The Genetics of Lignin Biosynthesis: Connecting Genotype to Phenotype
journal, December 2010


Phytozome: a comparative platform for green plant genomics
journal, November 2011

  • Goodstein, David M.; Shu, Shengqiang; Howson, Russell
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr944

The NAC Transcription Factors NST1 and NST2 of Arabidopsis Regulate Secondary Wall Thickenings and Are Required for Anther Dehiscence
journal, October 2005

  • Mitsuda, Nobutaka; Seki, Motoaki; Shinozaki, Kazuo
  • The Plant Cell, Vol. 17, Issue 11
  • DOI: 10.1105/tpc.105.036004

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres
journal, December 2012

  • Paterson, Andrew H.; Wendel, Jonathan F.; Gundlach, Heidrun
  • Nature, Vol. 492, Issue 7429
  • DOI: 10.1038/nature11798

Differential analysis of gene regulation at transcript resolution with RNA-seq
journal, December 2012

  • Trapnell, Cole; Hendrickson, David G.; Sauvageau, Martin
  • Nature Biotechnology, Vol. 31, Issue 1
  • DOI: 10.1038/nbt.2450

Plant cellulose synthesis: CESA proteins crossing kingdoms
journal, April 2015


Three Distinct Rice Cellulose Synthase Catalytic Subunit Genes Required for Cellulose Synthesis in the Secondary Wall
journal, August 2003

  • Tanaka, Katsuyuki; Murata, Kazumasa; Yamazaki, Muneo
  • Plant Physiology, Vol. 133, Issue 1
  • DOI: 10.1104/pp.103.022442

Secondary Cell Walls: Biosynthesis, Patterned Deposition and Transcriptional Regulation
journal, October 2014

  • Zhong, Ruiqin; Ye, Zheng-Hua
  • Plant and Cell Physiology, Vol. 56, Issue 2
  • DOI: 10.1093/pcp/pcu140

Cell wall glucomannan in Arabidopsis is synthesised by CSLA glycosyltransferases, and influences the progression of embryogenesis
journal, November 2009


Proteomic profiling of developing cotton fibers from wild and domesticated Gossypium barbadense
journal, June 2013

  • Hu, Guanjing; Koh, Jin; Yoo, Mi-Jeong
  • New Phytologist, Vol. 200, Issue 2
  • DOI: 10.1111/nph.12381

Transcriptional Regulation of Grass Secondary Cell Wall Biosynthesis: Playing Catch-Up with Arabidopsis thaliana
journal, January 2012


SND1, a NAC Domain Transcription Factor, Is a Key Regulator of Secondary Wall Synthesis in Fibers of Arabidopsis
journal, November 2006


The Acetyl Bromide Method Is Faster, Simpler and Presents Best Recovery of Lignin in Different Herbaceous Tissues than Klason and Thioglycolic Acid Methods
journal, October 2014

  • Moreira-Vilar, Flavia Carolina; Siqueira-Soares, Rita de Cássia; Finger-Teixeira, Aline
  • PLoS ONE, Vol. 9, Issue 10
  • DOI: 10.1371/journal.pone.0110000

β-1,3-Glucan in Developing Cotton Fibers: Structure, Localization, and Relationship of Synthesis to That of Secondary Wall Cellulose
journal, June 1979

  • Maltby, David; Carpita, Nicholas C.; Montezinos, David
  • Plant Physiology, Vol. 63, Issue 6
  • DOI: 10.1104/pp.63.6.1158

Genome-wide investigation and transcriptome analysis of the WRKY gene family in Gossypium
journal, September 2014

  • Ding, Mingquan; Chen, Jiadong; Jiang, Yurong
  • Molecular Genetics and Genomics, Vol. 290, Issue 1
  • DOI: 10.1007/s00438-014-0904-7

Lignins: Natural polymers from oxidative coupling of 4-hydroxyphenyl- propanoids
journal, January 2004


Phylogenetically Distinct Cellulose Synthase Genes Support Secondary Wall Thickening in Arabidopsis Shoot Trichomes and Cotton Fiber
journal, February 2010


The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
journal, December 2011

  • Lamesch, Philippe; Berardini, Tanya Z.; Li, Donghui
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1090

Perturbation of Brachypodium distachyon CELLULOSE SYNTHASE A4 or 7 results in abnormal cell walls
journal, January 2013

  • Handakumbura, Pubudu P.; Matos, Dominick A.; Osmont, Karen S.
  • BMC Plant Biology, Vol. 13, Issue 1
  • DOI: 10.1186/1471-2229-13-131

Ectopic expression of MYB46 identifies transcriptional regulatory genes involved in secondary wall biosynthesis in Arabidopsis
journal, November 2009


Functional characterization of the switchgrass (Panicum virgatum) R2R3-MYB transcription factor PvMYB4 for improvement of lignocellulosic feedstocks
journal, October 2011


g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments
journal, July 2007

  • Reimand, Jüri; Kull, Meelis; Peterson, Hedi
  • Nucleic Acids Research, Vol. 35, Issue suppl_2
  • DOI: 10.1093/nar/gkm226

The maize ZmMYB42 represses the phenylpropanoid pathway and affects the cell wall structure, composition and degradability in Arabidopsis thaliana
journal, February 2009

  • Sonbol, Fathi-Mohamed; Fornalé, Silvia; Capellades, Montserrat
  • Plant Molecular Biology, Vol. 70, Issue 3
  • DOI: 10.1007/s11103-009-9473-2

Dissection of the Transcriptional Program Regulating Secondary Wall Biosynthesis during Wood Formation in Poplar
journal, September 2011

  • Zhong, Ruiqin; McCarthy, Ryan L.; Lee, Chanhui
  • Plant Physiology, Vol. 157, Issue 3
  • DOI: 10.1104/pp.111.181354

Identification of Novel Genes in Arabidopsis Involved in Secondary Cell Wall Formation Using Expression Profiling and Reverse Genetics
journal, June 2005

  • Brown, David M.; Zeef, Leo A. H.; Ellis, Joanne
  • The Plant Cell, Vol. 17, Issue 8
  • DOI: 10.1105/tpc.105.031542

Lignin isolated from primary walls of hybrid aspen cell cultures indicates significant differences in lignin structure between primary and secondary cell wall
journal, August 2005

  • Christiernin, Maria; Ohlsson, Anna B.; Berglund, Torkel
  • Plant Physiology and Biochemistry, Vol. 43, Issue 8
  • DOI: 10.1016/j.plaphy.2005.07.007

EgMYB2, a new transcriptional activator from Eucalyptus xylem, regulates secondary cell wall formation and lignin biosynthesis
journal, July 2005


Two NAC domain transcription factors, SND1 and NST1, function redundantly in regulation of secondary wall synthesis in fibers of Arabidopsis
journal, March 2007


BEDTools: a flexible suite of utilities for comparing genomic features
journal, January 2010


Characterisation of a pine MYB that regulates lignification
journal, December 2003


NAC Transcription Factors, NST1 and NST3, Are Key Regulators of the Formation of Secondary Walls in Woody Tissues of Arabidopsis
journal, January 2007

  • Mitsuda, N.; Iwase, A.; Yamamoto, H.
  • The Plant Cell, Vol. 19, Issue 1, p. 270-280
  • DOI: 10.1105/tpc.106.047043

Heteromannan and Heteroxylan Cell Wall Polysaccharides Display Different Dynamics During the Elongation and Secondary Cell Wall Deposition Phases of Cotton Fiber Cell Development
journal, July 2015

  • Hernandez-Gomez, Mercedes C.; Runavot, Jean-Luc; Guo, Xiaoyuan
  • Plant and Cell Physiology, Vol. 56, Issue 9
  • DOI: 10.1093/pcp/pcv101

Solution-state 2D NMR of ball-milled plant cell wall gels in DMSO-d6/pyridine-d5
journal, January 2010

  • Kim, Hoon; Ralph, John
  • Org. Biomol. Chem., Vol. 8, Issue 3
  • DOI: 10.1039/B916070A

Lignification: different mechanisms for a versatile polymer
journal, February 2015


Xyloglucan and Its Biosynthesis
journal, January 2012


Global Analysis of Direct Targets of Secondary Wall NAC Master Switches in Arabidopsis
journal, November 2010

  • Zhong, Ruiqin; Lee, Chanhui; Ye, Zheng-Hua
  • Molecular Plant, Vol. 3, Issue 6
  • DOI: 10.1093/mp/ssq062

Navigating the transcriptional roadmap regulating plant secondary cell wall deposition
journal, January 2013

  • Hussey, Steven G.; Mizrachi, Eshchar; Creux, Nicky M.
  • Frontiers in Plant Science, Vol. 4
  • DOI: 10.3389/fpls.2013.00325

Large-scale screening of transcription factor–promoter interactions in spruce reveals a transcriptional network involved in vascular development
journal, April 2014

  • Duval, Isabelle; Lachance, Denis; Giguère, Isabelle
  • Journal of Experimental Botany, Vol. 65, Issue 9
  • DOI: 10.1093/jxb/eru116

Comparison of the Acetyl Bromide Spectrophotometric Method with Other Analytical Lignin Methods for Determining Lignin Concentration in Forage Samples
journal, June 2004

  • Fukushima, Romualdo S.; Hatfield, Ronald D.
  • Journal of Agricultural and Food Chemistry, Vol. 52, Issue 12, p. 3713-3720
  • DOI: 10.1021/jf035497l

Comparative Evolutionary and Developmental Dynamics of the Cotton (Gossypium hirsutum) Fiber Transcriptome
journal, January 2014


SND2, a NAC transcription factor gene, regulates genes involved in secondary cell wall development in Arabidopsis fibres and increases fibre cell area in Eucalyptus
journal, January 2011

  • Hussey, Steven G.; Mizrachi, Eshchar; Spokevicius, Antanas V.
  • BMC Plant Biology, Vol. 11, Issue 1
  • DOI: 10.1186/1471-2229-11-173

Mannan synthase activity in the CSLD family
journal, October 2011

  • Verhertbruggen, Yves; Yin, Lan; Oikawa, Ai
  • Plant Signaling & Behavior, Vol. 6, Issue 10
  • DOI: 10.4161/psb.6.10.17989

A Novel Isoform of Sucrose Synthase Is Targeted to the Cell Wall during Secondary Cell Wall Synthesis in Cotton Fiber
journal, July 2011

  • Brill, Elizabeth; van Thournout, Michel; White, Rosemary G.
  • Plant Physiology, Vol. 157, Issue 1
  • DOI: 10.1104/pp.111.178574

Transcriptional regulation of secondary wall formation controlled by NAC domain proteins
journal, January 2010


An Arabidopsis gene regulatory network for secondary cell wall synthesis
journal, December 2014

  • Taylor-Teeples, M.; Lin, L.; de Lucas, M.
  • Nature, Vol. 517, Issue 7536
  • DOI: 10.1038/nature14099

Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis
journal, May 2015


A Genetic and Metabolic Analysis Revealed that Cotton Fiber Cell Development Was Retarded by Flavonoid Naringenin
journal, March 2013


Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets
journal, June 2005

  • Persson, S.; Wei, H.; Milne, J.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 24
  • DOI: 10.1073/pnas.0503392102

Whole-exome sequencing for finding de novo mutations in sporadic mental retardation
journal, January 2010


Lignin engineering
journal, June 2008

  • Vanholme, R.; Morreel, K.; Ralph, J.
  • Current Opinion in Plant Biology, Vol. 11, Issue 3, p. 278-285
  • DOI: 10.1016/j.pbi.2008.03.005

Wood cell walls: biosynthesis, developmental dynamics and their implications for wood properties
journal, June 2008


What Do We Really Know about Cellulose Biosynthesis in Higher Plants?
journal, February 2010


MYB58 and MYB63 Are Transcriptional Activators of the Lignin Biosynthetic Pathway during Secondary Cell Wall Formation in Arabidopsis
journal, January 2009


    Works referencing / citing this record:

    DNA N6-Methyladenosine modification role in transmitted variations from genomic DNA to RNA in Herrania umbratica
    journal, June 2019


    Transciptome profiling at early infection of Elaeis guineensis by Ganoderma boninense provides novel insights on fungal transition from biotrophic to necrotrophic phase
    journal, December 2018

    • Bahari, Mohammad Nazri Abdul; Sakeh, Nurshafika Mohd; Abdullah, Siti Nor Akmar
    • BMC Plant Biology, Vol. 18, Issue 1
    • DOI: 10.1186/s12870-018-1594-9