Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation

[1]  H. Tokumoto,et al.  Changes in the sugar composition and molecular mass distribution of matrix polysaccharides during cotton fiber development. , 2002, Plant & cell physiology.

[2]  C. Wilkerson,et al.  Expression of cellulose synthase-like (Csl) genes in insect cells reveals that CslA family members encode mannan synthases. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Jun Cao The Pectin Lyases in Arabidopsis thaliana: Evolution, Selection and Expression Profiles , 2012, PloS one.

[4]  Ryan A. Rapp,et al.  Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication , 2010, BMC Biology.

[5]  Anne M. Evans,et al.  Organization of GC/MS and LC/MS metabolomics data into chemical libraries , 2010, J. Cheminformatics.

[6]  Y. Dorokhov,et al.  Cell wall methanol as a signal in plant immunity , 2014, Front. Plant Sci..

[7]  R. Dixon,et al.  Transcriptional networks for lignin biosynthesis: more complex than we thought? , 2011, Trends in plant science.

[8]  C. Haigler,et al.  Cool temperature hinders flux from glucose to sucrose during cellulose synthesis in secondary wall stage cotton fibers , 2004 .

[9]  M. Giband,et al.  Deep Sequencing Reveals Differences in the Transcriptional Landscapes of Fibers from Two Cultivated Species of Cotton , 2012, PloS one.

[10]  Corey D. DeHaven,et al.  Categorizing Ion -Features in Liquid Chromatography/Mass Spectrometry Metobolomics Data , 2012 .

[11]  Andreas Hansson,et al.  Oxidative modifications to cellular components in plants. , 2007, Annual review of plant biology.

[12]  J. Pelloux,et al.  Homogalacturonan-modifying enzymes: structure, expression, and roles in plants. , 2014, Journal of experimental botany.

[13]  Monika S. Doblin,et al.  Dimerization of cotton fiber cellulose synthase catalytic subunits occurs via oxidation of the zinc-binding domains , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[14]  K. Alleva,et al.  AtTIP1;3 and AtTIP5;1, the only highly expressed Arabidopsis pollen‐specific aquaporins, transport water and urea , 2008, FEBS letters.

[15]  Sixue Chen,et al.  Proteomic profiling of developing cotton fibers from wild and domesticated Gossypium barbadense. , 2013, The New phytologist.

[16]  Yuxian Zhu,et al.  Cotton GhPOX1 encoding plant class III peroxidase may be responsible for the high level of reactive oxygen species production that is related to cotton fiber elongation. , 2009, Journal of genetics and genomics = Yi chuan xue bao.

[17]  D. Delmer,et al.  Changes in biochemical composition of the cell wall of the cotton fiber during development. , 1977, Plant physiology.

[18]  R. Olsen,et al.  Dihydromyricetin As a Novel Anti-Alcohol Intoxication Medication , 2012, The Journal of Neuroscience.

[19]  Lokesh Kumar,et al.  Mfuzz: A software package for soft clustering of microarray data , 2007, Bioinformation.

[20]  Y. Cheng,et al.  Molecular Mechanisms of Fiber Differential Development between G. barbadense and G. hirsutum Revealed by Genetical Genomics , 2012, PloS one.

[21]  J. Ryals,et al.  Metabolomic profiling in Selaginella lepidophylla at various hydration states provides new insights into the mechanistic basis of desiccation tolerance. , 2013, Molecular plant.

[22]  Guang H. Yu,et al.  Exogenous γ-aminobutyric acid (GABA) affects pollen tube growth via modulating putative Ca2+-permeable membrane channels and is coupled to negative regulation on glutamate decarboxylase , 2014, Journal of experimental botany.

[23]  R. Seagull Cytoskeletal involvement in cotton fiber growth and development , 1993 .

[24]  D. Soltis,et al.  Polyploidy and Genome Evolution , 2012, Springer Berlin Heidelberg.

[25]  Juan Miguel García-Gómez,et al.  BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Manipulation of FASTQ data with Galaxy , 2005 .

[26]  A. Lorence,et al.  Engineering Elevated Vitamin C in Plants to Improve their Nutritional Content, Growth, and Tolerance to Abiotic Stress , 2014 .

[27]  J. Olsen,et al.  Changes in metabolite profiles in Norway spruce shoot tips during short-day induced winter bud development and long-day induced bud flush , 2014, Metabolomics.

[28]  C. Haigler,et al.  Cotton Fiber Cell Walls of Gossypium hirsutum and Gossypium barbadense Have Differences Related to Loosely-Bound Xyloglucan , 2013, PloS one.

[29]  J. Whelan,et al.  Alternative oxidase: a target and regulator of stress responses. , 2009, Physiologia plantarum.

[30]  P. Choler,et al.  Methyl-beta-D-glucopyranoside in higher plants: accumulation and intracellular localization in Geum montanum L. leaves and in model systems studied by 13C nuclear magnetic resonance. , 2004, Journal of experimental botany.

[31]  F. Ferrini,et al.  Stress-induced flavonoid biosynthesis and the antioxidant machinery of plants , 2011, Plant signaling & behavior.

[32]  C. Haigler,et al.  Genomics of Cotton Fiber Secondary Wall Deposition and Cellulose Biogenesis , 2009 .

[33]  D. Llewellyn,et al.  Pectin Methylesterase and Pectin Remodelling Differ in the Fibre Walls of Two Gossypium Species with Very Different Fibre Properties , 2013, PloS one.

[34]  Ryan A. Rapp,et al.  Phylogenetically distinct cellulose synthase genes support secondary wall thickening in arabidopsis shoot trichomes and cotton fiber. , 2010, Journal of integrative plant biology.

[35]  Yanbin Yin,et al.  A survey of plant and algal genomes and transcriptomes reveals new insights into the evolution and function of the cellulose synthase superfamily , 2014, BMC Genomics.

[36]  Hua Cassan-Wang,et al.  Identification of novel transcription factors regulating secondary cell wall formation in Arabidopsis. , 2013, Frontiers in plant science.

[37]  Hong S. Moon,et al.  Functional analyses of cotton (Gossypium hirsutum L.) immature fiber (im) mutant infer that fiber cell wall development is associated with stress responses , 2013, BMC Genomics.

[38]  Lex E. Flagel,et al.  Jeans, Genes, and Genomes: Cotton as a Model for Studying Polyploidy , 2012 .

[39]  A. Bennett,et al.  Constitutively expressed DHAR and MDHAR influence fruit, but not foliar ascorbate levels in tomato. , 2011, Plant physiology and biochemistry : PPB.

[40]  Tianzhen Zhang,et al.  The essential role of GhPEL gene, encoding a pectate lyase, in cell wall loosening by depolymerization of the de-esterified pectin during fiber elongation in cotton , 2010, Plant Molecular Biology.

[41]  D. Fang,et al.  Elevated Growing Degree Days Influence Transition Stage Timing During Cotton Fiber Development Resulting in Increased Fiber‐Bundle Strength , 2011 .

[42]  Tetsuro Mimura,et al.  Transcription switches for protoxylem and metaxylem vessel formation. , 2005, Genes & development.

[43]  D. Bassham,et al.  Degradation of Oxidized Proteins by Autophagy during Oxidative Stress in Arabidopsis1[W][OA] , 2006, Plant Physiology.

[44]  Tianzhen Zhang,et al.  Effect of H2O2 on fiber initiation using fiber retardation initiation mutants in cotton (Gossypium hirsutum). , 2010, Journal of plant physiology.

[45]  Yuxian Zhu,et al.  A cotton ascorbate peroxidase is involved in hydrogen peroxide homeostasis during fibre cell development. , 2007, The New phytologist.

[46]  M. Jarvis Cellulose Biosynthesis: Counting the Chains , 2013, Plant Physiology.

[47]  M. Milburn,et al.  Analysis of the adult human plasma metabolome. , 2008, Pharmacogenomics.

[48]  C. Foyer,et al.  ASCORBATE AND GLUTATHIONE: Keeping Active Oxygen Under Control. , 1998, Annual review of plant physiology and plant molecular biology.

[49]  Lawrance Hunter,et al.  Cotton Fiber Chemistry and Technology , 2006 .

[50]  F. Guo,et al.  A role for CSLD3 during cell-wall synthesis in apical plasma membranes of tip-growing root-hair cells , 2011, Nature Cell Biology.

[51]  C. Haigler,et al.  Cotton fiber: a powerful single-cell model for cell wall and cellulose research , 2012, Front. Plant Sci..

[52]  J. Ryals,et al.  A Sister Group Contrast Using Untargeted Global Metabolomic Analysis Delineates the Biochemical Regulation Underlying Desiccation Tolerance in Sporobolus stapfianus[C][W][OA] , 2011, Plant Cell.

[53]  Hanbo Chen,et al.  VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R , 2011, BMC Bioinformatics.

[54]  Efficacy of Antioxidant Overproduction on Fiber Growth and Maturation in Cotton , 2009 .

[55]  N. Raikhel,et al.  A gene from the cellulose synthase-like C family encodes a beta-1,4 glucan synthase. , 2007, Proceedings of the National Academy of Sciences of the United States of America.

[56]  Transcriptome analysis of extant cotton progenitors revealed tetraploidization and identified genome-specific single nucleotide polymorphism in diploid and allotetraploid cotton , 2014, BMC Research Notes.

[57]  T. Lumley,et al.  gplots: Various R Programming Tools for Plotting Data , 2015 .

[58]  D. Llewellyn,et al.  Transcript profiling during fiber development identifies pathways in secondary metabolism and cell wall structure that may contribute to cotton fiber quality. , 2009, Plant & cell physiology.

[59]  A. ElSayed,et al.  Physiological aspects of raffinose family oligosaccharides in plants: protection against abiotic stress. , 2014, Plant biology.

[60]  N. Raikhel,et al.  A gene from the cellulose synthase-like C family encodes a β-1,4 glucan synthase , 2007, Proceedings of the National Academy of Sciences.

[61]  Yixiong Tang,et al.  Cotton proteomics for deciphering the mechanism of environment stress response and fiber development. , 2014, Journal of proteomics.

[62]  Assessing the monophyly of polyploid Gossypium species , 2012, Plant Systematics and Evolution.

[63]  Jin-yuan Liu,et al.  Comparative proteomic analysis provides new insights into the fiber elongating process in cotton. , 2008, Journal of proteome research.

[64]  C. Lapierre,et al.  Flavonoid Accumulation in Arabidopsis Repressed in Lignin Synthesis Affects Auxin Transport and Plant Growth , 2007, The Plant Cell Online.

[65]  Lex E. Flagel,et al.  The Evolution of Spinnable Cotton Fiber Entailed Prolonged Development and a Novel Metabolism , 2008, PLoS genetics.

[66]  C. Wilkerson,et al.  A Specialized Outer Layer of the Primary Cell Wall Joins Elongating Cotton Fibers into Tissue-Like Bundles1[W][OA] , 2009, Plant Physiology.

[67]  Y. Pei,et al.  The Dual Functions of WLIM1a in Cell Elongation and Secondary Wall Formation in Developing Cotton Fibers[C][W] , 2013, Plant Cell.

[68]  H. Tokumoto,et al.  Xyloglucan breakdown during cotton fiber development. , 2003, Journal of plant physiology.

[69]  Li Zhou,et al.  Cotton KNL1, encoding a class II KNOX transcription factor, is involved in regulation of fibre development , 2014, Journal of experimental botany.

[70]  C. Wilkerson,et al.  Biotechnological improvement of cotton fibre maturity , 2005 .

[71]  Lili Tu,et al.  A Genetic and Metabolic Analysis Revealed that Cotton Fiber Cell Development Was Retarded by Flavonoid Naringenin1[W][OA] , 2013, Plant Physiology.

[72]  Adi Doron-Faigenboim,et al.  Ecology, Evolution and Organismal Biology Publications Ecology, Evolution and Organismal Biology Repeated Polyploidization of Gossypium Genomes and the Evolution of Spinnable Cotton Fibres , 2022 .

[73]  Ling-Jian Wang,et al.  Gene expression and metabolite profiles of cotton fiber during cell elongation and secondary cell wall synthesis , 2007, Cell Research.

[74]  Haibao Tang,et al.  Comparative analysis of Gossypium and Vitis genomes indicates genome duplication specific to the Gossypium lineage. , 2011, Genomics.

[75]  Wangyu Liu,et al.  Gradual transition zone between cell wall layers and its influence on wood elastic modulus , 2013, Journal of Materials Science.

[76]  D. Bowles,et al.  Arabidopsis glycosyltransferases as biocatalysts in fermentation for regioselective synthesis of diverse quercetin glucosides , 2004, Biotechnology and bioengineering.

[77]  Y. Hsieh,et al.  A Developmental Study of Single Fiber Strength: Greenhouse Grown SJ-2 Acala Cotton , 1995 .

[78]  B. Forde Glutamate signalling in roots. , 2014, Journal of experimental botany.

[79]  T. Brembu,et al.  The small GTPase AtRAC2/ROP7 is specifically expressed during late stages of xylem differentiation in Arabidopsis. , 2005, Journal of experimental botany.

[80]  Levine,et al.  The involvement of hydrogen peroxide in the differentiation of secondary walls in cotton fibers , 1999, Plant physiology.

[81]  D. Delmer,et al.  Genes encoding small GTP-binding proteins analogous to mammalian rac are preferentially expressed in developing cotton fibers , 1995, Molecular and General Genetics MGG.

[82]  Sixue Chen,et al.  Proteomics profiling of fiber development and domestication in upland cotton (Gossypium hirsutum L.) , 2014, Planta.

[83]  J. Selbig,et al.  Understanding the Relationship between Cotton Fiber Properties and Non-Cellulosic Cell Wall Polysaccharides , 2014, PloS one.

[84]  Corey D. DeHaven,et al.  Integrated, nontargeted ultrahigh performance liquid chromatography/electrospray ionization tandem mass spectrometry platform for the identification and relative quantification of the small-molecule complement of biological systems. , 2009, Analytical chemistry.

[85]  Mohammad Pessarakli,et al.  Reactive Oxygen Species, Oxidative Damage, and Antioxidative Defense Mechanism in Plants under Stressful Conditions , 2012 .

[86]  S. Fry Oxidative scission of plant cell wall polysaccharides by ascorbate-induced hydroxyl radicals. , 1998, The Biochemical journal.

[87]  Michael D. Gonzales,et al.  Functional genomics of cell elongation in developing cotton fibers , 2004, Plant Molecular Biology.

[88]  Ryan A. Rapp,et al.  Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense , 2008, Evolution & development.

[89]  P. Choler,et al.  Methyl-β-D-glucopyranoside in higher plants: accumulation and intracellular localization in Geum montanum L. leaves and in model systems studied by 13C nuclear magnetic resonance , 2004 .

[90]  P. Bauer,et al.  Identification of the family of aquaporin genes and their expression in upland cotton (Gossypium hirsutum L.) , 2010, BMC Plant Biology.

[91]  M. Uddin,et al.  Overexpression of dehydroascorbate reductase, but not monodehydroascorbate reductase, confers tolerance to aluminum stress in transgenic tobacco , 2010, Planta.

[92]  R. Furbank,et al.  Genotypic and Developmental Evidence for the Role of Plasmodesmatal Regulation in Cotton Fiber Elongation Mediated by Callose Turnover1 , 2004, Plant Physiology.

[93]  Chris Somerville,et al.  Cellulose synthesis in higher plants. , 2006, Annual review of cell and developmental biology.

[94]  R. Zhong,et al.  Evolutionary conservation of the transcriptional network regulating secondary cell wall biosynthesis. , 2010, Trends in plant science.

[95]  Xiaoming Hao,et al.  Molecular and biochemical evidence for phenylpropanoid synthesis and presence of wall-linked phenolics in cotton fibers. , 2009, Journal of integrative plant biology.

[96]  Y. Nagato,et al.  Rice SLENDER LEAF 1 gene encodes cellulose synthase-like D4 and is specifically expressed in M-phase cells to regulate cell proliferation , 2013, Journal of experimental botany.

[97]  P. Nowak,et al.  Protective effects of D-glucaro 1,4-lactone against oxidative/nitrative modifications of plasma proteins. , 2007, Nutrition.

[98]  S. Shigeoka,et al.  Galactinol and Raffinose Constitute a Novel Function to Protect Plants from Oxidative Damage1[W][OA] , 2008, Plant Physiology.

[99]  Jonathan D. G. Jones,et al.  Reactive oxygen species produced by NADPH oxidase regulate plant cell growth , 2003, Nature.

[100]  L. Dolan,et al.  Local Positive Feedback Regulation Determines Cell Shape in Root Hair Cells , 2008, Science.

[101]  K. Chapman,et al.  Identification and quantification of glycerolipids in cotton fibers: Reconciliation with metabolic pathway predictions from DNA databases , 2005, Lipids.

[102]  N. Eckardt Oxylipin Signaling in Plant Stress Responses , 2008, The Plant Cell Online.

[103]  Jun Zhuang,et al.  Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation. , 2005, The Plant journal : for cell and molecular biology.

[104]  S. Mongrand,et al.  Lipids of plant membrane rafts. , 2012, Progress in lipid research.

[105]  W. Sakamoto,et al.  Vegetative and Sperm Cell-Specific Aquaporins of Arabidopsis Highlight the Vacuolar Equipment of Pollen and Contribute to Plant Reproduction1[W] , 2014, Plant Physiology.

[106]  C. Chapple,et al.  The Phenylpropanoid Pathway in Arabidopsis , 2011, The arabidopsis book.

[107]  A. Meyer The integration of glutathione homeostasis and redox signaling. , 2008, Journal of plant physiology.

[108]  H. Fukuda Programmed cell death of tracheary elements as a paradigm in plants , 2000, Plant Molecular Biology.

[109]  H. Pritchard,et al.  Glutathione half-cell reduction potential: a universal stress marker and modulator of programmed cell death? , 2006, Free radical biology & medicine.

[110]  L. Macías-Rodríguez,et al.  Serotonin, a tryptophan-derived signal conserved in plants and animals, regulates root system architecture probably acting as a natural auxin inhibitor in Arabidopsis thaliana. , 2011, Plant & cell physiology.

[111]  J. Wendel New World tetraploid cottons contain Old World cytoplasm. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[112]  F. Van Breusegem,et al.  Plant proteins under oxidative attack , 2013, Proteomics.

[113]  A. Myburg,et al.  Navigating the transcriptional roadmap regulating plant secondary cell wall deposition , 2013, Front. Plant Sci..

[114]  C. Jan,et al.  Linoleamide, a brain lipid that induces sleep, increases cytosolic Ca2+ levels in MDCK renal tubular cells. , 2001, Life sciences.

[115]  J. Dumville,et al.  Solubilisation of tomato fruit pectins by ascorbate: a possible non-enzymic mechanism of fruit softening , 2003, Planta.