title: Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation.
abstract: BACKGROUND
  The morphogenesis of single-celled cotton fiber includes extreme elongation and staged cell wall differentiation. Designing strategies for improving cotton fiber for textiles and other uses relies on uncovering the related regulatory mechanisms. In this research we compared the transcriptomes and metabolomes of two Gossypium genotypes, Gossypium barbadense cv Phytogen 800 and G. hirsutum cv Deltapine 90. When grown in parallel, the two types of fiber developed similarly except for prolonged fiber elongation in the G. barbadense cultivar. The data were collected from isolated fibers between 10 to 28 days post anthesis (DPA) representing: primary wall synthesis to support elongation; transitional cell wall remodeling; and secondary wall cellulose synthesis, which was accompanied by continuing elongation only in G. barbadense fiber.
  
  
  RESULTS
  Of 206 identified fiber metabolites, 205 were held in common between the two genotypes. Approximately 38,000 transcripts were expressed in the fiber of each genotype, and these were mapped to the reference set and interpreted by homology to known genes. The developmental changes in the transcriptomes and the metabolomes were compared within and across genotypes with several novel implications. Transitional cell wall remodeling is a distinct stable developmental stage lasting at least four days (18 to 21 DPA). Expression of selected cell wall related transcripts was similar between genotypes, but cellulose synthase gene expression patterns were more complex than expected. Lignification was transcriptionally repressed in both genotypes. Oxidative stress was lower in the fiber of G. barbadense cv Phytogen 800 as compared to G. hirsutum cv Deltapine 90. Correspondingly, the G. barbadense cultivar had enhanced capacity for management of reactive oxygen species during its prolonged elongation period, as indicated by a 138-fold increase in ascorbate concentration at 28 DPA.
  
  
  CONCLUSIONS
  The parallel data on deep-sequencing transcriptomics and non-targeted metabolomics for two genotypes of single-celled cotton fiber showed that a discrete developmental stage of transitional cell wall remodeling occurs before secondary wall cellulose synthesis begins. The data showed how lignification can be transcriptionally repressed during secondary cell wall synthesis, and they implicated enhanced capacity to manage reactive oxygen species through the ascorbate-glutathione cycle as a positive contributor to fiber length.
authors.affiliation: Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA. jrtuttle@ncsu.edu.
authors.forename: John R
authors.initials: JR
authors.lastname: Tuttle
authors.affiliation: Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA. gyoungju.nah@gmail.com.
authors.forename: Gyoungju
authors.initials: G
authors.lastname: Nah
authors.affiliation: USDA ARS Genomics and Bioinformatics Research Unit, Stoneville, MS, 38776, USA. Mary.Duke@ars.usda.gov.
authors.forename: Mary V
authors.initials: MV
authors.lastname: Duke
authors.affiliation: Metabolon Inc, Durham, NC, 27713, USA. dalexander@metabolon.com.
authors.forename: Danny C
authors.initials: DC
authors.lastname: Alexander
authors.affiliation: Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA. xueying107@gmail.com.
authors.forename: Xueying
authors.initials: X
authors.lastname: Guan
authors.affiliation: Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA. qingxinsong@gmail.com.
authors.forename: Qingxin
authors.initials: Q
authors.lastname: Song
authors.affiliation: Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA. zjchen@mail.utexas.edu.
authors.forename: Z Jeffrey
authors.initials: ZJ
authors.lastname: Chen
authors.affiliation: USDA ARS Genomics and Bioinformatics Research Unit, Stoneville, MS, 38776, USA. brian.scheffler@ars.usda.gov.
authors.forename: Brian E
authors.initials: BE
authors.lastname: Scheffler
authors.affiliation: Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA. candace_haigler@ncsu.edu.|Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA. candace_haigler@ncsu.edu.
authors.forename: Candace H
authors.initials: CH
authors.lastname: Haigler
mesh_terms: D050260:Carbohydrate Metabolism / Q000235:genetics; D002473:Cell Wall / Q000235:genetics*; D032561:Cotton Fiber / Q000379:methods; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D005964:Glucosyltransferases / Q000235:genetics; D003368:Gossypium / Q000235:genetics*; D055442:Metabolome / Q000235:genetics*; D055432:Metabolomics / Q000379:methods; D059467:Transcriptome / Q000235:genetics*
chemical_list: D005964:Glucosyltransferases; C478648:cellulose synthase