Insight into Key Control Points in Cotton Fiber Development through Comparative Transcriptomics and Metabolomics in Gossypium hirsutum and Gossypium barbadense

We analyzed and compared the transcriptome and metabolome of the 10 - 28 days post anthesis (DPA) fiber of Gossypium hirsutum cv Deltapine90 and Gossypium barbadense cv Phytogen800 in the context of precisely understood fiber developmental profiles. The five days analyzed (10, 15, 18, 21, and 28 DPA) included the stages of rapid elongation, transitional cell wall remodeling, and secondary wall cellulose synthesis. A total of 41,566 transcripts were identified as expressed (RPKM of 2 or more) by Illumina sequencing (in collaboration with Dr. Brian Sheffler and coworkers) and mapped to the reference sequences (in collaboration with Dr. Jeff Chen, and coworkers). Approximately 38,000 transcripts were expressed in each fiber type. The corresponding fiber metabolome (acquired at Metabolon, Durham NC) included 205 identified metabolites held in common between the fiber types, with no unidentified peaks. For the transcriptome and the metabolome, comparisons were made and statistically analyzed during development of the fiber of each species and between fiber types at each DPA. Analysis of the results had several novel implications, including new insights into the transition stage, control of lignin content, and how G. barbadense fiber is able to sustain elongation.