Cotton fibers elongate rapidly after initiation of elongation, eventually leading to the deposit of a large amount ofcellulose. To reveal features of cotton fiber cells at the fast elongation and the secondary cell wall synthesis stages, wecompared the respective transcriptomes and metabolite profiles. Comparative analysis of transcriptomes by cDNA arrayidentified 633 genes that were differentially regulated during fiber development. Principal component analysis (PCA)using expressed genes as variables divided fiber samples into four groups, which are diagnostic of developmental stages.Similar grouping results are also found if we use non-polar or polar metabolites as variables for PCA of developingfibers. Auxin signaling, wall-loosening and lipid metabolism are highly active during fiber elongation, whereas cellulosebiosynthesis is predominant and many other metabolic pathways are downregulated at the secondary cell wall synthesisstage. Transcript and metabolite profiles and enzyme activities are consistent in demonstrating a specialization process ofcotton fiber development toward cellulose synthesis. These data demonstrate that cotton fiber cell at a certain stage has itsown unique feature, and developmental stages of cotton fiber cells can be distinguished by their transcript and metaboliteprofiles. During the secondary cell wall synthesis stage, metabolic pathways are streamed into cellulose synthesis. Cotton fibers elongate rapidly after initiation of elongation, eventually leading to the deposit of a large amount ofcellulose. To reveal features of cotton fiber cells at the fast elongation and the secondary cell wall synthesis stages, we compared the respective transcriptomes and metabolite profiles. Comparative analysis of transcriptomes by cDNA arrayidentified 633 genes that were differentially regulated during fiber development. Principal component analysis (PCA) using expressed genes as variables divided fiber samples into four groups, which are diagnostic of developmental stages. like grouping results are also found if we use non- polar or polar metabolites as variables for PCA of developing fibbers. Auxin signaling, wall-loosening and lipid metabolism are highly active during fiber elongation, dairy cellulose biosynthesis is predominant and many other metabolic pathwayways are downregulated at the secondary cell wall synthesis stage. Transcript and metabolite profiles and enzyme act These data demonstrate that cotton fiber cell at a certain stage has itsown unique feature, and developmental stages of cotton fiber cells can be distinguished by their transcript and metaboliteprofiles. During the secondary cell wall synthesis stage, metabolic pathways are streamed into cellulose synthesis.