ABSTRACT: The purpose of this study was to find candidate genes related to fiber strength by comparing the differences in gene expression levels of different samples at different stages of fiber development. Methods: PimaS-7 and 5917, two Gossypium barbadense materials with significant difference in fiber strength, were used as experimental materials. Transcriptome sequencing was performed on the fibers at 0,5,10,15,20,25,30,35 dPA after flowering, with three biological replicates。Sequence reads that were quality-screened were analyzed at the transcriptional subtype level using two methods :Burrows-Wheeler Aligner (BWA), then Aova (Aova) and Tophat, then Cufflinks. Results: Transcriptome analysis of 48 samples was completed, and a total of 317.57Gb of Clean Data was obtained. The Clean Data of all samples reached 5.78Gb, and the percentage of Q30 bases was 92.78% or above.The Clean Reads of each sample were sequenced with the designated reference genome, and the alignment efficiency ranged from 85.56% to 94.79%.Based on the comparison results, alternative splicing prediction analysis, gene structure optimization analysis and discovery of new genes were performed. 7,726 new genes were discovered, of which 6,612 were functional annotations. Conclusion: In this study, RNA-seq technology was used to analyze the changes of gene expression during the development of Gossypium barbadense fiber.Our results suggest that NGS provides a comprehensive and more accurate quantitative and qualitative assessment of RNA content in tissues.we conclusion that based on RNA-seq technology, the genes related to target traits can be obtained quickly.
