Cotton fiber development is still an intriguing question to understand fiber commitment and development. At different fiber developmental stages, many genes change their expression pattern and have a pivotal role in fiber quality and yield. Recently, numerous studies have been conducted for transcriptional regulation of fiber, and raw data were deposited to the public repository for comprehensive integrative analysis. Here, we remapped > 380 cotton RNAseq data with uniform mapping strategies that span ∼400 fold coverage to the genome. We identified stage-specific features related to fiber cell commitment, initiation, elongation, and Secondary Cell Wall (SCW) synthesis and their putative cis-regulatory elements for the specific regulation in fiber development. We also mined Exclusively Expressed Transcripts (EETs) that were positively selected during cotton fiber evolution and domestication. Furthermore, the expression of EETs was validated in 100 cotton genotypes through the nCounter assay and correlated with different fiber-related traits. Thus, our data mining study reveals several important features related to cotton fiber development and improvement, which were consolidated in the “CottonExpress-omics” database.

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Cotton fiber development is still an intriguing question to understand the fiber commitment and development. Here, we remapped >350 publicly available cotton RNA sequencing data on recently published cotton genome with ~400 fold coverage. The differentially expressed genes were clustered in six modules whose functions are specific to commitment, initiation, elongation and Secondary Cell Wall (SCW) fiber development stages. Gene Ontology analysis of commitment and initiation specific modules suggests enrichment of genes involved in organ development. The modules specific for elongation and SCW showed significant enrichment of hydroxyproline-rich proteins and hydrolases. Transcription factors (TFs) binding frequency of defined modules suggested that homeodomain, MYB and NAC expresses at commitment stages but their expression was governed by other TFs. We also mined the stage-specific transcriptional biomarker and Exclusively Expressed Transcripts (EETs) for fiber. These EETs were positively selected during fiber evolution and cotton domestication. The extensive expression profiling of six EETs in 100 cotton genotypes at different fiber developmental stages using nCounter assay and their correlation with eight fiber-related suggests that several EETs are correlated with different fiber quality-related traits. Thus, our study reveals several important genes and pathways that may be important for cotton fiber development and future improvement of cotton.