| Summary: | Histone modification is an important epigenetic modification that controls gene transcriptional regulation in eukaryotes. Histone methylation is accomplished by histone methyltransferase and can occur on two amino acid residues, arginine and lysine. JumonjiC (JmjC) domain-containing histone demethylase regulates gene transcription and chromatin structure by changing the methylation state of the lysine residue site and plays an important role in plant growth and development. In this study, we carried out genome-wide identification and comprehensive analysis of <i>JmjC</i> genes in the allotetraploid cotton species <i>Gossypium hirsutum</i>. In total, 50 <i>JmjC</i> genes were identified and in <i>G. hirsutum</i>, and 25 <i>JmjC</i> genes were identified in its two diploid progenitors,<i> G. arboreum</i> and <i>G. raimondii</i>, respectively. Phylogenetic analysis divided these <i>JmjC</i> genes into five subfamilies. A collinearity analysis of the two subgenomes of <i>G. hirsutum</i> and the genomes of <i>G. arboreum</i> and <i>G. raimondii</i> uncovered a one-to-one relationship between homologous genes of the <i>JmjC</i> gene family. Most homologs in the <i>JmjC</i> gene family between A and D subgenomes of <i>G. hirsutum</i> have similar exon-intron structures, which indicated that <i>JmjC</i> family genes were conserved after the polyploidization. All <i>G. hirsutum</i><i>JmjC</i> genes were found to have a typical JmjC domain, and some genes also possess other special domains important for their function. Analysis of promoter regions revealed that <i>cis</i>-acting elements, such as those related to hormone and abiotic stress response, were enriched in <i>G. hirsutum JmjC</i> genes. According to a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, most<i> G. hirsutum</i><i>JmjC</i> genes had high abundance expression at developmental stages of fibers, suggesting that they might participate in cotton fiber development. In addition, some <i>G. hirsutum</i><i>JmjC</i> genes were found to have different degrees of response to cold or osmotic stress, thus indicating their potential role in these types of abiotic stress response. Our results provide useful information for understanding the evolutionary history and biological function of <i>JmjC</i> genes in cotton.
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