Characterization and Stress Response of the JmjC Domain-Containing Histone Demethylase Gene Family in the Allotetraploid Cotton Species Gossypium hirsutum

Abstract

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 JmjC genes in the allotetraploid cotton species Gossypium hirsutum. In total, 50 JmjC genes were identified and in G. hirsutum, and 25 JmjC genes were identified in its two diploid progenitors, G. arboreum and G. raimondii, respectively. Phylogenetic analysis divided these JmjC genes into five subfamilies. A collinearity analysis of the two subgenomes of G. hirsutum and the genomes of G. arboreum and G. raimondii uncovered a one-to-one relationship between homologous genes of the JmjC gene family. Most homologs in the JmjC gene family between A and D subgenomes of G. hirsutum have similar exon-intron structures, which indicated that JmjC family genes were conserved after the polyploidization. All G. hirsutumJmjC 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 cis-acting elements, such as those related to hormone and abiotic stress response, were enriched in G. hirsutum JmjC genes. According to a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, most G. hirsutumJmjC genes had high abundance expression at developmental stages of fibers, suggesting that they might participate in cotton fiber development. In addition, some G. hirsutumJmjC 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 JmjC genes in cotton.

Genome-wide Characterization of the JmjC Domain-Containing Histone Demethylase Gene Family Reveals GhJMJ24 and GhJMJ49 Involving in Somatic Embryogenesis Process in Cotton

“…To examine the evolutionary relationships of JmjC genes in cotton, O. sativa and A. thaliana , we constructed a phylogenetic tree of JmjC based on 145 full-length JmjC protein sequences, including 51, 25, 28, 20, and 21 sequences from G. hirsutum , G. raimondii , G. arboreum, O. sativa , and A. thaliana , respectively. It appears that JmjC could be categorized into six distinct groups rather than the five groups reported in recent studies ( Zhang et al, 2020 ; Sun et al, 2021 ), which are denoted group I to group VI ( Figure 1 ). Group VI, relative to other five groups, contains more genes from each of the five species.…”

“…Previous studies in rice and maize revealed that hypomethylation events were observed more frequently than hypermethylation in the process of tissue culture and somatic embryogenesis ( Stroud et al, 2013 ; Stelpflug et al, 2014 ). A number of G. hirsutum JmjC genes have been found to respond to cold, salt, and osmotic stress to some extent ( Zhang et al, 2020 ; Sun et al, 2021 ), the question of whether JmjC plays a role in cotton tissue culture and somatic embryogenesis remains unanswered until this study.…”

Genome-wide identification, classification, and expression analysis of the JmjC domain-containing histone demethylase gene family in birch

“…The JHDM gene family in different species shows various tissue-specific expression patterns. For example, in cotton, the JHDM gene family is mainly expressed in 20 and 30 days post-anthes (DPA) fibers [31]. In maize, the expression level in roots, stems, and leaves are relatively low, and also different genes exhibit various expressions in different tissues.…”

JmjC Domain-containing Histone Demethylase Gene Family in Chinese Cabbage: Genome-wide Identification and Expressional Profiling

“…As lysine-specific demethylases (KDMs), JmjC gene family members have important biological functions in unicellular microorganisms to mammals [6]. Although the JmjC family has been characterized in several plant species including Arabidopsis [32], rice [33], birch [34], soybean [6], maize [27], pear [36], and cotton [37], it remains poorly examine in Chinese cabbage.…”