Objective Demethylation mediated by histone demethylases (HDMs) containing the JMJ domain plays a crucial role in chromatin conformation and the physiological activities it governs, such as replication and transcription. Identifying members of the JMJ histone demethylase gene family in bottle gourd (Lagenaria siceraria) and analysing their expression patterns could provide a reference for studying its growth and development.

Method The genome-wide identification of the JMJ histone demethylase family genes in bottle gourd was performed by HMM, and the expression patterns of the JMJ histone demethylase family genes were analysed by bioinformatics, RNA-Seq data and RT-qPCR in the roots, cotyledons, real leaves, hypocotyls, terminal buds, pistillate flowers, staminate flowers and tendrils of bottle gourd.

Result 17 JMJ family members was identified from bottle gourd genome, dividing into 5 subfamilies, named LsiJMJ1-LsiJMJ17 according to chromosome distribution. Physical and chemical property analysis and subcellular localisation prediction results showed that L. siceraria JMJ proteins ranged in length from 412 to 1852 aa, and most were weakly acidic nuclear localisation proteins. Chromosome localisation and collinearity analysis found that LsiJMJ genes were unevenly distributed across nine chromosomes, containing one pair of highly homologous genes, and multiple pairs of homologous genes with species such as Arabidopsis thaliana and Cucumis melo. Conserved motif analysis indicated that proteins within the same subgroup share similar motifs. Additionally, gene structure and encoded protein domain analysis revealed that most homologous genes exhibit similar exon-intron structures, and encoded sequences contain approximately 6 to 33 exons. Cis-acting element analysis identified stress response, hormone response, growth and development regulation, light response, and other types of elements in JMJ family genes. Protein network interaction analysis suggests that LsiJMJ3 co-express with LsiJMJ9, LsiJMJ2, and LsiJMJ12, while LsiJMJ12, LsiJMJ5, and LsiJMJ7 or LsiJMJ11 co-express in pairs. Expression analysis indicates that LsiJMJ4 and LsiJMJ9 are significantly highly expressed in all tissues, particularly in pistillate flowers and terminal buds, LsiJMJ11 is specifically highly expressed in staminate flowers, and LsiJMJ8 is lowly expressed in five tissue types.

Conclusion Seventeen members of the JMJ family have been successfully identified. Their conserved domains may play an important role in influencing the demethylase activity. The expression of LsiJMJs may be affected by development and abiotic stress. For instance, LsiJMJ4, LsiJMJ7 and LsiJMJ9 were involved in basic growth and development processes such as pistillate flower development or terminal bud differentiation regulation, LsiJMJ11 is related to staminate flower development, and LsiJMJ8 may be induced to express under specific conditions.