Jumonji family histone demethylases in Epinephelus coioides gonad

Genome-wide identification, evolution of histone lysine demethylases (KDM) genes and their expression during gonadal development in Nile tilapia

Histone lysine demethylases (KDM) are responsible for histone demethylation and are involved in gene expression regulation. Previous studies have shown that histone lysine demethylation plays an important role in gonadal development of vertebrates. The KDM family consists of eight subfamilies, i.e., kdm1, kdm2, kdm3, kdm4, kdm5, kdm6, kdm7 and JmjC-only subfamily. In this study, 13 to 63 KDM genes in 23 representative species were identified based on the available version of genome assembly. Phylogenetic relationships, domain architecture, and synteny of these genes were comprehensively analyzed and the results suggested KDM genes probably originated from the early diverging metazoan and significantly expanded in vertebrates with multiple whole genome duplication, especially in the third-round whole genome duplication (3R-WGD) and polyploidization of teleosts. The subfamilies of kdm2, kdm3, kdm4, kdm5, kdm6 and kdm7 were duplicated with 1R-2R events, and duplicates of kdm2a, kdm4a, kdm5b and kdm6b were resulted from 3R-WGD. Based on transcriptome data, the KDM genes were found to be dominantly expressed in the ovary and testis. More than 80% of KDM genes displayed sexual dimorphic expression, with 15 genes dominantly expressed in ovaries, and 12 genes dominantly expressed in testes. Importantly, from transcriptome data, qRT-PCR and fluorescence in situ hybridization during sex reversal, genes with higher expression in ovary than testis, such as kdm1b and two JmjC-only subfamily members hspbap1 and riox1, were downregulated, while other genes, such as kdm3c, kdm5bb, kdm6ba, kdm6bb and kdm7b, with higher expression in testis than ovary, were upregulated in ovotestis, indicating these genes play critical roles in the gonadal development and sex reversal. This study provided new insights into the evolution of the KDM genes and a fundamental clue for understanding their important roles in sex differentiation and gonadal development in teleosts.

Localization of RNA Pol II CTD (S5) and Transcriptome Analysis of Testis in Diploid and Tetraploid Hybrids of Red Crucian Carp (♀) × Common Carp (♂)

Polyploidy occurs naturally in fish; however, the appearance of these species is an occasional and gradual process, which makes it difficult to trace the changes in phenotypes, genotypes, and regulation of gene expression. The allotetraploid hybrids (4nAT) of red crucian carp (RCC; ♀) × common carp (CC; ♂) generated from interspecies crossing are a good model to investigate the initial changes after allopolyploidization. In the present study, we focused on the changes in the active sites of the testicular transcriptome of the allotetraploid by localization of RNA Pol II CTD YSPTSPS (phospho S5) using immunofluorescence and RNA-seq data via bioinformatic analysis. The results showed that there was no significant difference in signal counts of the RNA Pol II CTD (S5) between the different types of fish at the same stages, including RCC, CC, 2nF₁, and 4nAT, which means that the number of transcriptionally active sites on germ cell chromosomes was not affected by the increase in chromosome number. Similarly, RNA-seq analysis indicated that in the levels of chromosomes and 10-kb regions in the genome, there were no significant changes in the highly active sites in RCC, 2nF₁, and 4nAT. These findings suggest that at the beginning of tetraploid origin, the active transcriptome site of 4nAT in the testis was conserved in the regions of the genome compared to that in RCC and 2nF₁. In conclusion, 4nAT shared a similar gene expression model in the regions of the genome with RCC and 2nF₁ with significantly different expression levels.