Genome-Wide identification of doublesex and Mab-3-Related transcription factor (DMRT) genes in nile tilapia (oreochromis niloticus)

Genome-wide identification and expression analysis of Dmrt genes in bivalves

In recent years, some common themes in the development of sex-specific traits in different animal lineages have started to emerge since the discovery of the Dmrt (doublesex-mab3-related transcription factor gene) genes. Bivalves are characterized by a diversity of sexual systems, including simultaneous hermaphroditism, sequential hermaphroditism, and strict gonochorism. However, to date, no research has focused on the genome-wide characterization and analysis of Dmrt genes in bivalves. In this study, the identification and analysis of Dmrt genes in 15 bivalves were performed using bioinformatics methods. A total of 55 Dmrt genes were retrieved in the studied bivalve genomes. The number of Dmrt genes in different species ranged from 3 to 5. The phylogenetic tree showed that Dmrt genes in bivalves can be subdivided into 5 classes: the Dmrt2-like class, Dmrt3-like class, Dmrt4/5-like class, Dsx-like class, and scallop-specific Dmrt class. The Ka/Ks ratios suggested that all Dmrt classes underwent purifying selection pressure. Furthermore, the spatiotemporal expression of Dmrt genes in four bivalve species suggested that different Dmrt genes may have different functions, and scallop-specific Dmrt genes may play a key role in sex determination/differentiation. In general, this study provides a molecular basis for in-depth examination of the functions of Dmrt genes and phylogenomic analyses in bivalves.

Genome-wide identification and comparative analysis of Dmrt genes in echinoderms

The Dmrt (Doublesex-mab3-related transcription factor) gene family is a class of crucial transcription factors characterized by one or several conserved DM (Doublesex/Mab-3) domains. Dmrt family genes can participate in various physiological developmental processes, especially in sex determination/differentiation. Echinoderms are extremely important research objects in various fields, such as sex determination/differentiation and neuroscience. However, to date, the genome-wide characterization and analysis of Dmrt genes in echinoderms have not been investigated. In this study, the identification and analysis of Dmrt genes in 11 representative echinoderms were performed using bioinformatics methods. A total of 43 Dmrt genes have been found in the studied echinoderms, and the number of Dmrt genes in different species ranges from 2 to 5. The phylogenetic tree showed that all Dmrt genes from echinoderms can be subdivided into 5 classes, the Dmrt2-like class, Dmrt3-like class, Dmrt4/5-like class, Dsx-like class, and a novel Dmrt (starfish-specific) class. Furthermore, selective pressure assessment suggested that the Dmrt genes underwent purifying selection pressure. In general, this study provides a molecular basis for echinoderm Dmrt genes and may serve as a reference for in-depth phylogenomics.

Sex Reversal Induced by Dietary Supplementation with 17α-Methyltestosterone during the Critical Period of Sex Differentiation in Oriental River Prawn (Macrobrachium nipponense)

The steroid 17α-methyltestosterone (MT) inhibits ovarian function and is often used to induce sex reversal artificially in vertebrates. In the present study, different concentrations of MT were added as dietary supplementation, and the effects on sex ratio, growth, and gonadal development were examined. After 40 days, the sex ratio (male:female) in each group increased at different degrees with 50 (1.36:1), 100 (1.57:1), and 200 (2.61:1) mg/kg MT, and neo-males with testis-ovary coexistence were observed in the 200 mg/kg MT group. Furthermore, 50 and 100 mg/kg MT could induce female reversion in neo-males. Histologically, the development of the testes in experimental groups was slower, but the ovaries of the experimental and control groups had similar developmental rates. The expression levels of DMRT11E, Foxl2, and SoxE1 in males at 200 mg/kg MT were 8.65-, 3.75-, and 3.45-fold greater than those of the control group. In crustaceans, sex reversal through vertebrate sex hormones can be observed. Neo-males (sex-reversed female prawns) were maintained by exogenous androgen, and over-reliance led to slow testis growth, small body size, and low growth rate, but sperm was still produced. In female prawns, MT inhibited ovary development and promoted growth.

Identification and functional analysis of Dmrt1 gene and the SoxE gene in the sexual development of sea cucumber, Apostichopus japonicus

Members of the Doublesex and Mab-3-related transcription factor (Dmrt) gene family handle various vital functions in several biological processes, including sex determination/differentiation and gonad development. Dmrt1 and Sox9 (SoxE in invertebrates) exhibit a very conserved interaction function during testis formation in vertebrates. However, the dynamic expression pattern and functional roles of the Dmrt gene family and SoxE have not yet been identified in any echinoderm species. Herein, five members of the Dmrt gene family (Dmrt1, 2, 3a, 3b and 5) and the ancestor SoxE gene were identified from the genome of Apostichopus japonicus. Expression studies of Dmrt family genes and SoxE in different tissues of adult males and females revealed different expression patterns of each gene. Transcription of Dmrt2, Dmrt3a and Dmrt3b was higher expressed in the tube feet and coelomocytes instead of in gonadal tissues. The expression of Dmrt1 was found to be sustained throughout spermatogenesis. Knocking-down of Dmrt1 by means of RNA interference (RNAi) led to the downregulation of SoxE and upregulation of the ovarian regulator foxl2 in the testes. This indicates that Dmrt1 may be a positive regulator of SoxE and may play a role in the development of the testes in the sea cucumber. The expression level of SoxE was higher in the ovaries than in the testes, and knocking down of SoxE by RNAi reduced SoxE and Dmrt1 expression but conversely increased the expression of foxl2 in the testes. In summary, this study indicates that Dmrt1 and SoxE are indispensable for testicular differentiation, and SoxE might play a functional role during ovary differentiation in the sea cucumber.

Full-length gonad transcriptome analysis of Amur sturgeon Dmrt family genes: identification, characterization, and expression patterns during gonadal differentiation

The regulatory mechanisms that govern sex differentiation in sturgeon are still poorly understood. The doublesex and Mab-3-related transcription factor (Dmrt) gene family is known for its extensive roles in sex determination and differentiation across vertebrates. This study aimed to identify new members of sturgeon Dmrt family genes and core actors in the gonadal differentiation of Amur sturgeon. A full-length gonad transcriptome database was exploited to identify Dmrt gene orthologs. Analyses of phylogenetic relationships and selection pressure were performed, and tissue expression profiles and spatiotemporal expression patterns in gonads were then analyzed using real-time PCR. In total, five Dmrt family genes were identified from the full-length gonad transcriptome, including Dmrt2, DmrtA1, DmrtA2, DmrtB1a, and DmrtB1b. Phylogenetic analysis showed that these genes were clustered into clades corresponding to the doublesex/Mav-3 (DM) genes of vertebrates. Furthermore, the analysis of evolutionary selective pressure indicated that DmrtB1a and DmrtB1b were subject to positive selection, suggesting the existence of adaptive evolution in sturgeon. The extensive tissue expression profiling of each Dmrt family gene revealed typical characteristics. Remarkably, according to a spatiotemporal expression pattern analysis, in later stages, DmrtB1b expression increased in testes and was significantly higher in testes than in ovaries at 24 months after hatching (M) and 36 M. This study provides a genetic resource of full-length Dmrt family genes and increases the understanding of Dmrt functions in sex differentiation in sturgeon.

Genome wide identification, phylogeny, and synteny analysis of sox gene family in common carp (Cyprinus carpio)

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27 SOX (high-mobility group HMG-box) genes were identified in the C. carp genome.

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SOX genes ranging from 3496 (SOX6) to 924bp (SOX17b) which coded with putative protein series from 307 to 509 amino acids.

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Gene ontology revealed SOX proteins maximum involvement is in metabolic process 49.796 %.

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Chromosomal location and synteny analysis display all SOX gene are located on different chromosomes.

Common carp (Cyprinus carpio) is a commercial fish species valuable for nutritious components and plays a vital role in human healthy nutrition. The SOX (SRY-related genes systematically characterized by a high-mobility group HMG-box) encoded important gene regulatory proteins, a family of transcription factors found in a broad range of animal taxa and extensively known for its contribution in multiple developmental processes including contribution in sex determination across phyla. In our current study, we initially accomplished a genome-wide analysis to report the SOX gene family in common carp fish based on available genomic sequences of zebrafish retrieved from gene repository databases, we focused on the global identification of the Sox gene family in Common carp among wide range of vertebrates and teleosts based on bioinformatics tools and techniques and explore the evolutionary relationships. In our results, a total of 27 SOX (high-mobility group HMG-box) domain genes were identified in the C. carp genome. The full length sequences of SOX genes ranging from 3496 (SOX6) to 924bp (SOX17b) which coded with putative proteins series from 307 to 509 amino acids and all gene having exon number expect SOX9 and SOX13. All the SOX proteins contained at least one conserved DNA-binding HMG-box domain and two (SOX7 and SOX18) were found C terminal. The Gene ontology revealed SOX proteins maximum involvement is in metabolic process 49.796 %, average in biological regulation 45.188 %, biosynthetic process (19.992 %), regulation of cellular process 39.68, 45.508 % organic substance metabolic process, multicellular organismal process 23.23 %,developmental process 21.74 %, system development 16.59 %, gene expression 16.05 % and 14.337 % of RNA metabolic process. Chromosomal location and syntanic analysis show all SOX gene are located on different chromosomes and apparently does not fallow the unique pattern. The maximum linkage of chromosome is (2) on Unplaced Scaffold region. Finally, our results provide important genomic suggestion for upcoming studies of biochemical, physiological, and phylogenetic understanding on SOX genes among teleost.

The genomic structure of the highly-conserved dmrt1 gene in Solea senegalensis (Kaup, 1868) shows an unexpected intragenic duplication

Knowing the factors responsible for sex determination in a species has significant theoretical and practical implications; the dmrt1 gene (Doublesex and Mab-3 (DM)-related Transcription factor 1) plays this role in diverse animal species. Solea senegalensis is a commercially important flat fish in which females grow 30% faster than males. It has 2n = 42 chromosomes and an XX / XY chromosome system for sex determination, without heteromorph chromosomes but with sex proto-chromosome. In the present study, we are providing the genomic structure and nucleotide sequence of dmrt1 gene obtained from cDNA from male and female adult gonads. A cDNA of 2027 containing an open-reading frame (ORF) of 1206 bp and encoding a 402 aa protein it is described for dmrt1 gene of S. senegalensis. Multiple mRNA isoforms indicating a high variable system of alternative splicing in the expression of dmrt1 of the sole in gonads were studied. None isoforms could be related to sex of individuals. The genomic structure of the dmrt1 of S. senegalensis showed a gene of 31400 bp composed of 7 exons and 6 introns. It contains an unexpected duplication of more than 10399 bp, involving part of the exon I, exons II and III and a SINE element found in the sequence that it is proposed as responsible for the duplication. A mature miRNA of 21 bp in length was localized at 336 bp from exon V. Protein-protein interacting networks of the dmrt1 gene showed matches with dmrt1 protein from Cynoglossus semilaevis and a protein interaction network with 11 nodes (dmrt1 plus 10 other proteins). The phylogenetic relationship of the dmrt1 gene in S. senegalensis is consistent with the evolutionary position of its species. The molecular characterization of this gene will enhance its functional analysis and the understanding of sex differentiation in Solea senegalensis and other flatfish.

Molecular characterization, computational analysis and expression profiling of Dmrt1 gene in Indian major carp, Labeo rohita (Hamilton 1822)

Sexual dimorphism of fish morphology, physiology and behavior is diverse and complex in nature. Doublesex and mab-3 related transcription factor (Dmrt) is a large protein family whose function is sexual development and differentiation in vertebrates. Here, we report a full-length cDNA sequence of Labeo rohita (rohu) Dmrt1 of 907 bp length having 798 bp of open reading frame encoding 265 amino acids. The molecular weight of rohu DMRT1 protein was found to be 28.74 KDa and isoelectric point was 7.53. DMRT1 protein contains 23 positively and 24 negatively charged amino acids with a GRAVY score of -0.618. A characteristic DM domain was found in DMRT1 protein, which is a novel DNA-binding domain. Phylogenetic analysis showed maximum similarity with Cyprinus carpio when compared with DMRT1 of other vertebrates. Molecular docking study identified active sites to be targeted for drug designing. Rohu DMRT1 was observed to interact with other proteins such as FOXL2, CYP19a1a, AMH and SOX9a. Differential expression study revealed higher expression in testis tissue implying its role in male sex differentiation and testicular development. The information generated in the present work could facilitate further research to resolve the issues related to gonadal maturation and reproduction of commercially important aquaculture species.