Coordinated microRNA and messenger RNA expression profiles for understanding sexual dimorphism of gonads and the potential roles of microRNA in the steroidogenesis pathway in Nile tilapia (Oreochromis niloticus)

Histomorphic analysis and expression of mRNA and miRNA in embryonic gonadal differentiation in Chinese soft-shelled turtle (Pelodiscus sinensis)

The Chinese soft-shelled turtle (Pelodiscus sinensis) is extensively cultured in Asia for its nutritional and medical value. Gonadal differentiation is fantastic in turtles, whereas morphologic, mRNA, and miRNA expressions were insufficient in the turtle. In this study, ovaries and testes histomorphology analysis of 14-23 stage embryos were performed, and mRNA and miRNA expression profiles were analyzed. Histomorphology analysis revealed that gonads were undifferentiated at embryonic stage 14. Ovarian morphological differentiation became evident from stage 15, which was characterized by the development of the cortical region and degeneration of the medullary region. Concurrently, testicular morphological differentiation was apparent from stage 15, marked by the development of the medullary region and degeneration of the cortical region. qRT-PCR results showed that Cyp19a1 and Foxl2 exhibited female-specific expression at stage 15 and the expression increased throughout most of the embryonic development. Dmrt1, Amh, and Sox9 displayed male-specific expression at stage 15 and tended to increase substantially at later developmental stages. The expression of miR-8356 and miR-3299 in ZZ gonads were significantly higher than that in ZW gonads at stage 15, 17 and 19, and they had the highest expression at stage 15. While the expression of miR-8085 and miR-7982 had the highest expression at stage 19. Furthermore, chromatin remodeler genes showed differential expression in female and male P. sinensis gonads. These results of master sex-differentiation genes and morphological characteristics would provide a reference for the research of sex differentiation and sex reversal in turtles. Additionally, the expression of chromatin remodeler genes indicated they might be involved in gonadal differentiation of P. sinensis.

Differential Expression of miRNAs, lncRNAs, and circRNAs between Ovaries and Testes in Common Carp (Cyprinus carpio)

Female common carp grow faster than male individuals, implying that rearing females could be more profitable in aquaculture. Non-coding RNAs (ncRNAs) serve as versatile regulators with multiple functions in diverse biological processes. However, the roles of ncRNAs in the sex differentiation of common carp are less studied. In this study, we investigated the expression profiles of ncRNAs, including miRNAs, lncRNAs, and circRNAs, in the gonads to comprehend the roles of ncRNAs in sex differentiation in common carp. A substantial number of differentially expressed (DE) ncRNAs in ovaries and testes were identified. Some miRNAs, notably miR-205, miR-214, and miR-460-5p, might modulate hormone synthesis and thus maintain sex. A novel miRNA, novel_158, was predicted to suppress the expression of foxl3. DE lncRNAs were associated with oocyte meiosis, GnRH signaling pathways, and steroid biosynthesis, while DE circRNA target genes were enriched in the WNT signaling pathway and MAPK signaling pathway. We also analyzed ncRNA-mRNA interactions to shed light on the crosstalk between competing endogenous RNAs (ceRNAs), which is the critical mechanism by which lncRNAs and circRNAs function. Some lncRNAs and circRNAs may be able to competitively bind novel_313, a new miRNA, and thus regulate hsd17β3. Our research will provide a valuable resource for understanding the genetic basis of gonadal differentiation and development in common carp.

Exosome delivery to the testes for dmrt1 suppression: A powerful tool for sex-determining gene studies

Exosomes are endosome-derived extracellular vesicles about 100 nm in diameter. They are emerging as promising delivery platforms due to their advantages in biocompatibility and engineerability. However, research into and applications for engineered exosomes are still limited to a few areas of medicine in mammals. Here, we expanded the scope of their applications to sex-determining gene studies in early vertebrates. An integrated strategy for constructing the exosome-based delivery system was developed for efficient regulation of dmrt1, which is one of the most widely used sex-determining genes in metazoans. By combining classical methods in molecular biology and the latest technology in bioinformatics, isomiR-124a was identified as a dmrt1 inhibitor and was loaded into exosomes and a testis-targeting peptide was used to modify exosomal surface for efficient delivery. Results showed that isomiR-124a was efficiently delivered to the testes by engineered exosomes and revealed that dmrt1 played important roles in maintaining the regular structure and function of testis in juvenile fish. This is the first de novo development of an exosome-based delivery system applied in the study of sex-determining gene, which indicates an attractive prospect for the future applications of engineered exosomes in exploring more extensive biological conundrums.

Identification and Characterization of Sex-Biased miRNAs in the Golden Pompano (Trachinotus blochii)

The golden pompano (Trachinotus blochii) is a marine fish of considerable commercial importance in China. It shows notable sexual size dimorphism; the growth rate of females is faster than that of males. Therefore, sex-biased research is of great importance in T. blochii breeding. However, there have been few studies on sex differentiation and mechanisms underlying sex determination in T. blochii. MicroRNAs (miRNAs) play crucial roles in sex differentiation and determination in animals. However, limited miRNA data are available on fish. In this study, two small RNA libraries prepared from the gonads of T. blochii were constructed and sequenced. The RNA-seq analysis yielded 1366 known and 69 novel miRNAs with 289 significantly differentially expressed miRNAs (p < 0.05). Gene ontology (GO) analysis confirmed that the TFIIA transcription factor complex (GO: 0005672) was the most significantly enriched GO term. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the differentially expressed miRNAs and target genes were mainly related to sex determination and gonadal developmental signaling pathways, specifically the Wnt signaling pathway, MAPK signaling pathway, and steroid biosynthetic pathway. MiRNA-mRNA co-expression network analysis strongly suggested a role for sex-biased miRNAs in sex determination/differentiation and gonadal development. For example, gata4, foxo3, wt1, and sf1 genes were found to be regulated by bta-miR-2898; esr2 and foxo3 by novel_176, and ar by oar-let-7b. Quantitative real-time polymerase chain reaction analysis of selected mRNAs and miRNAs validated the integrated analysis. This study established a set of sex-biased miRNAs that are potential regulatory factors in gonadal development in T. blochii. These results provide new insight into the function of miRNAs in sex differentiation and determination in T. blochii and highlight some key miRNAs for future studies.

Small RNA sequencing reveals sex-related miRNAs in Collichthys lucidus

Collichthys lucidus (C. lucidus) is an economically important fish species, exhibiting sexual dimorphism in its growth rate. However, there is a lack of research on its underlying sex-related mechanisms. Therefore, small RNA sequencing was performed to better comprehend these sex-related molecular mechanisms. In total, 171 differentially expressed miRNAs (DE-miRNAs) were identified between the ovaries and testes. Functional enrichment analysis revealed that the target genes of DE-miRNAs were considerably enriched in the p53 signaling, PI3K–Akt signaling, and TGF-beta signaling pathways. In addition, sex-related miRNAs were identified, and the expression of miR-430c-3p and miR-430f-3p was specifically observed in the gonads compared with other organs and their expression was markedly upregulated in the testes relative to the ovaries. Bmp15 was a target of miR-430c-3p and was greatly expressed in the ovaries compared with the testes. Importantly, miR-430c-3p and bmp15 co-expressed in the ovaries and testes. This research provides the first detailed miRNA profiles for C. lucidus concerning sex, likely laying the basis for further studies on sex differentiation in C. lucidus.

Nuclear microRNAs may regulate mitochondrial gene expression following effluent exposure in darter (Etheostoma) species

Wastewater effluent is a metabolic stressor to aquatic organisms, though the mechanisms regulating metabolic rate in fish are not fully understood. Changes in metabolism may be regulated by microRNA (miRNA), small RNA molecules that post-transcriptionally regulate target mRNA translation in fish. Nuclear encoded miRNA are present in mammalian mitochondria where they regulate translation of mitochondrial genes, namely subunits for oxidative phosphorylation complexes; though this mechanism has not been identified in fish. This study aimed to identify if miRNA are present in darter (Etheostoma spp.) mitochondria, and if the metabolic stress occurring in darters in the Grand River, Waterloo, is partly regulated by miRNAs supressing translation of target mitochondrial genes. Three species of darters (E. caeruleum; E. nigrum; E. flabellare) were collected from upstream and downstream of the Waterloo wastewater treatment plant, and qPCR analysis confirmed the presence of four miRNA bioinformatically predicted to target mitochondrial mRNAs within the mitochondria, namely let-7a, miR-1, miR-122 and miR-20. E. caeruleum collected from downstream had lower cytochrome c oxidase activity, with a respective higher miR-1 abundance in the mitochondria, while E. nigrum had both a higher miR-20 abundance and cytochrome c oxidase activity downstream. E. flabellare was the only species that exhibited a lower miR-122 abundance downstream, despite no difference in cytochrome c oxidase activity between sites. Overall, this study confirmed the presence of miRNA within the mitochondria of daters, predicted a relationship between miR-1, and miR-20 abundance and cytochrome c oxidase activity, and identified one sex-specific miRNA, miR-20.

Comprehensive Characterization of Circular RNAs in Ovary and Testis From Nile Tilapia

Circular RNA (circRNA) is an endogenous biomolecule in eukaryotes. It has tissue- and cell-specific expression patterns and can act as a microRNA sponge or competitive endogenous RNA. Although circRNA has been found in several species in recent years, the expression profiles in fish gonad are still not fully understood. We detected the expression of circRNA in the ovary, testis, and sex-changed gonad of tilapia by high-throughput deep sequencing, and circRNA-specific computing tools. A total of 20,607 circRNAs were obtained, of which 141 were differentially expressed in the testis and ovary. Among these circRNAs, 135 circRNAs were upregulated and 6 circRNAs were downregulated in female fish. In addition, GO annotation and KEGG pathway analysis of the host genes of circRNAs indicated that these host genes were mainly involved in adherens junction, androgen production, and reproductive development, such as ZP3, PLC, delta 4a, ARHGEF10, and HSD17b3. It is worth noting that we found that circRNAs in tilapia gonads have abundant miRNA-binding sites. Among them, 935 circRNAs have a regulatory effect on miR-212, 856 circRNAs have a regulatory effect on miR-200b-3p, and 529 circRNAs have a regulatory effect on miR-200b-5p. Thus, our findings provide a new evidence for circRNA–miRNA networks in the gonads in tilapia.

Identification and in silico characterization of structural and functional impacts of genetic variants in milk protein genes in the Zebu breeds Guzerat and Gyr

Whole genome sequencing of bovine breeds has allowed identification of genetic variants in milk protein genes. However, functional repercussion of such variants at a molecular level has seldom been investigated. Here, the results of a multistep Bioinformatic analysis for functional characterization of recently identified genetic variants in Brazilian Gyr and Guzerat breeds is described, including predicted effects on the following: (i) evolutionary conserved nucleotide positions/regions; (ii) protein function, stability, and interactions; (iii) splicing, branching, and miRNA binding sites; (iv) promoters and transcription factor binding sites; and (v) collocation with QTL. Seventy-one genetic variants were identified in the caseins (CSN1S1, CSN2, CSN1S2, and CSN3), LALBA, LGB, and LTF genes. Eleven potentially regulatory variants and two missense mutations were identified. LALBA Ile60Val was predicted to affect protein stability and flexibility, by reducing the number the disulfide bonds established. LTF Thr546Asn is predicted to generate steric clashes, which could mildly affect iron coordination. In addition, LALBA Ile60Val and LTF Thr546Asn affect exonic splicing enhancers and silencers. Consequently, both mutations have the potential of affecting immune response at individual level, not only in the mammary gland. Although laborious, this multistep procedure for classifying variants allowed the identification of potentially functional variants for milk protein genes.

The emerging role of microRNAs in fish ovary: A mini review

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression primarily at the post-transcriptional levels. It is now well established that miRNAs are crucial regulators of many developmental and physiological processes, including reproduction. In teleosts, expression profiling studies have shown that miRNAs are expressed in the fish ovary and their levels are regulated during follicle development and by hormones. Using CRISPR/Cas9 mediated gene knockout strategies, several recent studies have provided strong evidence that miR-202 and miR-200s on chromosome 23 play critical roles in regulating ovarian development, oogenesis, and ovulation. In this mini review, we provide a brief overview of canonical miRNA biogenesis and functions; summarize miRNAs that are expressed in fish ovary; and discuss the emerging role of miRNAs in regulating fish ovarian functions.

Expression profile of miRNAs involved in the hepatoprotective effects of curcumin against oxidative stress in Nile tilapia

Curcumin is a polyphenol with antioxidant activity that has been used to protect the health of fish livers. Our previous studies about comparative transcriptome have shown that curcumin can enhance the Nrf2-Keap1 signaling pathway and induce downstream anti-stress genes to maintain cell viability. However, the possible role of miRNAs in the protective mechanism of curcumin is not understood. In this study, the tilapia hepatocyte H₂O₂ stress model was used, and the miRNA expression profile for four groups (control group, curcumin group, H₂O₂ group, and protection group) were established by high-throughput sequencing. In our results, 278-333 types of Oreochromis niloticus miRNAs, 309-543 types of conserved miRNAs, and 535-746 types of novel miRNAs were identified in different samples. Differentially expressed miRNAs were identified by comparing miRNA expression profiles among the four groups. The expression levels were confirmed by q-PCR. The target genes of these differentially expressed miRNAs were predicted, and their functional annotations were enriched by GO and KEGG analysis, which revealed that many target genes were involved in "response to stimulus" and "antioxidant activity" in each pair of groups. Several miRNAs related to oxidative stress showed differential expression. For example, in the H₂O₂ group, the expression of miR-122 was decreased, and the expression of miR-21 and miR-489 increased significantly. In the curcumin group, the expression of miR-153b was decreased, and the expression of miR-200a and miR-29 was increased significantly. miR-153b, miR-200a, and miR-29 may be involved in the regulation of the Nrf2-Keap1 signaling pathway by curcumin. This work might provide insights into the molecular mechanisms of miRNA regulation of curcumin on the prevention and alleviation of liver diseases in fish.

Integrated Analysis of miR-430 on Steroidogenesis-Related Gene Expression of Larval Rice Field Eel Monopterus albus

The present study aims to reveal the mechanism by which miR-430s regulate steroidogenesis in larval rice field eel Monopterus albus. To this end, M. albus embryos were respectively microinjected with miRNA-overexpressing mimics (agomir430a, agomir430b, and agomir430c) or miRNA-knockdown inhibitors (antagomir430a, antagomir430b, and antagomir430c). Transcriptome profiling of the larvae indicated that a total of more than 149 differentially expressed genes (DEGs) were identified among the eight treatments. Specifically, DEGs related to steroidogenesis, the GnRH signaling pathway, the erbB signaling pathway, the Wnt signaling pathway, and other pathways were characterized in the transcriptome. We found that steroidogenesis-related genes (hydroxysteroid 17-beta dehydrogenase 3 (17β-hsdb3), hydroxysteroid 17-beta dehydrogenase 7 (17β-hsdb7), hydroxysteroid 17-beta dehydrogenase 12 (17β-hsdb12), and cytochrome P450 family 19 subfamily a (cyp19a1b)) were significantly downregulated in miR-430 knockdown groups. The differential expressions of miR-430 in three gonads indicated different roles of three miR-430 (a, b, and c) isoforms in regulating steroidogenesis and sex differentiation. Mutation of the miR-430 sites reversed the downregulation of cytochrome P450 family 17 (cyp17), cyp19a1b, and forkhead box L2 (foxl2) reporter activities by miR-430, indicating that miR-430 directly interacted with cyp17, cyp19a1b, and foxl2 genes to inhibit their expressions. Combining these findings, we concluded that miR-430 regulated the steroidogenesis and the biosynthesis of steroid hormones by targeting cyp19a1b in larval M. albus. Our results provide a novel insight into steroidogenesis at the early stage of fish at the molecular level.

Identification and Characterization of Osmoregulation Related MicroRNAs in Gills of Hybrid Tilapia Under Three Types of Osmotic Stress

Researchers have increasingly suggested that microRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression and protein translation in organs and respond to abiotic and biotic stressors. To understand the function of miRNAs in osmotic stress regulation of the gills of hybrid tilapia (Oreochromis mossambicus ♀ × Oreochromis urolepis hornorum ♂), high-throughput Illumina deep sequencing technology was used to investigate the expression profiles of miRNAs under salinity stress (S, 25‰), alkalinity stress (A, 4‰) and salinity-alkalinity stress (SA, S: 15‰, A: 4‰) challenges. The results showed that 31, 41, and 27 upregulated and 33, 42, and 40 downregulated miRNAs (P < 0.05) were identified in the salt stress, alkali stress, and saline-alkali stress group, respectively, which were compared with those in the control group (C). Fourteen significantly differently expressed miRNAs were selected randomly and then validated by a quantitative polymerase chain reaction. On the basis of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, genes related to osmoregulation and biosynthesis were enriched in the three types of osmotic stress. In addition, three miRNAs and three predicted target genes were chosen to conduct a quantitative polymerase chain reaction in the hybrid tilapia and its parents during 96-h osmotic stress. Differential expression patterns of miRNAs provided the basis for research data to further investigate the miRNA-modulating networks in osmoregulation of teleost.

Identification of sex differentiation-related microRNA and long non-coding RNA in Takifugu rubripes gonads

Although sex determination and differentiation are key developmental processes in animals, the involvement of non-coding RNA in the regulation of this process is still not clarified. The tiger pufferfish (Takifugu rubripes) is one of the most economically important marine cultured species in Asia, but analyses of miRNA and long non-coding RNA (lncRNA) at early sex differentiation stages have not been conducted yet. In our study, high-throughput sequencing technology was used to sequence transcriptome libraries from undifferentiated gonads of T. rubripes. In total, 231 (107 conserved, and 124 novel) miRNAs were obtained, while 2774 (523 conserved, and 2251 novel) lncRNAs were identified. Of these, several miRNAs and lncRNAs were predicted to be the regulators of the expression of sex-related genes (including fru-miR-15b/foxl2, novel-167, novel-318, and novel-538/dmrt1, novel-548/amh, lnc_000338, lnc_000690, lnc_000370, XLOC_021951, and XR_965485.1/gsdf). Analysis of differentially expressed miRNAs and lncRNAs showed that three mature miRNAs up-regulated and five mature miRNAs were down-regulated in male gonads compared to female gonads, while 79 lncRNAs were up-regulated and 51 were down-regulated. These findings could highlight a group of interesting miRNAs and lncRNAs for future studies and may reveal new insights into the function of miRNAs and lncRNAs in sex determination and differentiation.

Genome-Wide DNA Methylation and Transcriptome Analyses Reveal Epigenetic and Genetic Mechanisms Underlying Sex Maintenance of Adult Chinese Alligator

The sexes of Chinese alligators are determined during embryonic development and remain fixed thereafter. In this study, we investigated the genetic and epigenetic mechanisms underlying sex maintenance in Chinese alligators through RNA sequencing and bisulfite sequencing data analyses of the adult gonads. We identified the genes and pathways (e. g., DMRT1-SOX9-AMH pathway for males and oocyte meiotic maturation pathway for females) involved in male and female sex maintenance and gonadal development of adult Chinese alligators. In contrast to their expression patterns in the embryo, both DMRT1 and the steroid hormone biosynthesis related genes showed a male-biased expression in adult gonads. The overall DNA methylation density and level were higher in testes than in ovaries. Hypermethylation in the gene bodies enhanced the expression of male-biased genes (such as DMRT1-SOX9-AMH and steroid hormone biosynthesis related genes) in the testis, as opposed to the normalization of gene expression. Our results provide insights into the genetic and epigenetic mechanisms underlying sex maintenance in adult Chinese alligators, and are expected to contribute to the development of scientific programs for the successful conservation of this endangered species.

Non-coding RNA Expression Patterns of Two Different Teleost Gonad Maturation Stages

Non-coding RNAs (ncRNAs) are involved in several different regulatory pathways including reproduction. In teleost fish, efficacious reproduction is heavily dependent on the completion of the reproductive cycle. The presence of ncRNA, however, and their expression dynamics and putative regulatory role in mature and immature gonads have not yet been extensively explored. Therefore, the abundance of ncRNAs in mature and immature female sharpsnout seabream (Diplodus puntazzo) was investigated. The sharpsnout seabream is a rudimentary hermaphrodite which, in captivity, displays dysfunctions in the gonad maturation process. Our analyses revealed a gonad specific read length distribution with two main peaks representing miRNAs (21-26 nt) and PIWI RNA (27-34 nt). Besides, distinct expression patterns for several ncRNA biotypes including microRNAs (miRNAs), PIWI RNAs (piRNAs), and ribosomal RNAs (rRNAs) were detected. Identified miRNA accounted to 938, corresponding to ~ 13% of obtained transcripts. Among the differential expressed ncRNAs, 10 (~ 7%) were annotated as miRNA, out of which 2 were found in higher abundance in immature gonads (miR-125c and miR-24) and 8 (miR-451, miR-7a, miR-122-1, miR190a, miR129, ENSGACT00000029608, ENSGACT00000029489, and ENSGACT00000029667) were found to be higher expressed in mature gonads. Putative miRNA targets, including long non-coding RNAs (lncRNAs) and genes, are proposed. Target genes are involved in several processes of fish oocyte development, such as steroidogenesis, proteolysis, and apoptosis, and may explain hormone regulation. This study demonstrates a gonad maturation biased ncRNA profile which in turn may support the role of ncRNAs in ovarian physiology and reproductive performance of fish, stressing the specific function of each RNA biotype in oocyte development.

Comparison of Adult Testis and Ovary MicroRNA Expression Profiles in Reeves' Pond Turtles (Mauremys reevesii) With Temperature-Dependent Sex Determination

Some differentially expressed genes (DEGs) that encode key enzymes involved in steroidogenic biosynthesis (CYP19A1) and key molecules related to gonadal functions (DMRT1, SOX9, AMH, FOXL2, WNT4, RSPO2, and GDF9) have been identified in adult gonadal RNA-seq studies of Reeves' pond turtle (Mauremys reevesii) with temperature-dependent sex determination (TSD). Gonadal functional maintenance and gametogenesis comprises a highly regulated and coordinated biological process, and increasing evidence indicates that microRNAs (miRNAs) may be involved in this dynamic program. However, it is not clear how the regulatory network comprising miRNAs changes the expression levels of these genes. In this study, miRNA sequencing of adult testis and ovary tissues from M. reevesii detected 25 known and 379 novel miRNAs, where 60 miRNAs were differentially expressed in the testis and ovary. A total of 1,477 target genes based on the differentially expressed miRNAs were predicted, where 221 target genes also exhibited differential expression. To verify the accuracy of the sequencing data, 10 differentially expressed miRNAs were validated by quantitative reverse transcription real-time PCR, and were found to be consistent with the transcriptome sequencing results. Moreover, several miRNA/target gene pairs, i.e., mre-let-7a-5p/mre-let-7e-5p and CYP19A1, mre-miR-200a-3p and DMRT1, mre-miR-101-3p and SOX9, and mre-miR-138-5p and AMH were identified. To explore the regulatory role of miRNAs, we conducted target gene enrichment analysis of the miRNAs and 221 target genes in the regulatory network. The signaling pathways related to gonadal functional maintenance and gametogenesis based on the DEGs and target genes were then compared. Our findings provide crucial information to facilitate further research into the regulatory mechanisms involving miRNAs in turtle species with TSD.

Identification and characterization of microRNAs in the gonads of Crassostrea hongkongensis using high-throughput sequencing

Crassostrea hongkongensis is one of the three most-commonly cultivated oyster species in China. Although microRNAs (miRNAs) expression in the gonads have been widely investigated, few studies of miRNAs in mollusk gonads are available, particularly in oyster. In the present study, we analyzed the miRNAs expressed in the ovaries and testes of C. hongkongensis. We obtained 14,166,409 and 15,133,900 raw reads from the ovaries and testes, respectively, yielding 13,634,997 (ovarian) and 14,494,149 (testicular) 18-35-nt sequences. We mapped these sequences to the C. hongkongensis genome reference sequence, and identified 8,771,717 (ovarian) and 9,926,014 (testicular) sequences corresponding to miRNAs in the Rfam database. After blasting the miRNA sequences against the miRBase database, we identified 50 known mature miRNAs and 53 novel miRNAs. Of these, 27 miRNAs were significantly upregulated in ovaries as compared to the testes, and 43 miRNAs were significantly upregulated in the testes as compared to the ovaries. To validate the differential expression results generated by Illumina sequencing, we used RT-real-time quantitative PCR (RT-qPCR) to characterize the expression patterns of the six most differently expressed miRNAs (lgi-miR-1990, lgi-miR-1986, lgi-miR-263b, lgi-miR-279, lgi-miR-1992, and novel_98) as well as two miRNAs associated with gonad development (lgi-miR-29 and lgi-miR-8). Most of the RT-qPCR miRNA expression patterns were similar to those recovered by high-throughput sequencing with the exceptions of novel_98 and lgi-miR-1992. Gene Ontology (GO) annotations indicated that the multi-organism cellular process GO category was enriched with the target genes of the differentially expressed miRNAs. Additionally, the target genes were enriched in several KEGG pathways, including the ECM-receptor interaction, galactose metabolism, phagosome, and notch signaling pathway. These pathways are involved in gonadal differentiation and the maintenance of gonad function. This identification and characterization of the miRNAs differentially expressed between the ovaries and testes of C. hongkongensis will increase our understanding of the role of miRNAs in gonad differentiation in the oyster.

Seminal Plasma Exosomes: Promising Biomarkers for Identification of Male and Pseudo-Males in Cynoglossus semilaevis

In mammals, small RNAs enclosed in exosomes have been identified as appropriate signatures for disease diagnosis. However, there is limited information on exosomes derived from seminal plasma, and few studies have reported analyzed the composition of exosomes and enclosed small RNAs in fish. The half-smooth tongue sole (Cynoglossus semilaevis) is an economically important fish for aquaculture, and it exhibits sexual dimorphism: the female gender show higher growth rates and larger body sizes than males. Standard karyotype analysis and artificial gynogenesis tests have revealed that this species uses heterogametic sex determination (ZW/ZZ), and so-called sex-reversed pseudo-males exist. In this study, we successfully identified exosomes in the seminal plasma of C. semilaevis; to the best of our knowledge, this is the first report of exosomes in fish seminal plasma. Analysis of the nucleotide composition showed that miRNAs were dominant in the exosomes, and the miRNAs were sequenced and compared to identify signature miRNAs as sexual biomarkers. Moreover, target genes of the signature miRNAs were predicted by sequence matching and annotation. Finally, four miRNAs (dre-miR-141-3P, dre-miR-10d-5p, ssa-miR-27b-3p, and ssa-miR-23a-3p) with significant differential expression in the males and pseudo-males were selected from the signature candidate miRNAs as markers for sex identification, and their expression profiles were verified using real-time quantitative PCR. Our findings could provide an effective detection method for sex differentiation in fish.

Deep sequencing identification of miRNAs in pigeon ovaries illuminated with monochromatic light

Background

The use of light of different wavelengths has grown popular in the poultry industry. An optimum wavelength is believed to improve pigeon egg production, but little is known about the role of microRNAs (miRNAs) in the effects of monochromatic light on ovarian pigeon function. Herein, we harvested ovaries from pigeons reared under monochromatic light of different wavelength and performed deep sequencing on various tissues using an Illumina Solexa high-throughput instrument.

Results

We obtained 66,148,548, 67,873,805, and 71,661,771 clean reads from ovaries of pigeons reared under red light (RL), blue light (BL), and white light (WL), respectively. We identified 1917 known miRNAs in nine libraries, of which 524 were novel. Three and five differentially expressed miRNAs were identified in BL vs. WL and RL vs. WL groups, respectively. Quantitative reverse transcription PCR was used to validate differentially expressed miRNAs (miR-200, miR-122, and miR-205b). In addition, 5824 target genes were annotated as differentially expressed miRNAs, most of which are involved in reproductive pathways including oestrogen signalling, cell cycle, and oocyte maturation. Notably, ovarian miR-205b expression was significantly negatively correlated with its target 11β-hydroxysteroid dehydrogenase type 1 (HSD11B1).

Conclusions

miRNA–mRNA network analysis suggests that miR-205b targeting of HSD11B1 plays a key role in the effects of monochromatic light on pigeon egg production. These findings indicate that monochromatic light shortens the oviposition interval of pigeons, which may be useful for egg production and pigeon breeding.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4831-6) contains supplementary material, which is available to authorized users.

Comparative Profiling of MicroRNAs Reveals the Underlying Toxicological Mechanism in Mice Testis Following Carbon Ion Radiation

This study investigated the toxicity of heavy ion radiation to mice testis by microRNA (miRNA) sequencing and bioinformatics analyses. Testicular indices and histology were measured following enterocoelia irradiation with a 2 Gy carbon ion beam, with the testes exhibiting the most serious injuries at 4 weeks after carbon ion radiation (CIR) exposure. Illumina sequencing technology was used to sequence small RNA libraries of the control and irradiated groups at 4 weeks after CIR. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses implicated differential miRNAs in the regulation of target genes involved in metabolism, development, and reproduction. Here, 8 miRNAs, including miR-34c-5p, miR-138, and 6 let-7 miRNA family members previously reported in testis after radiation, were analyzed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) to validate miRNA sequencing data. The differentially expressed miRNAs described here provided a novel perspective for the role of miRNAs in testis toxicity following CIR.

Fishing Into the MicroRNA Transcriptome

In the last decade, several studies have been focused on revealing the microRNA (miRNA) repertoire and determining their functions in farm animals such as poultry, pigs, cattle, and fish. These small non-protein coding RNA molecules (18-25 nucleotides) are capable of controlling gene expression by binding to messenger RNA (mRNA) targets, thus interfering in the final protein output. MiRNAs have been recognized as the main regulators of biological features of economic interest, including body growth, muscle development, fat deposition, and immunology, among other highly valuable traits, in aquatic livestock. Currently, the miRNA repertoire of some farmed fish species has been identified and characterized, bringing insights about miRNA functions, and novel perspectives for improving health and productivity. In this review, we summarize the current advances in miRNA research by examining available data on Neotropical and other key species exploited by fisheries and in aquaculture worldwide and discuss how future studies on Neotropical fish could benefit from this knowledge. We also make a horizontal comparison of major results and discuss forefront strategies for miRNA manipulation in aquaculture focusing on forward-looking ideas for forthcoming research.

Integrative testis transcriptome analysis reveals differentially expressed miRNAs and their mRNA targets during early puberty in Atlantic salmon

BACKGROUND

Our understanding of the molecular mechanisms implementing pubertal maturation of the testis in vertebrates is incomplete. This topic is relevant in Atlantic salmon aquaculture, since precocious male puberty negatively impacts animal welfare and growth. We hypothesize that certain miRNAs modulate mRNAs relevant for the initiation of puberty. To explore which miRNAs regulate mRNAs during initiation of puberty in salmon, we performed an integrated transcriptome analysis (miRNA and mRNA-seq) of salmon testis at three stages of development: an immature, long-term quiescent stage, a prepubertal stage just before, and a pubertal stage just after the onset of single cell proliferation activity in the testis.

RESULTS

Differentially expressed miRNAs clustered into 5 distinct expression profiles related to the immature, prepubertal and pubertal salmon testis. Potential mRNA targets of these miRNAs were predicted with miRmap and filtered for mRNAs displaying negatively correlated expression patterns. In summary, this analysis revealed miRNAs previously known to be regulated in immature vertebrate testis (miR-101, miR-137, miR-92b, miR-18a, miR-20a), but also miRNAs first reported here as regulated in the testis (miR-new289, miR-30c, miR-724, miR-26b, miR-new271, miR-217, miR-216a, miR-135a, miR-new194 and the novel predicted n268). By KEGG enrichment analysis, progesterone signaling and cell cycle pathway genes were found regulated by these differentially expressed miRNAs. During the transition into puberty we found differential expression of miRNAs previously associated (let7a/b/c), or newly associated (miR-15c, miR-2184, miR-145 and the novel predicted n7a and b) with this stage. KEGG enrichment analysis revealed that mRNAs of the Wnt, Hedgehog and Apelin signaling pathways were potential regulated targets during the transition into puberty. Likewise, several regulated miRNAs in the pubertal stage had earlier been associated (miR-20a, miR-25, miR-181a, miR-202, let7c/d/a, miR-125b, miR-222a/b, miR-190a) or have now been found connected (miR-2188, miR-144, miR-731, miR-8157 and the novel n2) to the initiation of puberty.

CONCLUSIONS

This study has - for the first time - linked testis maturation to specific miRNAs and their inversely correlated expressed targets in Atlantic salmon. The study indicates a broad functional conservation of already known miRNAs and associated pathways involved in the transition into puberty in vertebrates. The analysis also reveals miRNAs not previously associated with testis tissue or its maturation, which calls for further functional studies in the testis.

Identification of male-biased microRNA-107 as a direct regulator for nuclear receptor subfamily 5 group A member 1 based on sexually dimorphic microRNA expression profiling from chicken embryonic gonads

Several studies indicate that sexual dimorphic microRNAs (miRNAs) in chicken gonads are likely to have important roles in sexual development, but a more global understanding of the roles of miRNAs in sexual differentiation is still needed. To this end, we performed miRNA expression profiling in chicken gonads at embryonic day 5.5 (E5.5). Among the sex-biased miRNAs validated by qRT-PCR, twelve male-biased and six female-biased miRNAs were consistent with the sequencing results. Bioinformatics analysis revealed that some sex-biased miRNAs were potentially involved in gonadal development. Further functional analysis found that over-expression of miR-107 directly inhibited nuclear receptor subfamily 5 group A member 1 (NR5a1), and its downstream cytochrome P450 family 19 subfamily A, polypeptide 1 (CYP19A1). However, anti-Mullerian hormone (AMH) was not directly or indirectly regulated by miR-107. Overall results indicate that miR-107 may specifically mediate avian ovary-development by post-transcriptional regulation of NR5a1 and CYP19A1 in estrogen signaling pathways.

Integrated analysis of miRNA and mRNA expression profiles in tilapia gonads at an early stage of sex differentiation

Background

MicroRNAs (miRNAs) represent a second regulatory network that has important effects on gene expression and protein translation during biological process. However, the possible role of miRNAs in the early stages of fish sex differentiation is not well understood. In this study, we carried an integrated analysis of miRNA and mRNA expression profiles to explore their possibly regulatory patterns at the critical stage of sex differentiation in tilapia.

Results

We identified 279 pre-miRNA genes in tilapia genome, which were highly conserved in other fish species. Based on small RNA library sequencing, we identified 635 mature miRNAs in tilapia gonads, in which 62 and 49 miRNAs showed higher expression in XX and XY gonads, respectively. The predicted targets of these sex-biased miRNAs (e.g., miR-9, miR-21, miR-30a, miR-96, miR-200b, miR-212 and miR-7977) included genes encoding key enzymes in steroidogenic pathways (Cyp11a1, Hsd3b, Cyp19a1a, Hsd11b) and key molecules involved in vertebrate sex differentiation (Foxl2, Amh, Star1, Sf1, Dmrt1, and Gsdf). These genes also showed sex-biased expression in tilapia gonads at 5 dah. Some miRNAs (e.g., miR-96 and miR-737) targeted multiple genes involved in steroid synthesis, suggesting a complex miRNA regulatory network during early sex differentiation in this fish.

Conclusions

The sequence and expression patterns of most miRNAs in tilapia are conserved in fishes, indicating the basic functions of vertebrate miRNAs might share a common evolutionary origin. This comprehensive analysis of miRNA and mRNA at the early stage of molecular sex differentiation in tilapia XX and XY gonads lead to the discovery of differentially expressed miRNAs and their putative targets, which will facilitate studies of the regulatory network of molecular sex determination and differentiation in fishes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2636-z) contains supplementary material, which is available to authorized users.