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Ramos-Júdez S, Danis T, Angelova N, Tsakogiannis A, Giménez I, Tsigenopoulos CS, Duncan N, Manousaki T. Transcriptome analysis of flathead grey mullet ( Mugil cephalus) ovarian development induced by recombinant gonadotropin hormones. Front Physiol 2022; 13:1033445. [PMID: 36388126 PMCID: PMC9664002 DOI: 10.3389/fphys.2022.1033445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023] Open
Abstract
Background: Treatment with recombinant gonadotropin hormones (rGths), follicle-stimulating hormone (rFsh) and luteinizing hormone (rLh), was shown to induce and complete vitellogenesis to finally obtain viable eggs and larvae in the flathead grey mullet (Mugil cephalus), a teleost arrested at early stages of gametogenesis in intensive captivity conditions. This study aimed to investigate the transcriptomic changes that occur in the ovary of females during the rGths-induced vitellogenesis. Methods: Ovarian samples were collected through biopsies from the same five females at four stages of ovarian development. RNASeq libraries were constructed for all stages studied, sequenced on an Illumina HiSeq4000, and a de novo transcriptome was constructed. Differentially expressed genes (DEGs) were identified between stages and the functional properties of DEGs were characterized by comparison with the gene ontology and Kyoto Encyclopedia. An enrichment analysis of molecular pathways was performed. Results: The de novo transcriptome comprised 287,089 transcripts after filtering. As vitellogenesis progressed, more genes were significantly upregulated than downregulated. The rFsh application induced ovarian development from previtellogenesis to early-to-mid-vitellogenesis with associated pathways enriched from upregulated DEGs related to ovarian steroidogenesis and reproductive development, cholesterol metabolism, ovarian growth and differentiation, lipid accumulation, and cell-to-cell adhesion pathways. The application of rFsh and rLh at early-to-mid-vitellogenesis induced the growth of oocytes to late-vitellogenesis and, with it, the enrichment of pathways from upregulated DEGs related to the production of energy, such as the lysosomes activity. The application of rLh at late-vitellogenesis induced the completion of vitellogenesis with the enrichment of pathways linked with the switch from vitellogenesis to oocyte maturation. Conclusion: The DEGs and enriched molecular pathways described during the induced vitellogenesis of flathead grey mullet with rGths were typical of natural oogenesis reported for other fish species. Present results add new knowledge to the rGths action to further raise the possibility of using rGths in species that present similar reproductive disorders in aquaculture, the aquarium industry as well as the conservation of endangered species.
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Affiliation(s)
| | - Theodoros Danis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
| | - Nelina Angelova
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
| | - Alexandros Tsakogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
| | | | - Costas S. Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
| | | | - Tereza Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
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Optimized Method for the Identification of Candidate Genes and Molecular Maker Development Related to Drought Tolerance in Oil Palm (Elaeis guineensis Jacq.). PLANTS 2022; 11:plants11172317. [PMID: 36079700 PMCID: PMC9460821 DOI: 10.3390/plants11172317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022]
Abstract
Drought is a major constraint in oil palm (Elaeis guineensis Jacq.) production. As oil palm breeding takes a long time, molecular markers of genes related to drought tolerance characteristics were developed for effective selection. Two methods of gene identification associated with drought, differential display reverse transcription polymerase chain reaction (DDRT-PCR) and pyrosequencing platform, were conducted before developing the EST-SSR marker. By DDRT-PCR, fourteen out of twenty-four primer combinations yielded the polymorphism in leaf as 77.66% and root as 96.09%, respectively. BLASTN and BLASTX revealed nucleotides from 8 out of 236 different banding similarities to genes associated with drought stress. Five out of eight genes gave a similarity with our pyrosequencing sequencing database. Furthermore, pyrosequencing analysis of two oil palm libraries, drought-tolerant, and drought sensitive, found 117 proteins associated with drought tolerance. Thirteen out of sixty EST-SSR primers could be distinguished in 119 oil palm parents in our breeding program. All of our found genes revealed an ability to develop as a molecular marker for drought tolerance. However, the function of the validated genes on drought response in oil palm must be evaluated.
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A Comparison of Reproductive Performances in Young and Old Females: A Case Study on the Atlantic Bluefin Tuna in the Mediterranean Sea. Animals (Basel) 2021; 11:ani11123340. [PMID: 34944116 PMCID: PMC8697984 DOI: 10.3390/ani11123340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 12/23/2022] Open
Abstract
Simple Summary The Atlantic bluefin tuna Thunnus thynnus is a species characterized by complex trans-oceanic migrations linked to size, which rely on the delicate trade-off between somatic growth and reproduction before and during the migratory movements to reach spawning grounds. Therefore, understanding the processes that drive reproduction and elucidating its age-related regulation is essential in the context of sustainable fishery management. In this study, carried out in the Mediterranean Sea, older bluefin tuna females were found to have greater reproductive performances than younger females according to a molecular biology approach (i.e., gene expression), a result that likely mirrors a better physical condition, different habitat usage or migratory behaviour. This result highlights the importance of preserving large females for their major reproductive contribution at a stock level. Furthermore, the gonad-specific mir-202, which belongs to a class of non-coding RNA, called miRNA, that regulate the post-transcription of protein-coding genes, was identified as a potential candidate to play a role in egg quality and quantity (i.e., fecundity) during ovarian maturation through age- or stage-dependent reproductive processes. Overall, the present study contributes to improve the sustainability of the Atlantic bluefin tuna fishery in the Mediterranean Sea. Abstract In the Mediterranean Sea, a demographic substructure of the Atlantic bluefin tuna Thunnus thynnus has emerged over the last decade, with old and young individuals exhibiting different horizontal movements and spatial–temporal patterns of gonad maturation. In the present study, histology and molecular reproductive markers were integrated with the gonad-specific mir-202 gene expression and ovarian localization to provide a comprehensive picture of the reproductive performances in young and old females and investigate the role played by the mir-202 during gonadal maturation. During the reproductive period, old females (>100 kg; 194.6 ± 33.9 cm straight fork length; 11.3 ± 2.7 years old) were found to have greater reproductive performances than younger females (<80 kg; 139.3 ± 18.8 cm straight fork length; 8.4 ± 1.1 years old) according to gene expression results, suggesting a prolonged spawning season, earlier arrival on spawning grounds and/or better condition in older females. The mir-202-5p showed no global changes; it was abundantly expressed in granulosa cells and faintly present in the ooplasm. On the other hand, the mir-202-3p expression profile reflected levels of oocyte maturation molecular markers (star, lhr) and both histological and molecular (casp3) levels of follicular atresia. Overall, old females exhibited greater reproductive performances than younger females, likely reflecting different reproductive dynamics linked to the physical condition, habitat usage and migratory behaviour. These results highlight the importance of preserving large and old females in the context of fishery management. Finally, the mir-202 appears to be a good candidate to regulate the reproductive output of this species in an autocrine/paracrine manner through either stage- or age-dependent processes.
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Gomez-Sanchez EP, Gomez-Sanchez CE. 11β-hydroxysteroid dehydrogenases: A growing multi-tasking family. Mol Cell Endocrinol 2021; 526:111210. [PMID: 33607268 PMCID: PMC8108011 DOI: 10.1016/j.mce.2021.111210] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/02/2021] [Accepted: 02/07/2021] [Indexed: 02/06/2023]
Abstract
This review briefly addresses the history of the discovery and elucidation of the three cloned 11β-hydroxysteroid dehydrogenase (11βHSD) enzymes in the human, 11βHSD1, 11βHSD2 and 11βHSD3, an NADP+-dependent dehydrogenase also called the 11βHSD1-like dehydrogenase (11βHSD1L), as well as evidence for yet identified 11βHSDs. Attention is devoted to more recently described aspects of this multi-functional family. The importance of 11βHSD substrates other than glucocorticoids including bile acids, 7-keto sterols, neurosteroids, and xenobiotics is discussed, along with examples of pathology when functions of these multi-tasking enzymes are disrupted. 11βHSDs modulate the intracellular concentration of glucocorticoids, thereby regulating the activation of the glucocorticoid and mineralocorticoid receptors, and 7β-27-hydroxycholesterol, an agonist of the retinoid-related orphan receptor gamma (RORγ). Key functions of this nuclear transcription factor include regulation of immune cell differentiation, cytokine production and inflammation at the cell level. 11βHSD1 expression and/or glucocorticoid reductase activity are inappropriately increased with age and in obesity and metabolic syndrome (MetS). Potential causes for disappointing results of the clinical trials of selective inhibitors of 11βHSD1 in the treatment of these disorders are discussed, as well as the potential for more targeted use of inhibitors of 11βHSD1 and 11βHSD2.
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Affiliation(s)
| | - Celso E Gomez-Sanchez
- Department of Pharmacology and Toxicology, Jackson, MS, USA; Medicine (Endocrinology), Jackson, MS, USA; University of Mississippi Medical Center and G.V. (Sonny) Montgomery VA Medical Center(3), Jackson, MS, USA
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Chen X, Zhu W, Du Y, Liu X, Geng Z. Genetic Parameters for Yolk Cholesterol and Transcriptional Evidence Indicate a Role of Lipoprotein Lipase in the Cholesterol Metabolism of the Chinese Wenchang Chicken. Front Genet 2019; 10:902. [PMID: 31632438 PMCID: PMC6786094 DOI: 10.3389/fgene.2019.00902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/26/2019] [Indexed: 11/13/2022] Open
Abstract
The yolk cholesterol has been reported to affect egg quality and breeding performance in chickens. However, the genetic parameters and molecular mechanisms regulating yolk cholesterol remain largely unknown. Here, we used the Wenchang chicken, a Chinese indigenous breed with a complete pedigree, as an experimental model, and we examined 24 sire families (24 males and 240 females) and their 362 daughters. First, egg quality and yolk cholesterol content were determined in 40-week-old chickens of two consecutive generations, and the heritability of these parameters was analyzed using the half-sib correlation method. Among first-generation individuals, the egg weight, egg shape index, shell strength, shell thickness, yolk weight, egg white height, Haugh unit, and cholesterol content were 45.36 ± 4.44 g, 0.81 ± 0.12, 3.07 ± 0.92 kg/cm2, 0.340 ± 0.032 mm, 15.57 ± 1.64 g, 3.36 ± 1.15 mm, 58.70 ± 12.33, and 274.3 ± 36.73 mg/egg, respectively. When these indexes were compared to those of the following generation, no statistically significant difference was detected. Although yolk cholesterol content was not associated with egg quality in females, an increase in yolk cholesterol content was correlated with increased yolk weight and albumin height in sire families (p < 0.05). Moreover, the heritability estimates for the yolk cholesterol content were 0.328 and 0.530 in female and sire families, respectively. Therefore, the yolk cholesterol content was more strongly associated with the sire family. Next, chickens with low and high yolk cholesterol contents were selected for follicular membrane collection. Total RNA was extracted from these samples and used as a template for transcriptional sequencing. In total, 375 down- and 578 upregulated genes were identified by comparing the RNA sequencing data of chickens with high and low yolk cholesterol contents. Furthermore, Gene Ontology term and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses indicated the involvement of energy metabolism and immune-related pathways in yolk cholesterol deposition. Several genes participating in the regulation of the yolk cholesterol content were located on the sex chromosome Z, among which lipoprotein lipase (LPL) was associated with the peroxisome proliferator-activated receptor signaling pathway and the Gene Ontology term cellular component. Collectively, our data suggested that the ovarian steroidogenesis pathway and the downregulation of LPL played critical roles in the regulation of yolk cholesterol content.
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Affiliation(s)
- Xingyong Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
| | - Wenjun Zhu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yeye Du
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xue Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zhaoyu Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, China
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Peri S, Kulkarni A, Feyertag F, Berninsone PM, Alvarez-Ponce D. Phylogenetic Distribution of CMP-Neu5Ac Hydroxylase (CMAH), the Enzyme Synthetizing the Proinflammatory Human Xenoantigen Neu5Gc. Genome Biol Evol 2018; 10:207-219. [PMID: 29206915 PMCID: PMC5767959 DOI: 10.1093/gbe/evx251] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2017] [Indexed: 01/25/2023] Open
Abstract
The enzyme CMP-N-acetylneuraminic acid hydroxylase (CMAH) is responsible for the synthesis of N-glycolylneuraminic acid (Neu5Gc), a sialic acid present on the cell surface proteins of most deuterostomes. The CMAH gene is thought to be present in most deuterostomes, but it has been inactivated in a number of lineages, including humans. The inability of humans to synthesize Neu5Gc has had several evolutionary and biomedical implications. Remarkably, Neu5Gc is a xenoantigen for humans, and consumption of Neu5Gc-containing foods, such as red meats, may promote inflammation, arthritis, and cancer. Likewise, xenotransplantation of organs producing Neu5Gc can result in inflammation and organ rejection. Therefore, knowing what animal species contain a functional CMAH gene, and are thus capable of endogenous Neu5Gc synthesis, has potentially far-reaching implications. In addition to humans, other lineages are known, or suspected, to have lost CMAH; however, to date reports of absent and pseudogenic CMAH genes are restricted to a handful of species. Here, we analyze all available genomic data for nondeuterostomes, and 322 deuterostome genomes, to ascertain the phylogenetic distribution of CMAH. Among nondeuterostomes, we found CMAH homologs in two green algae and a few prokaryotes. Within deuterostomes, putatively functional CMAH homologs are present in 184 of the studied genomes, and a total of 31 independent gene losses/pseudogenization events were inferred. Our work produces a list of animals inferred to be free from endogenous Neu5Gc based on the absence of CMAH homologs and are thus potential candidates for human consumption, xenotransplantation research, and model organisms for investigation of human diseases.
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Affiliation(s)
- Sateesh Peri
- Department of Biology, University of Nevada, Reno
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Nan F, Feng J, Lv J, Liu Q, Xie S. Transcriptome analysis of the typical freshwater rhodophytes Sheathia arcuata grown under different light intensities. PLoS One 2018; 13:e0197729. [PMID: 29813098 PMCID: PMC5973588 DOI: 10.1371/journal.pone.0197729] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/08/2018] [Indexed: 01/25/2023] Open
Abstract
The Rhodophyta Sheathia arcuata is exclusively distributed in freshwater, constituting an important component in freshwater flora. This study presents the first transcriptome profiling of freshwater Rhodophyta taxa. A total of 161,483 assembled transcripts were identified, annotated and classified into different biological categories and pathways based on BLAST against diverse databases. Different gene expression patterns were caused principally by different irradiances considering the similar water conditions of the sampling site when the specimens were collected. Comparison results of gene expression levels under different irradiances revealed that photosynthesis-related pathways significantly up-regulated under the weak light. Molecular responses for improved photosynthetic activity include the transcripts corresponding to antenna proteins (LHCA1 and LHCA4), photosynthetic apparatus proteins (PSBU, PETB, PETC, PETH and beta and gamma subunits of ATPase) and metabolic enzymes in the carbon fixation. Along with photosynthesis, other metabolic activities were also regulated to optimize the growing and development of S. arcuata under appropriate sunlight. Protein-protein interactive networks revealed the most responsive up-expressed transcripts were ribosomal proteins. The de-novo transcriptome assembly of S. arcuata provides a foundation for further investigation on the molecular mechanism of photosynthesis and environmental adaption for freshwater Rhodophyta.
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Affiliation(s)
- Fangru Nan
- School of Life Science, Shanxi University, Taiyuan, China
| | - Jia Feng
- School of Life Science, Shanxi University, Taiyuan, China
| | - Junping Lv
- School of Life Science, Shanxi University, Taiyuan, China
| | - Qi Liu
- School of Life Science, Shanxi University, Taiyuan, China
| | - Shulian Xie
- School of Life Science, Shanxi University, Taiyuan, China
- * E-mail:
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Arias Torres AJ, Páez JB, Zelarayán LI. Oocyte maturation in the toad Rhinella arenarum (Amphibia, Anura): Evidence of cAMP involvement in steroid production and action. Mol Reprod Dev 2018; 85:137-145. [PMID: 29247588 DOI: 10.1002/mrd.22944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 12/07/2017] [Indexed: 11/11/2022]
Abstract
In this work, we describe the participation of the adenylate cyclase/3'-5'-cyclic adenonsine monophosphate (cAMP) pathway in the seasonal follicular secretion of progesterone (P4 ) and testosterone (T), and its relationship with the maturation of Rhinella arenarum oocytes. Under gonadotropin stimulation, P4 secretion was the dominant steroid produced during the reproductive period, resulting in 100% germinal vesicle breakdown (GVBD) in oocytes in vitro; in contrast, T and estradiol (E2 ) secretion increased (∼16 nM/20 follicles and ∼80 pM/20 follicles, respectively) during the non-reproductive period, but only yielded 50% GVBD. Treatment of the follicles with dibutyryl-cAMP or forskolin induced a significant increase in T secretion during both periods, but P4 secretion did not significantly change and GVBD did not occur. These results suggest that high cAMP levels in the oocyte maintain meiotic arrest and prevent the induction effect of follicular steroids. An increase in cAMP levels in denuded oocytes, however, negatively regulated T-induced maturation since treatment with increasing db-cAMP or forskolin inhibited their maturation. Therefore, we hypothesize that an elevation in T during the non-reproductive period favors its aromatization to E2 , leading to follicle growth. During the reproductive period, P4 production might promote oocyte maturation when environmental conditions are favorable for reproduction. Together, the results indicate that steroidogenesis is seasonal and depends on gonadotropic activity in R. arenarum.
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Affiliation(s)
- Ana J Arias Torres
- Instituto Superior de Investigaciones Biológicas (INSIBIO)-CONICET-UNT, San Miguel de Tucumán, Tucumán, Argentina.,Instituto de Ambiente de Montaña y Regiones Áridas (IAMRA), Universidad Nacional de Chilecito (UNdeC), Chilecito, La Rioja, Argentina
| | - José B Páez
- Facultad de Bioquímica, Química y Farmacia, UNT, San Miguel de Tucumán, Tucumán, Argentina
| | - Liliana I Zelarayán
- Instituto Superior de Investigaciones Biológicas (INSIBIO)-CONICET-UNT, San Miguel de Tucumán, Tucumán, Argentina.,Facultad de Bioquímica, Química y Farmacia, UNT, San Miguel de Tucumán, Tucumán, Argentina
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Djordjevic D, Kusumi K, Ho JWK. XGSA: A statistical method for cross-species gene set analysis. Bioinformatics 2017; 32:i620-i628. [PMID: 27587682 DOI: 10.1093/bioinformatics/btw428] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION Gene set analysis is a powerful tool for determining whether an experimentally derived set of genes is statistically significantly enriched for genes in other pre-defined gene sets, such as known pathways, gene ontology terms, or other experimentally derived gene sets. Current gene set analysis methods do not facilitate comparing gene sets across different organisms as they do not explicitly deal with homology mapping between species. There lacks a systematic investigation about the effect of complex gene homology on cross-species gene set analysis. RESULTS In this study, we show that not accounting for the complex homology structure when comparing gene sets in two species can lead to false positive discoveries, especially when comparing gene sets that have complex gene homology relationships. To overcome this bias, we propose a straightforward statistical approach, called XGSA, that explicitly takes the cross-species homology mapping into consideration when doing gene set analysis. Simulation experiments confirm that XGSA can avoid false positive discoveries, while maintaining good statistical power compared to other ad hoc approaches for cross-species gene set analysis. We further demonstrate the effectiveness of XGSA with two real-life case studies that aim to discover conserved or species-specific molecular pathways involved in social challenge and vertebrate appendage regeneration. AVAILABILITY AND IMPLEMENTATION The R source code for XGSA is available under a GNU General Public License at http://github.com/VCCRI/XGSA CONTACT: jho@victorchang.edu.au.
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Affiliation(s)
- Djordje Djordjevic
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia, St Vincent's Clinical School, University of New South Wales Australia, Darlinghurst, NSW 2010, Australia
| | - Kenro Kusumi
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joshua W K Ho
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia, St Vincent's Clinical School, University of New South Wales Australia, Darlinghurst, NSW 2010, Australia
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Liu DT, Brewer MS, Chen S, Hong W, Zhu Y. Transcriptomic signatures for ovulation in vertebrates. Gen Comp Endocrinol 2017; 247:74-86. [PMID: 28111234 PMCID: PMC5410184 DOI: 10.1016/j.ygcen.2017.01.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/14/2017] [Accepted: 01/17/2017] [Indexed: 01/01/2023]
Abstract
The central roles of luteinizing hormone (LH), progestin and their receptors for initiating ovulation have been well established. However, signaling pathways and downstream targets such as proteases that are essential for the rupture of follicular cells are still unclear. Recently, we found anovulation in nuclear progestin receptor (Pgr) knockout (Pgr-KO) zebrafish, which offers a new model for examining genes and pathways that are important for ovulation and fertility. In this study, we examined expression of all transcripts using RNA-Seq in preovulatory follicular cells collected following the final oocyte maturation, but prior to ovulation, from wild-type (WT) or Pgr-KO fish. Differential expression analysis revealed 3567 genes significantly differentially expressed between WT and Pgr-KO fish (fold change⩾2, p<0.05). Among those, 1543 gene transcripts were significantly more expressed, while 2024 genes were significantly less expressed, in WT than those in Pgr-KO. We then retrieved and compared transcriptional data from online databases and further identified 661 conserved genes in fish, mice, and humans that showed similar levels of high (283 genes) or low (387) expression in animals that were ovulating compared to those with no ovulation. For the first time, ovulatory genes and their involved biological processes and pathways were also visualized using Enrichment Map and Cytoscape. Intriguingly, enrichment analysis indicated that the genes with higher expression were involved in multiple ovulatory pathways and processes such as inflammatory response, angiogenesis, cytokine production, cell migration, chemotaxis, MAPK, focal adhesion, and cytoskeleton reorganization. In contrast, the genes with lower expression were mainly involved in DNA replication, DNA repair, DNA methylation, RNA processing, telomere maintenance, spindle assembling, nuclear acid transport, catabolic processes, and nuclear and cell division. Our results indicate that a large set of genes (>3000) is differentially regulated in the follicular cells in zebrafish prior to ovulation, terminating programs such as growth and proliferation, and beginning processes including the inflammatory response and apoptosis. Further studies are required to establish relationships among these genes and an ovulatory circuit in the zebrafish model.
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Affiliation(s)
- Dong Teng Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian Province 361102, People's Republic of China; Department of Biology, East Carolina University, Greenville, NC 27858, United States
| | - Michael S Brewer
- Department of Biology, East Carolina University, Greenville, NC 27858, United States
| | - Shixi Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian Province 361102, People's Republic of China
| | - Wanshu Hong
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian Province 361102, People's Republic of China
| | - Yong Zhu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian Province 361102, People's Republic of China; Department of Biology, East Carolina University, Greenville, NC 27858, United States.
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Żarski D, Nguyen T, Le Cam A, Montfort J, Dutto G, Vidal MO, Fauvel C, Bobe J. Transcriptomic Profiling of Egg Quality in Sea Bass (Dicentrarchus labrax) Sheds Light on Genes Involved in Ubiquitination and Translation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:102-115. [PMID: 28181038 PMCID: PMC5323488 DOI: 10.1007/s10126-017-9732-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 01/09/2017] [Indexed: 05/31/2023]
Abstract
Variable and low egg quality is a major limiting factor for the development of efficient aquaculture production. This stems from limited knowledge on the mechanisms underlying egg quality in cultured fish. Molecular analyses, such as transcriptomic studies, are valuable tools to identify the most important processes modulating egg quality. However, very few studies have been devoted to this aspect so far. Within this study, the microarray-based transcriptomic analysis of eggs (of different quality) of sea bass (Dicentrarchus labrax) was performed. An Agilent oligo microarray experiment was performed on labelled mRNA extracted from 16 batches of eggs (each batch obtained from a different female) of sea bass, in which over 24,000 published probe arrays were used. We identified 39 differentially expressed genes exhibiting a differential expression between the groups of low (fertilization rate < 60 %) and high (fertilization rate > 60 %) quality. The mRNA levels of eight genes were further analyzed by quantitative PCR. Seven genes were confirmed by qPCR to be differentially expressed in eggs of low and high quality. This study confirmed the importance of some of the genes already reported to be potential molecular quality indicators (mainly rnf213 and irf7), but we also found new genes (mainly usp5, mem-prot, plec, cenpf), which had not yet been reported to be quality-dependent in fish. These results suggest the importance of genes involved in several important processes, such as protein ubiquitination, translation, DNA repair, and cell structure and architecture; these probably being the mechanisms that contribute to egg developmental competence in sea bass.
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Affiliation(s)
- Daniel Żarski
- Department of Lake and River Fisheries, University of Warmia and Mazury, ul. Oczapowskiego 2, 10-719, Olsztyn, Poland.
- Department of Aquaculture, Szent István University, Páter Károly 1, Gödöllo, 2100, Hungary.
| | | | | | | | - Gilbert Dutto
- IFREMER, UMR MARBEC (IRD, IFREMER, CNRS, Université de Montpellier), Station Expérimentale d'Aquaculture, Chemin de Maguelone, 34250, Palavas, France
| | - Marie Odile Vidal
- IFREMER, UMR MARBEC (IRD, IFREMER, CNRS, Université de Montpellier), Station Expérimentale d'Aquaculture, Chemin de Maguelone, 34250, Palavas, France
| | - Christian Fauvel
- IFREMER, UMR MARBEC (IRD, IFREMER, CNRS, Université de Montpellier), Station Expérimentale d'Aquaculture, Chemin de Maguelone, 34250, Palavas, France
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Babbucci M, Ferraresso S, Pauletto M, Franch R, Papetti C, Patarnello T, Carnier P, Bargelloni L. An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax). Sci Rep 2016; 6:38673. [PMID: 27929136 PMCID: PMC5144136 DOI: 10.1038/srep38673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/11/2016] [Indexed: 12/13/2022] Open
Abstract
Skeletal anomalies in farmed fish are a relevant issue affecting animal welfare and health and causing significant economic losses. Here, a high-density genetic map of European seabass for QTL mapping of jaw deformity was constructed and a genome-wide association study (GWAS) was carried out on a total of 298 juveniles, 148 of which belonged to four full-sib families. Out of 298 fish, 107 were affected by mandibular prognathism (MP). Three significant QTLs and two candidate SNPs associated with MP were identified. The two GWAS candidate markers were located on ChrX and Chr17, both in close proximity with the peaks of the two most significant QTLs. Notably, the SNP marker on Chr17 was positioned within the Sobp gene coding region, which plays a pivotal role in craniofacial development. The analysis of differentially expressed genes in jaw-deformed animals highlighted the “nervous system development” as a crucial pathway in MP. In particular, Zic2, a key gene for craniofacial morphogenesis in model species, was significantly down-regulated in MP-affected animals. Gene expression data revealed also a significant down-regulation of Sobp in deformed larvae. Our analyses, integrating transcriptomic and GWA methods, provide evidence for putative mechanisms underlying seabass jaw deformity.
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Affiliation(s)
- Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Rafaella Franch
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Chiara Papetti
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35121 Padova, Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Paolo Carnier
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
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Robertson C, Pauli BD, Trudeau VL, Navarro-Martín L. Characterization and Developmental Expression Profile of the Steroidogenic Acute Regulatory Protein (StAR) in the Gonad-Mesonephros Complex of Lithobates sylvaticus. Sex Dev 2016; 10:91-6. [PMID: 27110942 DOI: 10.1159/000445816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Indexed: 11/19/2022] Open
Abstract
The steroidogenic acute regulatory (StAR) protein is responsible for the movement of cholesterol across mitochondrial membranes and is therefore a key factor in regulating the timing and rate of steroidogenesis. In this study, we characterized the coding region of the star gene in the ranid Lithobates sylvaticus and studied star mRNA levels in steroidogenic tissues during development and under natural conditions. Our results support previous research showing that the StAR sequence is well conserved. We determined that star is expressed in both the interrenal and gonadal tissues of adults and in the tadpole gonad-mesonephros complex (GMC). The mRNA levels of star in the GMC were found to increase during tadpole development, reaching a maximum between Gosner stages (Gs) 32 and 38. We observed a significant drop in star mRNA levels at the end of prometamorphosis (Gs40-41), just before the start of the metamorphic climax. Significant differences in star levels between females and males, with males presenting higher levels than females, were detected at Gs36-38. To our knowledge, this is the first study that reports transitory star sex differences in tadpoles' developing GMC. Our results suggest an involvement of StAR in anuran late male GMC formation and development that requires further investigation.
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Affiliation(s)
- Courtney Robertson
- Centre for Advanced Research in Environmental Genomics (CAREG), Department of Biology, University of Ottawa, Ottawa, Ont., Canada
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Kim TS, Raveendar S, Suresh S, Lee GA, Lee JR, Cho JH, Lee SY, Ma KH, Cho GT, Chung JW. Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement. Genes (Basel) 2015; 6:1164-82. [PMID: 26540077 PMCID: PMC4690033 DOI: 10.3390/genes6041164] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 10/16/2015] [Accepted: 10/19/2015] [Indexed: 11/26/2022] Open
Abstract
The vetch (Vicia sativa) is one of the most important annual forage legumes globally due to its multiple uses and high nutritional content. Despite these agronomical benefits, many drawbacks, including cyano-alanine toxin, has reduced the agronomic value of vetch varieties. Here, we used 454 technology to sequence the two V. sativa subspecies (ssp. sativa and ssp. nigra) to enrich functional information and genetic marker resources for the vetch research community. A total of 86,532 and 47,103 reads produced 35,202 and 18,808 unigenes with average lengths of 735 and 601 bp for V. sativa sativa and V. sativa nigra, respectively. Gene Ontology annotations and the cluster of orthologous gene classes were used to annotate the function of the Vicia transcriptomes. The Vicia transcriptome sequences were then mined for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. About 13% and 3% of the Vicia unigenes contained the putative SSR and SNP sequences, respectively. Among those SSRs, 100 were chosen for the validation and the polymorphism test using the Vicia germplasm set. Thus, our approach takes advantage of the utility of transcriptomic data to expedite a vetch breeding program.
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Affiliation(s)
- Tae-Sung Kim
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 340-702, Korea.
| | - Sebastin Raveendar
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Sundan Suresh
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
- Department of Botany, Directorate of Distance Education, Madurai Kamaraj University, Madurai 625 021, India.
| | - Gi-An Lee
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Jung-Ro Lee
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Joon-Hyeong Cho
- Department of Biological and Environmental Science, Dongguk University, Seoul 100-175, Korea.
| | - Sok-Young Lee
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Kyung-Ho Ma
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Gyu-Taek Cho
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Jong-Wook Chung
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
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Construction, De-Novo Assembly and Analysis of Transcriptome for Identification of Reproduction-Related Genes and Pathways from Rohu, Labeo rohita (Hamilton). PLoS One 2015; 10:e0132450. [PMID: 26148098 PMCID: PMC4509579 DOI: 10.1371/journal.pone.0132450] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 06/15/2015] [Indexed: 01/22/2023] Open
Abstract
Rohu is a leading candidate species for freshwater aquaculture in South-East Asia. Unlike common carp the monsoon breeding habit of rohu restricts its seed production beyond season indicating strong genetic control over spawning. Genetic information is limited in this regard. The problem is exacerbated by the lack of genomic-resources. We identified 182 reproduction-related genes previously by Sanger-sequencing which were less to address the issue of seasonal spawning behaviour of this important carp. Therefore, the present work was taken up to generate transcriptome profile by mRNAseq. 16 GB, 72 bp paired end (PE) data was generated from the pooled-RNA of twelve-tissues from pre-spawning rohu using IlluminaGA-II-platform. There were 64.97 million high-quality reads producing 62,283 contigs and 88,612 numbers of transcripts using velvet and oases programs, respectively. Gene ontology annotation identified 940 reproduction-related genes consisting of 184 mainly associated with reproduction, 223 related to hormone-activity and receptor-binding, 178 receptor-activity and 355 embryonic-development related-proteins. The important reproduction-relevant pathways found in KEGG analysis were GnRH-signaling, oocyte-meiosis, steroid-biosynthesis, steroid-hormone biosynthesis, progesterone-mediated oocyte-maturation, retinol-metabolism, neuroactive-ligand-receptor interaction, neurotrophin-signaling and photo-transduction. Twenty nine simple sequence repeat containing sequences were also found out of which 12 repeat loci were polymorphic with mean expected-&-observed heterozygosity of 0.471 and 0.983 respectively. Quantitative RT-PCR analyses of 13-known and 6-unknown transcripts revealed differences in expression level between preparatory and post-spawning phase. These transcriptomic sequences have significantly increased the genetic-&-genomic resources for reproduction-research in Labeo rohita.
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Regnault C, Worms IAM, Oger-Desfeux C, MelodeLima C, Veyrenc S, Bayle ML, Combourieu B, Bonin A, Renaud J, Raveton M, Reynaud S. Impaired liver function in Xenopus tropicalis exposed to benzo[a]pyrene: transcriptomic and metabolic evidence. BMC Genomics 2014; 15:666. [PMID: 25103525 PMCID: PMC4141109 DOI: 10.1186/1471-2164-15-666] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/30/2014] [Indexed: 12/20/2022] Open
Abstract
Background Despite numerous studies suggesting that amphibians are highly sensitive to cumulative anthropogenic stresses, the role pollutants play in the decline of amphibian populations remains unclear. Amongst the most common aquatic contaminants, polycyclic aromatic hydrocarbons (PAHs) have been shown to induce several adverse effects on amphibian species in the larval stages. Conversely, adults exposed to high concentrations of the ubiquitous PAH, benzo[a]pyrene (BaP), tolerate the compound thanks to their highly efficient hepatic detoxification mechanisms. Due to this apparent lack of toxic effect on adults, no studies have examined in depth the potential toxicological impact of PAH on the physiology of adult amphibian livers. This study sheds light on the hepatic responses of Xenopus tropicalis when exposed to high environmentally relevant concentrations of BaP, by combining a high throughput transcriptomic approach (mRNA deep sequencing) and a characterization of cellular and physiological modifications to the amphibian liver. Results Transcriptomic changes observed in BaP-exposed Xenopus were further characterized using a time-dependent enrichment analysis, which revealed the pollutant-dependent gene regulation of important biochemical pathways, such as cholesterol biosynthesis, insulin signaling, adipocytokines signaling, glycolysis/gluconeogenesis and MAPK signaling. These results were substantiated at the physiological level with the detection of a pronounced metabolic disorder resulting in a possible insulin resistance-like syndrome phenotype. Hepatotoxicity induced by lipid and cholesterol metabolism impairments was clearly identified in BaP-exposed individuals. Conclusions Our data suggested that BaP may disrupt overall liver physiology, and carbohydrate and cholesterol metabolism in particular, even after short-term exposure. These results are further discussed in terms of how this deregulation of liver physiology can lead to general metabolic impairment in amphibians chronically exposed to contaminants, thereby illustrating the role xenobiotics might play in the global decline in amphibian populations. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-666) contains supplementary material, which is available to authorized users.
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Sahu DK, Panda SP, Panda S, Das P, Meher PK, Hazra RK, Peatman E, Liu ZJ, Eknath AE, Nandi S. Identification of reproduction-related genes and SSR-markers through expressed sequence tags analysis of a monsoon breeding carp rohu, Labeo rohita (Hamilton). Gene 2013; 524:1-14. [DOI: 10.1016/j.gene.2013.03.111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 03/20/2013] [Accepted: 03/25/2013] [Indexed: 12/20/2022]
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Nivet AL, Vigneault C, Blondin P, Sirard MA. Changes in granulosa cells' gene expression associated with increased oocyte competence in bovine. Reproduction 2013; 145:555-65. [PMID: 23564726 DOI: 10.1530/rep-13-0032] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
One of the challenges in mammalian reproduction is to understand the basic physiology of oocyte quality. It is believed that the follicle status is linked to developmental competence of the enclosed oocyte. To explore the link between follicles and competence in cows, previous research at our laboratory has developed an ovarian stimulation protocol that increases and then decreases oocyte quality according to the timing of oocyte recovery post-FSH withdrawal (coasting). Using this protocol, we have obtained the granulosa cells associated with oocytes of different qualities at selected times of coasting. Transcriptome analysis was done with Embryogene microarray slides and validation was performed by real-time PCR. Results show that the major changes in gene expression occurred from 20 to 44 h of coasting, when oocyte quality increases. Secondly, among upregulated genes (20-44 h), 25% were extracellular molecules, highlighting potential granulosa signaling cascades. Principal component analysis identified two patterns: one resembling the competence profile and another associated with follicle growth and atresia. Additionally, three major functional changes were identified: (i) the end of follicle growth (BMPR1B, IGF2, and RELN), involving interactions with the extracellular matrix (TFPI2); angiogenesis (NRP1), including early hypoxia, and potentially oxidative stress (GFPT2, TF, and VNN1) and (ii) apoptosis (KCNJ8) followed by iii) inflammation (ANKRD1). This unique window of analysis indicates a progressive hypoxia during coasting mixed with an increase in apoptosis and inflammation. Potential signaling pathways leading to competence have been identified and will require downstream testing. This preliminary analysis supports the potential role of the follicular differentiation in oocyte quality both during competence increase and decrease phases.
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Affiliation(s)
- Anne-Laure Nivet
- Département des sciences animales, Pavillon INAF, Faculté des sciences de l'agriculture et de l'alimentation, Centre de recherche en biologie de la reproduction, Université Laval, Quebec, Quebec, Canada G1V 0A6
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Paganini J, Gouret P. Reliable Phylogenetic Trees Building: A New Web Interface for FIGENIX. Evol Bioinform Online 2012; 8:417-21. [PMID: 22844195 PMCID: PMC3399708 DOI: 10.4137/ebo.s9179] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The community needed a reliable and user friendly tool to quickly produce robust phylogenetic trees which are crucial in evolutionary studies and genomes’ functional annotation. FIGENIX is software dedicated to this and was published in 2005. Several laboratories around the world use it in their research, but it was difficult to use for non-expert users, thus we developed a new graphical user interface for the benefit of all biologists.
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Affiliation(s)
- Julien Paganini
- UMR 7353, Evolutionary Biology and Modeling team, Aix-Marseille University, 3 place Victor Hugo, Marseille, France
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Powers TR, Virk SM, Trujillo-Provencio C, Serrano EE. Probing the Xenopus laevis inner ear transcriptome for biological function. BMC Genomics 2012; 13:225. [PMID: 22676585 PMCID: PMC3532188 DOI: 10.1186/1471-2164-13-225] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 05/21/2012] [Indexed: 01/27/2023] Open
Abstract
Background The senses of hearing and balance depend upon mechanoreception, a process that originates in the inner ear and shares features across species. Amphibians have been widely used for physiological studies of mechanotransduction by sensory hair cells. In contrast, much less is known of the genetic basis of auditory and vestibular function in this class of animals. Among amphibians, the genus Xenopus is a well-characterized genetic and developmental model that offers unique opportunities for inner ear research because of the amphibian capacity for tissue and organ regeneration. For these reasons, we implemented a functional genomics approach as a means to undertake a large-scale analysis of the Xenopus laevis inner ear transcriptome through microarray analysis. Results Microarray analysis uncovered genes within the X. laevis inner ear transcriptome associated with inner ear function and impairment in other organisms, thereby supporting the inclusion of Xenopus in cross-species genetic studies of the inner ear. The use of gene categories (inner ear tissue; deafness; ion channels; ion transporters; transcription factors) facilitated the assignment of functional significance to probe set identifiers. We enhanced the biological relevance of our microarray data by using a variety of curation approaches to increase the annotation of the Affymetrix GeneChip® Xenopus laevis Genome array. In addition, annotation analysis revealed the prevalence of inner ear transcripts represented by probe set identifiers that lack functional characterization. Conclusions We identified an abundance of targets for genetic analysis of auditory and vestibular function. The orthologues to human genes with known inner ear function and the highly expressed transcripts that lack annotation are particularly interesting candidates for future analyses. We used informatics approaches to impart biologically relevant information to the Xenopus inner ear transcriptome, thereby addressing the impediment imposed by insufficient gene annotation. These findings heighten the relevance of Xenopus as a model organism for genetic investigations of inner ear organogenesis, morphogenesis, and regeneration.
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Affiliation(s)
- TuShun R Powers
- Biology Department, New Mexico State University, Las Cruces, USA
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An ovary transcriptome for all maturational stages of the striped bass (Morone saxatilis), a highly advanced perciform fish. BMC Res Notes 2012; 5:111. [PMID: 22353237 PMCID: PMC3305648 DOI: 10.1186/1756-0500-5-111] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 02/21/2012] [Indexed: 12/30/2022] Open
Abstract
Background The striped bass and its relatives (genus Morone) are important fisheries and aquaculture species native to estuaries and rivers of the Atlantic coast and Gulf of Mexico in North America. To open avenues of gene expression research on reproduction and breeding of striped bass, we generated a collection of expressed sequence tags (ESTs) from a complementary DNA (cDNA) library representative of their ovarian transcriptome. Results Sequences of a total of 230,151 ESTs (51,259,448 bp) were acquired by Roche 454 pyrosequencing of cDNA pooled from ovarian tissues obtained at all stages of oocyte growth, at ovulation (eggs), and during preovulatory atresia. Quality filtering of ESTs allowed assembly of 11,208 high-quality contigs ≥ 100 bp, including 2,984 contigs 500 bp or longer (average length 895 bp). Blastx comparisons revealed 5,482 gene orthologues (E-value < 10-3), of which 4,120 (36.7% of total contigs) were annotated with Gene Ontology terms (E-value < 10-6). There were 5,726 remaining unknown unique sequences (51.1% of total contigs). All of the high-quality EST sequences are available in the National Center for Biotechnology Information (NCBI) Short Read Archive (GenBank: SRX007394). Informative contigs were considered to be abundant if they were assembled from groups of ESTs comprising ≥ 0.15% of the total short read sequences (≥ 345 reads/contig). Approximately 52.5% of these abundant contigs were predicted to have predominant ovary expression through digital differential display in silico comparisons to zebrafish (Danio rerio) UniGene orthologues. Over 1,300 Gene Ontology terms from Biological Process classes of Reproduction, Reproductive process, and Developmental process were assigned to this collection of annotated contigs. Conclusions This first large reference sequence database available for the ecologically and economically important temperate basses (genus Morone) provides a foundation for gene expression studies in these species. The predicted predominance of ovary gene expression and assignment of directly relevant Gene Ontology classes suggests a powerful utility of this dataset for analysis of ovarian gene expression related to fundamental questions of oogenesis. Additionally, a high definition Agilent 60-mer oligo ovary 'UniClone' microarray with 8 × 15,000 probe format has been designed based on this striped bass transcriptome (eArray Group: Striper Group, Design ID: 029004).
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Gohin M, Bodinier P, Fostier A, Bobe J, Chesnel F. Aromatase expression in Xenopus oocytes: a three cell-type model for the ovarian estradiol synthesis. J Mol Endocrinol 2011; 47:241-50. [PMID: 21768170 DOI: 10.1530/jme-11-0080] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In contrast to the classical model describing the synthesis of androgens and estrogens as restricted to somatic cells, a previous study demonstrated that Xenopus laevis oocytes participate in androgen synthesis. The objective of our study was to determine whether Xenopus oocytes are also involved in estrogen synthesis. More precisely, we analyzed aromatase expression by in situ hybridization and RT-QPCR and measured aromatase activity. Aromatase, the enzyme responsible for estrogen synthesis, appears to be expressed and active not only in the follicular cells but also in the vitellogenic oocytes. During late oogenesis, aromatase oocyte expression and activity decreased concomitantly with the trend observed in surrounding follicular layers. In order to investigate the role of estradiol-17β (E(2)), we studied its effect on oocyte meiotic resumption. It appears that, as in Rana pipiens, E(2) inhibited the follicle-enclosed maturation of Xenopus oocytes, likely through inhibition of LH-induced maturation-inducing steroid synthesis. In addition, E(2) exerted a slight enhancing action on denuded oocyte maturation whose biological significance remains unclear. Together, our results demonstrate that Xenopus oocyte significantly participates in ovarian E(2) synthesis and this may be a common feature of vitellogenic vertebrates.
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Affiliation(s)
- M Gohin
- CNRS/IGDR (UMR 6061), IFR140 GFAS, Université de Rennes I, 2 Avenue du Pr. Léon Bernard, 35043 Rennes Cedex, France
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Gohin M, Bodinier P, Fostier A, Chesnel F, Bobe J. Aromatase is expressed and active in the rainbow trout oocyte during final oocyte maturation. Mol Reprod Dev 2011; 78:510-8. [DOI: 10.1002/mrd.21335] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 05/13/2011] [Indexed: 02/04/2023]
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Moe KT, Chung JW, Cho YI, Moon JK, Ku JH, Jung JK, Lee J, Park YJ. Sequence information on simple sequence repeats and single nucleotide polymorphisms through transcriptome analysis of mungbean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2011; 53:63-73. [PMID: 21205180 DOI: 10.1111/j.1744-7909.2010.01012.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Mungbean (Vigna radiata (L.) Wilczek) is a unique species in its ability to fix atmospheric nitrogen, with early maturity, and relatively good drought resistance. We used 454 sequencing technology for transcriptome sequencing. A total of 150 159 and 142 993 reads produced 5 254 and 6 374 large contigs (≥ 500 bp) with an average length of 833 and 853 for Sunhwa and Jangan, respectively. Functional annotation to known sequences yielded 41.34% and 41.74% unigenes for Jangan and Sunhwa. A higher number of simple sequence repeat (SSR) motifs was identified in Jangan (1 630) compared with that of Sunhwa (1 334). A similar SSR distribution pattern was observed in both varieties. A total of 8 249 single nucleotide polymorphisms (SNPs) and indels with 2 098 high-confidence candidates were identified in the two mungbean varieties. The average distance between individual SNPs was approximately 860 bp. Our report demonstrates the utility of transcriptomic data for implementing a functional annotation and development of genetic markers. We also provide large resource sequence data for mungbean improvement programs.
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Affiliation(s)
- Kyaw Thu Moe
- Department of Palnt Resources, College of Industrial Sciences, Kongju National University, Yesan 304-702, Republic of Korea
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Rime H, Nguyen T, Bobe J, Fostier A, Monod G. Prochloraz-induced oocyte maturation in rainbow trout (Oncorhynchus mykiss), a molecular and functional analysis. Toxicol Sci 2010; 118:61-70. [PMID: 20805220 DOI: 10.1093/toxsci/kfq255] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In the present study, we aimed at characterizing the effect of prochloraz, an imidazole fungicide, on the oocyte meiotic maturation process in a freshwater teleost species, the rainbow trout (Oncorhynchus mykiss). Full-grown post-vitellogenic ovarian follicles were incubated in vitro with prochloraz, Luteinizing Hormone (LH), or a combination of prochloraz and LH. The occurrence of oocyte maturation was assessed by monitoring germinal vesicle breakdown (GVBD) after 62-h in vitro incubation. Experiments were repeated in presence of actinomycin D, cycloheximide, or trilostane. The effect of prochloraz on the production of 17,20β-dihydroxy-4-pregnen-3-one (17,20βP), the natural maturation-inducing steroid, was quantified by radioimmunoassay. In addition, the effect of prochloraz on ovarian expression of 12 genes was monitored by real-time PCR. Prochloraz (10(-5)M) administered alone was able to induce 100% GVBD in the most responsive females. The occurrence of GVBD observed after prochloraz stimulation of follicles originating from various females was similar and highly correlated with the occurrence of GVBD observed after stimulation with low LH concentration. In addition, oocyte maturation induced by LH or prochloraz was totally inhibited by actinomycin D, cycloheximide, and trilostane. Similarly to LH, prochloraz was able to trigger 17,20βP production by the ovarian follicle. Finally, prochloraz induced the overexpression of genes participating in 17,20βP production, intercellular communication, and paracrine control of preovulatory follicular differentiation such as igf, igf2, connexin 43, and 20β hydroxysteroid dehydrogenase (hsbd20). Together, our results demonstrate that prochloraz administered alone is able to trigger oocyte maturation through the induction of specific genes, some of them being also triggered by LH. Finally, our results clearly indicate that the effects of prochloraz and LH on oocyte maturation are synergistic.
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Affiliation(s)
- Hélène Rime
- Institut National de la Recherche Agronomique, UR1037 SCRIBE, F-35000 Rennes, France
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