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Luo H, Zhang Y, Liu F, Zhao Y, Peng J, Xu Y, Chen X, Huang Y, Ji C, Liu Q, He P, Feng P, Yang C, Wei P, Ma Z, Qin J, Zhou S, Dai S, Zhang Y, Zhao Z, Liu H, Zheng H, Zhang J, Lin Y, Chen X. The male and female genomes of golden pompano (Trachinotus ovatus) provide insights into the sex chromosome evolution and rapid growth. J Adv Res 2024; 65:1-17. [PMID: 38043610 PMCID: PMC11518962 DOI: 10.1016/j.jare.2023.11.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 12/05/2023] Open
Abstract
INTRODUCTION Golden pompano (Trachinotus ovatus) is economically significant important for offshore cage aquaculture in China and Southeast Asian countries. Lack of high-quality genomic data and accurate gene annotations greatly restricts its genetic breeding progress. OBJECTIVES To decode the mechanisms of sex determination and rapid growth in golden pompano and facilitate the sex- and growth-aimed genetic breeding. METHODS Genome assemblies of male and female golden pompano were generated using Illumina, PacBio, BioNano, genetic maps and Hi-C sequencing data. Genomic comparisons, whole genome re-sequencing of 202 F1 individuals, QTL mapping and gonadal transcriptomes were used to analyze the sex determining region, sex chromosome evolution, SNP loci, and growth candidate genes. Zebrafish model was used to investigate the functions of growth candidate gene. RESULTS Female (644.45 Mb) and male (652.12 Mb) genomes of golden pompano were assembled and annotated at the chromosome level. Both genomes are highly conserved and no new or highly differentiated sex chromosomes occur. A 3.5 Mb sex determining region on LG15 was identified, where Hsd17b1, Micall2 and Lmx1a were putative candidates for sex determination. Three SNP loci significantly linked to growth were pinpointed, and a growth-linked gene gpsstr1 was identified by locus BSNP1369 (G → C, 17489695, Chr23). Loss of sstr1a (homologue of gpsstr1) in zebrafish caused growth retardation. CONCLUSION This study provides insights into sex chromosome evolution, sex determination and rapid growth of golden pompano.
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Affiliation(s)
- Honglin Luo
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China; Institute of Oncology, Guangxi Academy of Medical Sciences, Nanning, Guangxi 530021, China
| | - Yongde Zhang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Fuyan Liu
- Biomarker Technologies, Beijing 101300, China; BGI-Beijing, Beijing 102601, China
| | - Yongzhen Zhao
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Jinxia Peng
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Yuhui Xu
- Biomarker Technologies, Beijing 101300, China
| | - Xiuli Chen
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Yin Huang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | | | - Qingyun Liu
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Pingping He
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Pengfei Feng
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Chunling Yang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Pinyuan Wei
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Zhenhua Ma
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Jianguang Qin
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Shengjie Zhou
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Shiming Dai
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Yaoyao Zhang
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Zhongquan Zhao
- College of Animal Science and Technology, Southwest University, Beibei, Chongqing 400715, China
| | | | | | - Jisen Zhang
- Center for Genomics and Biotechnology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China; State Key Lab for Conservation and Utilization of Subtropical Agro-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China.
| | - Yong Lin
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China.
| | - Xiaohan Chen
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China.
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Huo Y, Gu Y, Cao M, Mao Y, Wang Y, Wang X, Wang G, Li J. Identification and functional analysis of Tex11 and Meig1 in spermatogenesis of Hyriopsis cumingii. Front Physiol 2022; 13:961773. [PMID: 36091389 PMCID: PMC9449974 DOI: 10.3389/fphys.2022.961773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/04/2022] [Indexed: 11/23/2022] Open
Abstract
Abstract: The process of spermatogenesis is complex and controlled by many genes. In mammals, Testis-expressed gene 11 (Tex11) and meiosis expressed gene 1 (Meig1) are typical spermatogenesis-related genes. In this study, we obtained the full length cDNAs for Tex11 (3143bp) and Meig1 (1649bp) in Hyriopsis cumingii by cloning. Among them, Hc-Tex11 contains 930 amino acids and Hc-Meig1 contains 91 amino acids. The protein molecular masses (MW) of Hc-Tex11 and Hc-Meig1 were 105.63 kDa and 10.95 kDa, respectively. Protein secondary structure analysis showed that Hc-TEX11 protein has three TPR domains. The expression of Hc-Tex11 and Hc-Meig1 in different tissues showed higher levels in testes. At different ages, the expression of Hc-Tex11 and Hc-Meig1 was higher levels in 3-year-old male mussels. During spermatogenesis, the mRNA levels of Hc-Tex11, Hc-Meig1 gradually increased with the development of spermatogonia and reached a peak during sperm maturation. Hc-Tex11 and Hc-Meig1 mRNA signals were detected on spermatogonia and spermatocytes by in situ hybridization. In addition, RNA interference (RNAi) experiments of Hc-Tex11 caused a down-regulated of Dmrt1, KinaseX, Tra-2 and Klhl10 genes and an up-regulated of β-catenin gene. Based on the above experimental results, it can be speculated that Hc-Tex11 and Hc-Meig1 are important in the development of the male gonadal and spermatogenesis in H. cumingii, which can provide important clues to better comprehend the molecular mechanism of Tex11 and Meig1 in regulating spermatogenesis of bivalves.
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Affiliation(s)
- Yingduo Huo
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
| | - Yang Gu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
| | - Mulian Cao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
| | - Yingrui Mao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
| | - Yayu Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
| | - Xiaoqiang Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
| | - Guiling Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
- *Correspondence: Guiling Wang,
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
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Gatto KP, Timoshevskaya N, Smith JJ, Lourenço LB. Sequencing of laser captured Z and W chromosomes of the tocantins paradoxical frog (Pseudis tocantins) provides insights on repeatome and chromosomal homology. J Evol Biol 2022; 35:1659-1674. [PMID: 35642451 DOI: 10.1111/jeb.14027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/06/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022]
Abstract
Pseudis tocantins is the only frog species of the hylid genus Pseudis that possesses highly heteromorphic sex chromosomes. Z and W chromosomes of Ps. tocantins differ in size, morphology, position of the nucleolar organizer region (NOR) and the amount and distribution of heterochromatin. A chromosomal inversion and heterochromatin amplification on the W chromosome were previously inferred to be involved in the evolution of this sex chromosome pair. Despite these findings, knowledge related to the molecular composition of the large heterochromatic band of this W chromosome is restricted to the PcP190 satellite DNA, and no data are available regarding the gene content of either the W or the Z chromosome of Ps. tocantins. Here, we sequenced microdissected Z and W chromosomes of this species to further resolve their molecular composition. Comparative genomic analysis suggests that Ps. tocantins sex chromosomes are likely homologous to chromosomes 4 and 10 of Xenopus tropicalis. Analyses of the repetitive DNA landscape in the Z and W assemblies allowed for the identification of several transposable elements and putative satellite DNA sequences. Finally, some transposable elements from the W assembly were found to be highly diverse and divergent from elements found elsewhere in the genome, suggesting a rapid amplification of these elements on the W chromosome.
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Affiliation(s)
- Kaleb Pretto Gatto
- Laboratory of Chromosome Studies, Department of Structural and Functional Biology, Institute of Biology, University of Campinas, Campinas, Brazil.,Laboratory of Herpetology and Aquaculture Center, Department of Zoology, Institute of Biosciences, São Paulo State University, Rio Claro, Brazil
| | - Nataliya Timoshevskaya
- Department of Biology, College of Arts and Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Jeramiah J Smith
- Department of Biology, College of Arts and Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Luciana Bolsoni Lourenço
- Laboratory of Chromosome Studies, Department of Structural and Functional Biology, Institute of Biology, University of Campinas, Campinas, Brazil
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Tang Y, Chen JY, Ding GH, Lin ZH. Analyzing the gonadal transcriptome of the frog Hoplobatrachus rugulosus to identify genes involved in sex development. BMC Genomics 2021; 22:552. [PMID: 34281525 PMCID: PMC8290591 DOI: 10.1186/s12864-021-07879-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The tiger frog (Hoplobatrachus rugulosus) is listed as a national Class II protected species in China. In the context of global warming, the sex ratio of amphibians will be affected, and the development of the population will be limited. Therefore, considering the potential for a decrease in the number of amphibians, studying sex evolution and molecular regulation of gonadal development in H. rugulosus, phenomenon that are currently unclear, is of great significance. RESULTS Here, H. rugulosus was used to explore the mechanisms regulating gonadal development in amphibians. Illumina HiSeq 3000 was used to sequence the gonadal transcriptome of male and female H. rugulosus at two growth stages to identify genes related to gonadal development and analyze expression differences in the gonads. This analysis indicated that cyp17α, hsd3β, hsd11β1, cyp19α, and hsd17β12 perform vital functions in sex development in amphibians. Specifically, the expression of cyp3α, cyp17α, hsd3β, hsd11β1, sox2, sox9, sox30, soat, cyp19α, hsd17β12, and hspα1s was correlated with gonadal development and differentiation in H. rugulosus, as determined using the quantitative reverse transcriptase-polymerase chain reaction. CONCLUSION Significant differences were found in the gonadal gene expression levels in H. rugulosus of both sexes, and we identified a steroid hormone synthesis pathway in this species and analyzed related gene expression, but the changes during sex differentiation were still unclear. To our knowledge, this report presents the first analysis of the H. rugulosus gonadal transcriptome and lays the foundation for future research.
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Affiliation(s)
- Yun Tang
- Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University, Lishui, 323000, Zhejiang, People's Republic of China.,College of Life Sciences, Nanjing Normal University, Nanjing, 210046, Jiangsu, People's Republic of China
| | - Jing-Yi Chen
- Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University, Lishui, 323000, Zhejiang, People's Republic of China
| | - Guo-Hua Ding
- Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University, Lishui, 323000, Zhejiang, People's Republic of China.
| | - Zhi-Hua Lin
- Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University, Lishui, 323000, Zhejiang, People's Republic of China
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Roco ÁS, Ruiz-García A, Bullejos M. Testis Development and Differentiation in Amphibians. Genes (Basel) 2021; 12:578. [PMID: 33923451 PMCID: PMC8072878 DOI: 10.3390/genes12040578] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/08/2021] [Accepted: 04/14/2021] [Indexed: 11/17/2022] Open
Abstract
Sex is determined genetically in amphibians; however, little is known about the sex chromosomes, testis-determining genes, and the genes involved in testis differentiation in this class. Certain inherent characteristics of the species of this group, like the homomorphic sex chromosomes, the high diversity of the sex-determining mechanisms, or the existence of polyploids, may hinder the design of experiments when studying how the gonads can differentiate. Even so, other features, like their external development or the possibility of inducing sex reversal by external treatments, can be helpful. This review summarizes the current knowledge on amphibian sex determination, gonadal development, and testis differentiation. The analysis of this information, compared with the information available for other vertebrate groups, allows us to identify the evolutionarily conserved and divergent pathways involved in testis differentiation. Overall, the data confirm the previous observations in other vertebrates-the morphology of the adult testis is similar across different groups; however, the male-determining signal and the genetic networks involved in testis differentiation are not evolutionarily conserved.
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Affiliation(s)
| | | | - Mónica Bullejos
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Campus Las Lagunillas S/N, Universidad de Jaén, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.)
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Ma WJ, Carpentier F, Giraud T, Hood ME. Differential Gene Expression between Fungal Mating Types Is Associated with Sequence Degeneration. Genome Biol Evol 2020; 12:243-258. [PMID: 32058544 PMCID: PMC7150583 DOI: 10.1093/gbe/evaa028] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2020] [Indexed: 12/13/2022] Open
Abstract
Degenerative mutations in non-recombining regions, such as in sex chromosomes, may lead to differential expression between alleles if mutations occur stochastically in one or the other allele. Reduced allelic expression due to degeneration has indeed been suggested to occur in various sex-chromosome systems. However, whether an association occurs between specific signatures of degeneration and differential expression between alleles has not been extensively tested, and sexual antagonism can also cause differential expression on sex chromosomes. The anther-smut fungus Microbotryum lychnidis-dioicae is ideal for testing associations between specific degenerative signatures and differential expression because 1) there are multiple evolutionary strata on the mating-type chromosomes, reflecting successive recombination suppression linked to mating-type loci; 2) separate haploid cultures of opposite mating types help identify differential expression between alleles; and 3) there is no sexual antagonism as a confounding factor accounting for differential expression. We found that differentially expressed genes were enriched in the four oldest evolutionary strata compared with other genomic compartments, and that, within compartments, several signatures of sequence degeneration were greater for differentially expressed than non-differentially expressed genes. Two particular degenerative signatures were significantly associated with lower expression levels within differentially expressed allele pairs: upstream insertion of transposable elements and mutations truncating the protein length. Other degenerative mutations associated with differential expression included nonsynonymous substitutions and altered intron or GC content. The association between differential expression and allele degeneration is relevant for a broad range of taxa where mating compatibility or sex is determined by genes located in large regions where recombination is suppressed.
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Affiliation(s)
- Wen-Juan Ma
- Department of Biology, Amherst College, Amherst, MA
| | - Fantin Carpentier
- Ecologie Systematique et Evolution, Université Paris-Saclay, CNRS, AgroParisTech, Orsay, France
| | - Tatiana Giraud
- Ecologie Systematique et Evolution, Université Paris-Saclay, CNRS, AgroParisTech, Orsay, France
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Piprek RP, Damulewicz M, Tassan JP, Kloc M, Kubiak JZ. Transcriptome profiling reveals male- and female-specific gene expression pattern and novel gene candidates for the control of sex determination and gonad development in Xenopus laevis. Dev Genes Evol 2019; 229:53-72. [PMID: 30972573 PMCID: PMC6500517 DOI: 10.1007/s00427-019-00630-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/20/2019] [Indexed: 12/21/2022]
Abstract
Xenopus laevis is an amphibian (frog) species widely used in developmental biology and genetics. To unravel the molecular machinery regulating sex differentiation of Xenopus gonads, we analyzed for the first time the transcriptome of developing amphibian gonads covering sex determination period. We applied microarray at four developmental stages: (i) NF50 (undifferentiated gonad during sex determination), (ii) NF53 (the onset of sexual differentiation of the gonads), (iii) NF56 (sexual differentiation of the gonads), and (iv) NF62 (developmental progression of differentiated gonads). Our analysis showed that during the NF50, the genetic female (ZW) gonads expressed more sex-specific genes than genetic male (ZZ) gonads, which suggests that a robust genetic program is realized during female sex determination in Xenopus. However, a contrasting expression pattern was observed at later stages (NF56 and NF62), when the ZW gonads expressed less sex-specific genes than ZZ gonads, i.e., more genes may be involved in further development of the male gonads (ZZ). We identified sexual dimorphism in the expression of several functional groups of genes, including signaling factors, proteases, protease inhibitors, transcription factors, extracellular matrix components, extracellular matrix enzymes, cell adhesion molecules, and epithelium-specific intermediate filaments. In addition, our analysis detected a sexually dimorphic expression of many uncharacterized genes of unknown function, which should be studied further to reveal their identity and if/how they regulate gonad development, sex determination, and sexual differentiation. Comparison between genes sex-specifically expressed in developing gonads of Xenopus and available transcriptome data from zebrafish, two reptile species, chicken, and mouse revealed significant differences in the genetic control of sex determination and gonad development. This shows that the genetic control of gonad development is evolutionarily malleable.
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Affiliation(s)
- Rafal P Piprek
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387, Krakow, Poland.
| | - Milena Damulewicz
- Department of Cell Biology and Imaging, Institute of Zoology and Biomedical Research, Jagiellonian University, Krakow, Poland
| | - Jean-Pierre Tassan
- Univ Rennes, UMR 6290, Cell Cycle Group, Faculty of Medicine, Institute of Genetics and Development of Rennes, F-35000, Rennes, France
| | - Malgorzata Kloc
- The Houston Methodist Research Institute, Houston, TX, USA
- Department of Surgery, The Houston Methodist Hospital, Houston, TX, USA
- MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Jacek Z Kubiak
- Univ Rennes, UMR 6290, Cell Cycle Group, Faculty of Medicine, Institute of Genetics and Development of Rennes, F-35000, Rennes, France
- Laboratory of Regenerative Medicine and Cell Biology, Military Institute of Hygiene and Epidemiology (WIHE), Warsaw, Poland
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Identification of critical sex-biased genes in Andrias davidianus by de novo transcriptome. Mol Genet Genomics 2018; 294:287-299. [PMID: 30377773 DOI: 10.1007/s00438-018-1508-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023]
Abstract
The Chinese giant salamander Andrias davidianus is a protected amphibian with high nutritional and economic value. Understanding its sex determination mechanism is important for improving culture techniques and sex control in breeding. However, little information on the characterization of critical genes involved in sex is available. Herein, sequencing of ovary and test produced 40,783,222 and 46,128,902 raw reads, respectively, which were jointly assembled into 80,497 unigenes. Of these, 36,609 unigenes were annotated, of which 8907 were female-biased and 10,385 were male-biased. Several sex-related pathways were observed, including the Wnt signaling pathway. After elevated temperature and estrogen exposure, neomale and neofemale specimens were identified by a female-specific marker for the first time. RT-qPCR analysis showed the expression profile of ten selected sex-biased genes to be exhibited consistently in male and neomale and in female and neofemale, with the exception of the Amh and TfIIIa genes. Results suggested that these genes may play important roles in A. davidianus sex determination and gonad development. This provides a basis for further investigation of the molecular mechanisms of sex determination in amphibians.
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Ma WJ, Veltsos P, Sermier R, Parker DJ, Perrin N. Evolutionary and developmental dynamics of sex-biased gene expression in common frogs with proto-Y chromosomes. Genome Biol 2018; 19:156. [PMID: 30290841 PMCID: PMC6173898 DOI: 10.1186/s13059-018-1548-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 09/20/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The patterns of gene expression on highly differentiated sex chromosomes differ drastically from those on autosomes, due to sex-specific patterns of selection and inheritance. As a result, X chromosomes are often enriched in female-biased genes (feminization) and Z chromosomes in male-biased genes (masculinization). However, it is not known how quickly sexualization of gene expression and transcriptional degeneration evolve after sex-chromosome formation. Furthermore, little is known about how sex-biased gene expression varies throughout development. RESULTS We sample a population of common frogs (Rana temporaria) with limited sex-chromosome differentiation (proto-sex chromosome), leaky genetic sex determination evidenced by the occurrence of XX males, and delayed gonadal development, meaning that XY individuals may first develop ovaries before switching to testes. Using high-throughput RNA sequencing, we investigate the dynamics of gene expression throughout development, spanning from early embryo to froglet stages. Our results show that sex-biased expression affects different genes at different developmental stages and increases during development, reaching highest levels in XX female froglets. Additionally, sex-biased gene expression depends on phenotypic, rather than genotypic sex, with similar expression in XX and XY males; correlates with gene evolutionary rates; and is not localized to the proto-sex chromosome nor near the candidate sex-determining gene Dmrt1. CONCLUSIONS The proto-sex chromosome of common frogs does not show evidence of sexualization of gene expression, nor evidence for a faster rate of evolution. This challenges the notion that sexually antagonistic genes play a central role in the initial stages of sex-chromosome evolution.
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Affiliation(s)
- Wen-Juan Ma
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland
- Current address: Department of Biology, Amherst College, Amherst, MA USA
| | - Paris Veltsos
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland
| | - Roberto Sermier
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland
| | - Darren J Parker
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland
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Campbell DEK, Langlois VS. Thyroid hormones and androgens differentially regulate gene expression in testes and ovaries of sexually mature Silurana tropicalis. Gen Comp Endocrinol 2018; 267:172-182. [PMID: 29990494 DOI: 10.1016/j.ygcen.2018.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 05/05/2018] [Accepted: 07/03/2018] [Indexed: 02/04/2023]
Abstract
A series of ex vivo exposures using testicular and ovarian tissues of sexually mature Western clawed frogs (Silurana tropicalis) were designed to examine molecular mechanisms of thyroid hormone (TH) and androgen crosstalk sans hypophyseal feedback as well as investigate potential sex-specific differences. Tissues were exposed ex vivo to either triiodothyronine (T3), iopanoic acid (IOP), one co-treatment of IOP + 5α-dihydrotestosterone (5α-DHT), 5α-DHT, 5β-dihydrotestosterone (5β-DHT), or testosterone (T). Direct exposure to different androgens led to androgen specific increases in thyroid receptor and deiodinase transcripts in testes (trβ and dio1) but a decrease in expression in ovaries (trβ and dio3), suggesting that male and female frogs can be differently affected by androgenic compounds. Moreover, exposure to select androgens differentially increased estrogen-related transcription (estrogen receptor alpha (erα) and aromatase (cyp19)) and production (estradiol) in ovaries and testes indicating the activation of alternate metabolic pathways yielding estrogenic metabolites. Sex-steroid-related transcription (i.e., steroid 5α-reductase type 2 (srd5α2) and erα) and production (i.e., 5α-DHT) were also differentially regulated by THs. The presence and frequency of transcription factor binding sites in the putative promoter regions of TH- and sex steroid-related genes were also examined in S. tropicalis, rodent, and fish models using in silico analysis. In summary, this study provides an improved mechanistic understanding of TH- and androgen-mediated actions and reveals differential transcriptional effects as a function of sex in frogs.
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Affiliation(s)
- D E K Campbell
- Biology Department, Queen's University, Kingston, ON, Canada
| | - V S Langlois
- Biology Department, Queen's University, Kingston, ON, Canada; Institut national de la recherche scientifique (INRS) - Centre Eau Terre Environnement, Quebec City, QC, Canada; Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON, Canada.
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Janesick A, Tang W, Shioda T, Blumberg B. RARγ is required for mesodermal gene expression prior to gastrulation in Xenopus. Development 2018; 145:dev147769. [PMID: 30111657 DOI: 10.1242/dev.147769] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 07/31/2018] [Indexed: 12/12/2022]
Abstract
The developing vertebrate embryo is exquisitely sensitive to retinoic acid (RA) concentration, particularly during anteroposterior patterning. In contrast to Nodal and Wnt signaling, RA was not previously considered to be an instructive signal in mesoderm formation during gastrulation. Here, we show in Xenopus that RARγ is indispensable for the expression of early mesoderm markers and is, therefore, an obligatory factor in mesodermal competence and/or maintenance. We identified several novel targets upregulated by RA receptor signaling in the early gastrula that are expressed in the circumblastoporal ring and linked to mesodermal development. Despite overlapping expression patterns of the genes encoding the RA-synthesizing enzyme Aldh1a2 and the RA-degrading enzyme Cyp26a1, RARγ1 functions as a transcriptional activator in early mesoderm development, suggesting that RA ligand is available to the embryo earlier than previously appreciated. RARγ1 is required for cellular adhesion, as revealed by spontaneous dissociation and depletion of ncam1 mRNA in animal caps harvested from RARγ1 knockdown embryos. RARγ1 knockdown obliterates somite boundaries, and causes loss of Myod protein in the presomitic mesoderm, but ectopic, persistent expression of Myod protein in the trunk. Thus, RARγ1 is required for stabilizing the mesodermal fate, myogenic commitment, somite boundary formation, and terminal skeletal muscle differentiation.
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Affiliation(s)
- Amanda Janesick
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, 92697-2300, USA
| | - Weiyi Tang
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, 92697-2300, USA
| | - Toshi Shioda
- Center for Cancer Research, Massachusetts General Hospital, Building 149, 13th Street, Charlestown, MA 02129, USA
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, 92697-2300, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-2300, USA
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12
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Ma WJ, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries DL, Perrin N. Tissue Specificity and Dynamics of Sex-Biased Gene Expression in a Common Frog Population with Differentiated, Yet Homomorphic, Sex Chromosomes. Genes (Basel) 2018; 9:E294. [PMID: 29895802 PMCID: PMC6027210 DOI: 10.3390/genes9060294] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/04/2018] [Accepted: 06/11/2018] [Indexed: 02/06/2023] Open
Abstract
Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage- or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes.
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Affiliation(s)
- Wen-Juan Ma
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
| | - Paris Veltsos
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
- Department of Biology, Indiana University, Jordan Hall, 1001 East Third Street, Bloomington, IN 47405, USA.
| | - Melissa A Toups
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
| | - Nicolas Rodrigues
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
| | - Roberto Sermier
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
| | - Daniel L Jeffries
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
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Haselman JT, Kosian PA, Korte JJ, Olmstead AW, Degitz SJ. Effects of multiple life stage exposure to the fungicide prochloraz in Xenopus laevis: Manifestations of antiandrogenic and other modes of toxicity. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 199:240-251. [PMID: 29674245 PMCID: PMC6299828 DOI: 10.1016/j.aquatox.2018.03.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 05/14/2023]
Abstract
The Larval Amphibian Growth and Development Assay (LAGDA) is an internationally harmonized testing guideline for evaluating effects of chronic chemical exposure in amphibians. In order to evaluate the effects of chronic exposure to an antiandrogenic chemical in an amphibian model, prochloraz was tested using a variation of the LAGDA design. Exposure was initiated with <1d post-fertilization embryos at nominal concentrations of 0, 6.7, 20, 60 and 180 μg/L (0, 18, 53, 159, 478 nM) and continued in flow-through conditions until two months following the median time that controls completed metamorphosis. Growth, developmental rate, circulating thyroid hormone and thyroid gland histopathology were evaluated in a subsample at completion of metamorphosis. There were no effects on growth or development at this stage, but circulating thyroid hormone was elevated in the 20, 60 and 180 μg/L treatments and minimal to mild thyroid follicular cell hypertrophy was observed histologically in the 180 μg/L treatment. Growth, overt toxicity, and reproductive development were evaluated at test termination. There were no effects on growth in either gender, but livers and kidneys exhibited treatment-related pathologies consistent with organ toxicity related to metabolism and presumably impaired excretion of prochloraz metabolites. Histological assessments of female ovaries resulted in minimal pathologies only in the 180 μg/L treatment while male testes exhibited numerous treatment-related pathologies that are consistent with previously reported antiandrogenic effects of prochloraz in other species. The most severe testis pathologies occurred in the 180 μg/L treatment; however, incidences of treatment-related pathologies occurred in all prochloraz treatments. Müllerian duct regression in males was inhibited by prochloraz exposure while Müllerian duct maturation in females was accelerated, characteristic of a feminizing effect. Gene expression levels of potential biomarkers of testis function were also measured. Relative abundance of cyp17a1 transcripts was generally unaffected by prochloraz exposure whereas the Insl3 orthologue, rflcii, was elevated by 3 and >5-fold in the 60 and 180 μg/L treatments, respectively, indicating impaired Leydig cell maturation and testosterone signaling. Overall, prochloraz exposure caused effects characteristic of an antiandrogenic mode of action, which is consistent with previously reported results in other species and supports the utility of the LAGDA design for chemical testing.
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Affiliation(s)
- Jonathan T Haselman
- US EPA Mid-Continent Ecology Division, 6201 Congdon Blvd, Duluth, MN, 55804, USA.
| | - Patricia A Kosian
- US EPA Mid-Continent Ecology Division, 6201 Congdon Blvd, Duluth, MN, 55804, USA.
| | - Joseph J Korte
- US EPA Mid-Continent Ecology Division, 6201 Congdon Blvd, Duluth, MN, 55804, USA.
| | - Allen W Olmstead
- US EPA Mid-Continent Ecology Division, 6201 Congdon Blvd, Duluth, MN, 55804, USA.
| | - Sigmund J Degitz
- US EPA Mid-Continent Ecology Division, 6201 Congdon Blvd, Duluth, MN, 55804, USA.
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14
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Xu W, Li YY, Lou QQ, Chen XR, Qin ZF, Wie WJ. Low concentrations of dihydrotestosterone induce female-to-male sex reversal in the frog Pelophylax nigromaculatus. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2015; 34:2370-2377. [PMID: 26226837 DOI: 10.1002/etc.3072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 04/10/2015] [Accepted: 05/19/2015] [Indexed: 06/04/2023]
Abstract
Previous studies have demonstrated that some amphibian species can be sex-reversed by high concentrations of androgens. Little attention has focused on the effects of androgenic endocrine-disrupting chemicals (EDCs) on amphibians. The present study aimed to investigate the effects of lower concentrations of the androgenic EDC 5α-dihydrotestosterone (DHT) on gonadal differentiation and development in Pelophylax nigromaculatus, a true frog distributed widely in East Asia. Tadpoles at Gosner stage 24/25 were exposed to nominal concentrations of 40 ng/L, 400 ng/L, and 4000 ng/L DHT to complete metamorphosis. In all DHT treatment groups, males and ambiguous sexes were identified based on gonadal morphology, whereas no females were found; thus, all treatment groups exhibited male-skewed ratios compared with the control group. Gonadal histological examination revealed that ambiguous sexes displayed overall testicular structure with certain ovarian characteristics, demonstrating that DHT-induced sex-ambiguous gonads were incomplete ovary-to-testis reversals (IOTTRs). The expression levels of some ovary-biased genes in the IOTTRs were significantly higher than in the control testes but lower than in the control ovaries. These results show that low concentrations of DHT induced complete or incomplete female-to-male sex reversal in P. nigromaculatus, and incomplete sex reversal retained certain ovarian characteristics not only at gonadal morphological and histological levels but also at the molecular level. They present study highlights potential risks of DHT and other androgenic EDCs for P. nigromaculatus.
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Affiliation(s)
- Wei Xu
- College of Environment, Nanjing University of Technology, Nanjing, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yuan-Yuan Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Qin-Qin Lou
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Ran Chen
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhan-Fen Qin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Wu-Ji Wie
- College of Environment, Nanjing University of Technology, Nanjing, China
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