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Gao R, Yan H, Zhou H, Hu M, Wang J, Shen X, Li M, Chen J, Liu Q, Liu Y, Wang X, Sun Q, Zhou H. The potential regulatory role of non-coding RNAs in mifepristone-induced masculinization in Takifugu rubripes gonads. BMC Genomics 2025; 26:471. [PMID: 40355821 PMCID: PMC12067753 DOI: 10.1186/s12864-025-11647-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2025] [Accepted: 04/28/2025] [Indexed: 05/15/2025] Open
Abstract
BACKGROUND The regulatory roles of non-coding RNAs (ncRNAs) during sex differentiation in teleosts have received widespread attention recently. Mifepristone (RU486, a progesterone antagonist), which acts as an endocrine disruptor, can affect reproduction and sex differentiation in teleosts. RESULTS The expression of ncRNAs in the gonads of tiger puffer (Takifugu rubripes) during RU486 (500 µg/g diet) induced masculinization process was examined by RNA-sequencing. A total of 4,381 long non-coding RNAs (lncRNAs), 309 circular RNAs (circRNAs), and 1,020 microRNAs (miRNAs) were identified. The expression of 41 differentially expressed (DE) lncRNAs and 20 DE miRNAs, which showed sexual dimorphic expression patterns in genetic female gonads in the control group (C-XX) vs. genetic male gonads in the control group (C-XY), were altered in genetic female gonads in the RU486 treated group (RU-XX). The genes targeted by DE ncRNAs were mainly enriched in sex-related pathways, such as calcium signaling, ovarian steroidogenesis, and cortisol synthesis and secretion. The results of co-expression and competing endogenous RNA (ceRNA) network analysis indicated that miRNAs (e.g., miR-205-z and fru-miR-122) and lncRNAs (including XR_003890915.1 and XR_003885862.1) may have pivotal roles, and lncRNAs (including XR_003890295.1, MSTRG.11750.1, and XR_003888827.1) may act as miRNA sponges, involved in the competition between miRNAs and sex-related genes during tiger puffer masculinization process. Dual luciferase reporter assay results identified that ovarian steroidogenesis related gene hsd17b1 is a downstream target of fru-miR-122. The expression of 4 lncRNAs, 4 circRNAs, and 6 miRNAs were validated by qPCR, indicating the accuracy and dependability of RNA-Seq. CONCLUSIONS This study provided the evidence that ncRNAs may participate in RU486-induced masculinization in T. rubripes, and may enhance our understanding of the regulatory network of sex differentiation in fugu.
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Affiliation(s)
- Rui Gao
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, Beijing, 116023, China
- College of Marine Science and Environment Engineering, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Hongwei Yan
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, Beijing, 116023, China.
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China.
- The Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian, 116023, China.
| | - Huiting Zhou
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, Beijing, 116023, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Mingtao Hu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, Beijing, 116023, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Jia Wang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, Beijing, 116023, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Xufang Shen
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, Beijing, 116023, China
| | - Meiyuan Li
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, Beijing, 116023, China
- College of Marine Science and Environment Engineering, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Jinfeng Chen
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, Beijing, 116023, China
- College of Marine Science and Environment Engineering, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Qi Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, Beijing, 116023, China
- College of Marine Science and Environment Engineering, Dalian Ocean University, Dalian, Liaoning, 116023, China
- The Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian, 116023, China
| | - Ying Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, Beijing, 116023, China
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Xiuli Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
- The Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian, 116023, China
| | - Qunwen Sun
- Dalian Tian Zheng Co., Ltd, Dalian, Liaoning, China
| | - He Zhou
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
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Huang YQ, Zhang XH, Bian C, Jiao KZ, Zhang L, Huang Y, Yang W, Li Y, Shi G, Huang Y, Tian CX, Chen HP, Deng SP, Zhu CH, Shi Q, Li GL, Jiang DN. Allelic variation and duplication of the dmrt1 were associated with sex chromosome turnover in three representative Scatophagidae fish species. Commun Biol 2025; 8:627. [PMID: 40246974 PMCID: PMC12006487 DOI: 10.1038/s42003-025-08056-1] [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: 11/24/2024] [Accepted: 04/08/2025] [Indexed: 04/19/2025] Open
Abstract
Fish species of the family Scatophagidae possessing known candidate sex-determining genes (male-specific dmrt1Ys), offer suitable models for studying sex chromosome evolution. Here, we analyzed sex chromosome turnover events in three representative fish species of the family Scatophagidae, belonging to the genera Scatophagus and Selenotoca, which diverged 12.8 million years ago (Mya). Prior to the divergence of Sc. argus and Sc. tetracanthus 7.2 Mya, their dmrt1Y was differentiated from its locus, the truncated dmrt1ΔX, through allelic variation. The Y chromosome (Chr1) of Sc. tetracanthus is the result of the fusion of the original Y chromosome (Chr4) with an autosome (Chr13). The Se. multifasciata dmrt1Y arose from a duplication of dmrt1 on Chr4 and then translocated to the new Y chromosome (Chr18). The divergent evolutionary trajectories of the dmrt1Ys were accompanied by sex chromosome turnover in these three species. The sex chromosomes of the Scatophagidae family have evolved rapidly, albeit not randomly.
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Affiliation(s)
- Yuan-Qing Huang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Xin-Hui Zhang
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518057, China
| | - Chao Bian
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518057, China
| | - Kai-Zhi Jiao
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Lin Zhang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, Shenzhen, 518081, China
| | - Wei Yang
- Yangjiang Polytechnic, Yangjiang, 529566, China
| | - Yu Li
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Gang Shi
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yang Huang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Chang-Xu Tian
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Hua-Pu Chen
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Si-Ping Deng
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Chun-Hua Zhu
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Qiong Shi
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518057, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, Shenzhen, 518081, China.
| | - Guang-Li Li
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China.
| | - Dong-Neng Jiang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China.
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Zheng S, Tao H, Song Y, Li M, Yang H, Li J, Yan H, Sheraliev B, Tao W, Peng Z, Zhang Y, Wang D. The origin, evolution, and translocation of sex chromosomes in Silurus catfish mediated by transposons. BMC Biol 2025; 23:54. [PMID: 39984975 PMCID: PMC11846232 DOI: 10.1186/s12915-025-02160-8] [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: 08/09/2024] [Accepted: 02/13/2025] [Indexed: 02/23/2025] Open
Abstract
BACKGROUND Sex chromosome (SC) evolution is a longstanding topic of focus in evolutionary biology. Teleosts often exhibit rapid turnover of SCs and sex-determining (SD) genes, alongside a diverse range of SC differentiation mechanisms. RESULTS On the basis of new chromosome-scale assemblies of three Silurus species (S. microdorsalis, S. glanis, and S. lanzhouensis) and two outgroup species (Pterocryptis cochinchinensis and Kryptopterus bicirrhis), along with our previous assemblies of S. meridionalis and S. asotus, we traced the evolution of SC in the Silurus genus (Siluriformes), following the fate of the known SD gene amhr2y. Phylogenetic analysis showed that amhr2y occurred at least before the divergence of Pterocryptis, Kryptopterus, and Silurus and lost in P. cochinchinensis and K. bicirrhis. Chr24 has become the SC in the ancestor of five Silurus species due to the duplication-and-translocation of amhr2 mediated by LTR transposon. Then, a proto Y was formed and maintained with a shared 60 kb male-specific region of the Y chromosome (MSY) by transposable elements (TEs) expansion and gene gathering. Due to the continuous TEs accumulation, genes other than amhr2y in MSYs have degenerated or been lost, while non-recombinant regions continue to expend, forming MSYs of different sizes in different Silurus species (from 320 to 550 kb). Two turnover events, one homologous (from the left arm to the right arm of Chr24) and one nonhomologous (from Chr24 to Chr5), occurring among five Silurus species were possibly mediated by hAT and Helitron transposons. CONCLUSIONS Our results on the dynamic evolutionary trajectory of SD gene amhr2y, MSYs, and SCs in Silurus catfish indicated the variability and diversity of fish SCs and confirmed that frequent turnover is an important way to maintain the homology and low differentiation of fish SCs.
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Affiliation(s)
- Shuqing Zheng
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, 400715, China
| | - Hongyan Tao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, 400715, China
| | - Yuheng Song
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, 400715, China
| | - Mao Li
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, 400715, China
| | - Haowen Yang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, 400715, China
| | - Jianzhen Li
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, 730070, China
| | - Hongwei Yan
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Bakhtiyor Sheraliev
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, 400715, China
| | - Wenjing Tao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, 400715, China
| | - Zuogang Peng
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, 400715, China
| | - Yaoguang Zhang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, 400715, China
| | - Deshou Wang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, 400715, China.
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4
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Christensen KA, Flores AM, Joshi J, Shibata K, Fujimoto T, Koop BF, Devlin RH. Masu salmon species complex relationships and sex chromosomes revealed from analyses of the masu salmon (Oncorhynchus masou masou) genome assembly. G3 (BETHESDA, MD.) 2025; 15:jkae278. [PMID: 39607719 PMCID: PMC11797027 DOI: 10.1093/g3journal/jkae278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 11/15/2024] [Indexed: 11/29/2024]
Abstract
Masu salmon (Oncorhynchus masou) are the only Pacific salmon endemic to Asia. Some researchers prefer to categorize these salmon into 4 subspecies (masu-Oncorhynchus masou masou, amago-Oncorhynchus masou ishikawae, Biwa-Oncorhynchus masou subsp., and Formosan-Oncorhynchus masou formosanus), while others prefer individual species designations. Even though the masu salmon fishery is thousands of years old, classification of the diversity within the masu salmon species complex remains elusive. In this study, a genetic map and reference genome assembly were generated for 1 species/subspecies (masu) to provide resources for understanding the species complex. In O. m. masou, the sex chromosome was determined to be chromosome 7. Resequenced genomes from 2 other putative subspecies (amago and Biwa) provided evidence that they do not share the same sex chromosome. Principal component and admixture analyses clustered the amago and Biwa salmon close together. This supported previous findings of a close relationship between amago and Biwa salmon and a more distant relationship to masu salmon for both. Additional analyses of the masu salmon species complex will benefit from using the new reference genome assembly.
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Affiliation(s)
- Kris A Christensen
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada V8W 2Y2
| | - Anne-Marie Flores
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada V8W 2Y2
| | - Jay Joshi
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada V8W 2Y2
| | - Kiko Shibata
- Faculty and Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan
| | - Takafumi Fujimoto
- Faculty and Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada V8W 2Y2
| | - Robert H Devlin
- Fisheries and Oceans Canada, West Vancouver, British Columbia, Canada V7V 1N6
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5
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Zhao H, Li J, Xiao Z, Xiao Y. Dose-dependent role of AMH and AMHR2 signaling in male differentiation and regulation of sex determination in Spotted knifejaw (Oplegnathus punctatus) with X 1X 1X 2X 2/X 1X 2Y chromosome system. Cell Commun Signal 2025; 23:59. [PMID: 39893368 PMCID: PMC11786412 DOI: 10.1186/s12964-025-02038-w] [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: 09/14/2024] [Accepted: 01/10/2025] [Indexed: 02/04/2025] Open
Abstract
Sex determination mechanisms vary significantly across different chromosomal systems and evolutionary contexts. Nonetheless, the regulatory framework governing the multi-sex chromosome system (X1X1X2X2/X1X2Y) remains enigmatic. Through an examination of sex-related genes (dmrt1, hsd11b2, amh, sox9a, sox9b, foxl2, cyp19a), hormonal influences (E2, 11-KT), and histological analyses of gonadal development, we demonstrate that the critical period for sexual differentiation occurs between 35 to 60 days post-hatching (dph). Our multi-omics analysis identified amhr2 as a candidate sex-determining gene, revealing that the males possess three distinct amhr2 transcripts (amhr2ay, amhr2by, amhr2cy), whereas females express only one (amhr2a). In situ hybridization assays demonstrated that amhr2 is predominantly localized to primary spermatocyte and Sertoli cells of male testes. Notably, the specific mRNA expression of amhr2 is significantly enriched in amhr2cy, whose extracellular domain exhibits the highest binding affinity for Amh protein, with sexual expression differences manifesting as early as 5 dph. The outcomes of amhr2 interference (RNAi) experiments indicate that amhr2 knockdown leads to a reduction in the expression of male-related gene (dmrt1, amh, sox9a, sox9b), androgen synthesis genes (hsd11b2, cyp11a), and female-related genes (wnt4, foxl2, cyp19a, cyp19b). Conversely, overexpression of amhr2 yielded contrasting results. Our research supports the role of amhr2 as a pivotal candidate sex-determining gene. Furthermore, the dosage effect of amhr2, reflected in transcript abundance, mRNA expression levels, and binding efficacy, serves as a fundamental mechanism driving male differentiation and regulatory processes in Spotted knifejaw.
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Affiliation(s)
- Haixia Zhao
- State Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences (CAS), Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Marine Biology Institute of Shandong Province, Qingdao, Shandong, China
| | - Jun Li
- State Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences (CAS), Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Zhizhong Xiao
- State Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences (CAS), Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Yongshuang Xiao
- State Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences (CAS), Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
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6
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Johnson HA, Rondeau EB, Sutherland BJG, Minkley DR, Leong JS, Whitehead J, Despins CA, Gowen BE, Collyard BJ, Whipps CM, Farrell JM, Koop BF. Loss of genetic variation and ancestral sex determination system in North American northern pike characterized by whole-genome resequencing. G3 (BETHESDA, MD.) 2024; 14:jkae183. [PMID: 39115373 PMCID: PMC11457062 DOI: 10.1093/g3journal/jkae183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/28/2024] [Indexed: 10/08/2024]
Abstract
The northern pike Esox lucius is a freshwater fish with low genetic diversity but ecological success throughout the Northern Hemisphere. Here, we generate an annotated chromosome-level genome assembly of 941 Mbp in length with 25 chromosome-length scaffolds. We then genotype 47 northern pike from Alaska through New Jersey at a genome-wide scale and characterize a striking decrease in genetic diversity along the sampling range. Individuals west of the North American Continental Divide have substantially higher diversity than those to the east (e.g. Interior Alaska and St. Lawrence River have on average 181 and 64K heterozygous SNPs per individual, or a heterozygous SNP every 5.2 and 14.6 kbp, respectively). Individuals clustered within each population with strong support, with numerous private alleles observed within each population. Evidence for recent population expansion was observed for a Manitoba hatchery and the St. Lawrence population (Tajima's D = -1.07 and -1.30, respectively). Several chromosomes have large regions with elevated diversity, including LG24, which holds amhby, the ancestral sex determining gene. As expected amhby was largely male-specific in Alaska and the Yukon and absent southeast to these populations, but we document some amhby(-) males in Alaska and amhby(+) males in the Columbia River, providing evidence for a patchwork of presence of this system in the western region. These results support the theory that northern pike recolonized North America from refugia in Alaska and expanded following deglaciation from west to east, with probable founder effects resulting in loss of both neutral and functional diversity (e.g. amhby).
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Affiliation(s)
- Hollie A Johnson
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Eric B Rondeau
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Ben J G Sutherland
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
- Sutherland Bioinformatics, Lantzville V0R 2H0, British Columbia, Canada
| | - David R Minkley
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Jong S Leong
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Joanne Whitehead
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Cody A Despins
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Brent E Gowen
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Brian J Collyard
- Alaska Department of Fish and Game, Division of Sport Fish, 1300 College Rd, Fairbanks, AK 99701-1599, USA
| | - Christopher M Whipps
- Center for Applied Microbiology, Department of Environmental Biology, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - John M Farrell
- Thousand Island Biological Station, Department of Environmental and Forest Biology, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Ben F Koop
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
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Zhou Q, Wang J, Li J, Chen Z, Wang N, Li M, Wang L, Si Y, Lu S, Cui Z, Liu X, Chen S. Decoding the fish genome opens a new era in important trait research and molecular breeding in China. SCIENCE CHINA. LIFE SCIENCES 2024; 67:2064-2083. [PMID: 39145867 DOI: 10.1007/s11427-023-2670-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/01/2024] [Indexed: 08/16/2024]
Abstract
Aquaculture represents the fastest-growing global food production sector, as it has become an essential component of the global food supply. China has the world's largest aquaculture industry in terms of production volume. However, the sustainable development of fish culture is hindered by several concerns, including germplasm degradation and disease outbreaks. The practice of genomic breeding, which relies heavily on genome information and genotypephenotype relationships, has significant potential for increasing the efficiency of aquaculture production. In 2014, the completion of the genome sequencing and annotation of the Chinese tongue sole signified the beginning of the fish genomics era in China. Since then, domestic researchers have made dramatic progress in functional genomic studies. To date, the genomes of more than 60 species of fish in China have been assembled and annotated. Based on these reference genomes, evolutionary, comparative, and functional genomic studies have revolutionized our understanding of a wide range of biologically and economically important traits of fishes, including growth and development, sex determination, disease resistance, metamorphosis, and pigmentation. Furthermore, genomic tools and breeding techniques such as SNP arrays, genomic selection, and genome editing have greatly accelerated genetic improvement through the incorporation of functional genomic information into breeding activities. This review aims to summarize the current status, advances, and perspectives of the genome resources, genomic study of important traits, and genomic breeding techniques of fish in China. The review will provide aquaculture researchers, fish breeders, and farmers with updated information concerning fish genomic research and breeding technology. The summary will help to promote the genetic improvement of production traits and thus will support the sustainable development of fish aquaculture.
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Affiliation(s)
- Qian Zhou
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Jialin Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Jiongtang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100041, China
| | - Zhangfan Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Na Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Ming Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Lei Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Yufeng Si
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Sheng Lu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Zhongkai Cui
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Xuhui Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Songlin Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China.
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8
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Yu H, Du X, Chen X, Liu L, Wang X. Transforming growth factor-β (TGF-β): A master signal pathway in teleost sex determination. Gen Comp Endocrinol 2024; 355:114561. [PMID: 38821217 DOI: 10.1016/j.ygcen.2024.114561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/27/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Sex determination and differentiation in fish has always been a hot topic in genetic breeding of aquatic animals. With the advances in next-generation sequencing (NGS) in recent years, sex chromosomes and sex determining genes can be efficiently identified in teleosts. To date, master sex determination genes have been elucidated in 114 species, of which 72 species have sex determination genes belonging to TGF-β superfamily. TGF-β is the only signaling pathway that the largest proportion of components, which including ligands (amhy, gsdfy, gdf6), receptors (amhr, bmpr), and regulator (id2bby), have opportunity recognized as a sex determination gene. In this review, we focus on the recent studies about teleost sex-determination genes within TGF-β superfamily and propose several hypotheses on how these genes regulate sex determination process. Differing from other reviews, our review specifically devotes significant attention to all members of the TGF-β signal pathway, not solely the sex determination genes within the TGF-β superfamily. However, the functions of the paralogous genes of TGF superfamily are still needed ongoing research. Further studies are required to more accurately interpret the molecular mechanism of TGF-β superfamily sex determination genes.
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Affiliation(s)
- Haiyang Yu
- School of Life Science and Engineering, Jining University, Qufu, Shandong, China
| | - Xinxin Du
- School of Life Science and Engineering, Jining University, Qufu, Shandong, China
| | - Xue Chen
- School of Resource & Environment and Safety Engineering, Jining University, Qufu, Shandong, China
| | - Longxue Liu
- School of Life Science and Engineering, Jining University, Qufu, Shandong, China
| | - Xubo Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China.
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9
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Kuhl H, Euclide PT, Klopp C, Cabau C, Zahm M, Lopez-Roques C, Iampietro C, Kuchly C, Donnadieu C, Feron R, Parrinello H, Poncet C, Jaffrelo L, Confolent C, Wen M, Herpin A, Jouanno E, Bestin A, Haffray P, Morvezen R, de Almeida TR, Lecocq T, Schaerlinger B, Chardard D, Żarski D, Larson WA, Postlethwait JH, Timirkhanov S, Kloas W, Wuertz S, Stöck M, Guiguen Y. Multi-genome comparisons reveal gain-and-loss evolution of anti-Mullerian hormone receptor type 2 as a candidate master sex-determining gene in Percidae. BMC Biol 2024; 22:141. [PMID: 38926709 PMCID: PMC11209984 DOI: 10.1186/s12915-024-01935-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. RESULTS We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex-determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplicates (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been likely lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome 18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variations (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex-determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in the testis than in the ovary. CONCLUSIONS Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.
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Affiliation(s)
- Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587, Berlin, Germany.
| | - Peter T Euclide
- Department of Forestry and Natural Resources | Illinois-Indiana Sea Grant, Purdue University, West Lafayette, USA
| | - Christophe Klopp
- Sigenae, Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Cédric Cabau
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Margot Zahm
- Sigenae, Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | | | | | - Claire Kuchly
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hugues Parrinello
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Charles Poncet
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Lydia Jaffrelo
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Carole Confolent
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ming Wen
- INRAE, LPGP, 35000, Rennes, France
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | | | | | - Anastasia Bestin
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Pierrick Haffray
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Romain Morvezen
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes Cedex, France
| | | | | | | | | | - Daniel Żarski
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, ul. Tuwima 10, 10-748, Olsztyn, Poland
| | - Wesley A Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science Center, 17109 Point Lena Loop Road, Auke Bay LaboratoriesJuneau, AK, 99801, USA
| | | | | | - Werner Kloas
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587, Berlin, Germany
| | - Sven Wuertz
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587, Berlin, Germany
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587, Berlin, Germany
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10
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Čermáková E, Mukherjee S, Nováková D, Horká P, Zdeňková K, Demnerová K. Parvalbumin Gene: A Valuable Marker for Pike Authentication and Allergen Risk Assessment. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12788-12797. [PMID: 38778779 PMCID: PMC11157528 DOI: 10.1021/acs.jafc.4c01410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/02/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Fish from the pike (Esox) genus are valued in gastronomy for their superior meat quality. However, they can cause allergic reactions in sensitive consumers. This work aimed to fill the gap in the detection of pike allergens using molecular-biological techniques. New, fast, and accurate loop-mediated isothermal amplification (LAMP) and real-time PCR (qPCR) assays were designed to detect pike DNA using the parvalbumin gene as a marker. LAMP was assessed by electrophoresis, SYBR green optical detection, and real-time fluorescence detection. The latter was the most sensitive, detecting as little as 0.78 ng of pike DNA; the qPCR detection limit was 0.1 ng. The LAMP analysis took 20-70 min, which is significantly faster than qPCR. The study provides reliable detection and quantification of the parvalbumin gene in both fresh and processed samples and further highlights the versatility of the use of the parvalbumin gene for the authentication of food products and consumer protection via refined allergen risk assessment that is independent of the type of tissue or food processing method used.
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Affiliation(s)
- Eliška Čermáková
- Department
of Chemistry, Biochemistry and Food Microbiology, Food Research Institute Prague, Radiová 1285/7, Prague
10 102 00, Czech Republic
- Department
of Biochemistry and Microbiology, University
of Chemistry and Technology, Prague, Technická 5, Prague 6 166 28, Czech Republic
| | - Subham Mukherjee
- Department
of Chemistry, Biochemistry and Food Microbiology, Food Research Institute Prague, Radiová 1285/7, Prague
10 102 00, Czech Republic
- Lennard-Jones
School of Chemical and Physical Sciences, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institute
for Environmental Studies, Faculty of Science, Charles University, Benatska 2, Prague 2 128
01, Czech Republic
| | - Denisa Nováková
- Department
of Biochemistry and Microbiology, University
of Chemistry and Technology, Prague, Technická 5, Prague 6 166 28, Czech Republic
| | - Petra Horká
- Institute
for Environmental Studies, Faculty of Science, Charles University, Benatska 2, Prague 2 128
01, Czech Republic
| | - Kamila Zdeňková
- Department
of Biochemistry and Microbiology, University
of Chemistry and Technology, Prague, Technická 5, Prague 6 166 28, Czech Republic
| | - Kateřina Demnerová
- Department
of Biochemistry and Microbiology, University
of Chemistry and Technology, Prague, Technická 5, Prague 6 166 28, Czech Republic
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11
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Zhang Q, Huang J, Fu Y, Chen J, Wang W. Genome-wide identification and expression profiles of sex-related gene families in the Pacific abalone Haliotis discus hannai. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101205. [PMID: 38364653 DOI: 10.1016/j.cbd.2024.101205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/25/2024] [Accepted: 02/05/2024] [Indexed: 02/18/2024]
Abstract
In recent years, members of the Dmrt family, TGF-β superfamily and Sox family have been recognized as crucial genes for sex determination/differentiation across diverse animal species. Nevertheless, knowledge regarding the abundance and potential functions of these genes in abalone remains limited. In this study, a total of 5, 10, and 7 members of the Dmrt family, the TGF-β superfamily and the Sox family, respectively, were identified in the Pacific abalone Haliotis discus hannai. Sequence characteristics, phylogenetic relationships and spatiotemporal expression profiles of these genes were investigated. Notably, HdDmrt-04 (Dmrt1/1L-like) emerged as a potential mollusc-specific gene with a preponderance for expression in the testis. Interestingly, none of the TGF-β superfamily members exhibited specific or elevated expression in the gonads, highlighting the need for further investigation into their role in abalone sex differentiation. The Sox proteins in H. discus hannai were categorized into 7 subfamilies: B1, B2, C, D, E, F, and H. Among them, HdSox-07 (SoxH-like) was observed to play a crucial role in testis development, while HdSox-03 (SoxB1-like) and HdSox-04 (SoxC-like) probably cooperate in abalone ovary development. Taken together, the results of the present study suggested that HdDmrt-04 and HdSox-07 can be used as male-specific markers for gonad differentiation in H. discus hannai and imply conservation of their functions across invertebrates and vertebrates. Our findings provide new insights into the evolution and genetic structure of the Dmrt family, the TGF-β superfamily and the Sox family in abalone and pave the way for a deeper understanding of sex differentiation in gastropods.
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Affiliation(s)
- Qian Zhang
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China; Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou 350108, China
| | - Jianfang Huang
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China; Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou 350108, China
| | - Yangtao Fu
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China
| | - Jianming Chen
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China; Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou 350108, China.
| | - Wei Wang
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China; Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou 350108, China.
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12
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Webster TH, Vannan A, Pinto BJ, Denbrock G, Morales M, Dolby GA, Fiddes IT, DeNardo DF, Wilson MA. Lack of Dosage Balance and Incomplete Dosage Compensation in the ZZ/ZW Gila Monster (Heloderma suspectum) Revealed by De Novo Genome Assembly. Genome Biol Evol 2024; 16:evae018. [PMID: 38319079 PMCID: PMC10950046 DOI: 10.1093/gbe/evae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/07/2024] Open
Abstract
Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z chromosome scaffolds. These putative Z chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates.
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Affiliation(s)
- Timothy H Webster
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Annika Vannan
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Grant Denbrock
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Matheo Morales
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Greer A Dolby
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Dale F DeNardo
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ, USA
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13
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Kitano J, Ansai S, Takehana Y, Yamamoto Y. Diversity and Convergence of Sex-Determination Mechanisms in Teleost Fish. Annu Rev Anim Biosci 2024; 12:233-259. [PMID: 37863090 DOI: 10.1146/annurev-animal-021122-113935] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Sexual reproduction is prevalent across diverse taxa. However, sex-determination mechanisms are so diverse that even closely related species often differ in sex-determination systems. Teleost fish is a taxonomic group with frequent turnovers of sex-determining mechanisms and thus provides us with great opportunities to investigate the molecular and evolutionary mechanisms underlying the turnover of sex-determining systems. Here, we compile recent studies on the diversity of sex-determination mechanisms in fish. We demonstrate that genes in the TGF-β signaling pathway are frequently used for master sex-determining (MSD) genes. MSD genes arise via two main mechanisms, duplication-and-transposition and allelic mutations, with a few exceptions. We also demonstrate that temperature influences sex determination in many fish species, even those with sex chromosomes, with higher temperatures inducing differentiation into males in most cases. Finally, we review theoretical models for the turnover of sex-determining mechanisms and discuss what questions remain elusive.
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Affiliation(s)
- Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan;
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan;
| | - Yusuke Takehana
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan;
| | - Yoji Yamamoto
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan;
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14
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Pinto BJ, Nielsen SV, Sullivan KA, Behere A, Keating SE, van Schingen-Khan M, Nguyen TQ, Ziegler T, Pramuk J, Wilson MA, Gamble T. It's a trap?! Escape from an ancient, ancestral sex chromosome system and implication of Foxl2 as the putative primary sex-determining gene in a lizard (Anguimorpha; Shinisauridae). Evolution 2024; 78:355-363. [PMID: 37952174 PMCID: PMC10834058 DOI: 10.1093/evolut/qpad205] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/25/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023]
Abstract
Although sex determination is ubiquitous in vertebrates, mechanisms of sex determination vary from environmentally to genetically influenced. In vertebrates, genetic sex determination is typically accomplished with sex chromosomes. Groups like mammals maintain conserved sex chromosome systems, while sex chromosomes in most vertebrate clades are not conserved across similar evolutionary timescales. One group inferred to have an evolutionarily stable mode of sex determination is Anguimorpha, a clade of charismatic taxa including monitor lizards, Gila monsters, and crocodile lizards. The common ancestor of extant anguimorphs possessed a ZW system that has been retained across the clade. However, the sex chromosome system in the endangered, monotypic family of crocodile lizards (Shinisauridae) has remained elusive. Here, we analyze genomic data to demonstrate that Shinisaurus has replaced the ancestral anguimorph ZW system on LG7 with a novel ZW system on LG3. The linkage group, LG3, corresponds to chromosome 9 in chicken, and this is the first documented use of this syntenic block as a sex chromosome in amniotes. Additionally, this ~1 Mb region harbors approximately 10 genes, including a duplication of the sex-determining transcription factor, Foxl2, critical for the determination and maintenance of sexual differentiation in vertebrates, and thus a putative primary sex-determining gene for Shinisaurus.
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Affiliation(s)
- Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States
| | - Stuart V Nielsen
- Department of Biological Sciences, Museum of Life Sciences, Louisiana State University-Shreveport, Shreveport, LA, United States
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
| | - Kathryn A Sullivan
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Ashmika Behere
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Shannon E Keating
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | | | - Truong Q Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thomas Ziegler
- Cologne Zoo, Cologne, Germany
- Department of Biology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Jennifer Pramuk
- Former affiliation: Woodland Park Zoo, Seattle, WA, United States
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ, United States
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
- Bell Museum of Natural History, University of Minnesota, St Paul, MN, United States
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15
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Shen X, Hu J, Yáñez JM, Bastos Gomes G, Poon ZWJ, Foster D, Alarcon JF, Shao L, Guo X, Shao Y, Huerlimann R, Li C, Goulden E, Anderson K, Fan G, Domingos JA. Exploring the cobia (Rachycentron canadum) genome: unveiling putative male heterogametic regions and identification of sex-specific markers. Gigascience 2024; 13:giae034. [PMID: 38995143 PMCID: PMC11240236 DOI: 10.1093/gigascience/giae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/19/2024] [Accepted: 05/22/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Cobia (Rachycentron canadum) is the only member of the Rachycentridae family and exhibits considerable sexual dimorphism in growth rate. Sex determination in teleosts has been a long-standing basic biological question, and the molecular mechanisms of sex determination/differentiation in cobia are completely unknown. RESULTS Here, we reported 2 high-quality, chromosome-level annotated male and female cobia genomes with assembly sizes of 586.51 Mb (contig/scaffold N50: 86.0 kb/24.3 Mb) and 583.88 Mb (79.9 kb/22.5 Mb), respectively. Synteny inference among perciform genomes revealed that cobia and the remora Echeneis naucrates were sister groups. Further, whole-genome resequencing of 31 males and 60 females, genome-wide association study, and sequencing depth analysis identified 3 short male-specific regions within a 10.7-kb continuous genomic region on male chromosome 18, which hinted at an undifferentiated sex chromosome system with a putative XX/XY mode of sex determination in cobia. Importantly, the only 2 genes within/between the male-specific regions, epoxide hydrolase 1 (ephx1, renamed cephx1y) and transcription factor 24 (tcf24, renamed ctcf24y), showed testis-specific/biased gene expression, whereas their counterparts cephx1x and ctf24x, located in female chromosome 18, were similarly expressed in both sexes. In addition, male-specific PCR targeting the cephx1y gene revealed that this genomic feature is conserved in cobia populations from Panama, Brazil, Australia, and Japan. CONCLUSION The first comprehensive genomic survey presented here is a valuable resource for future studies on cobia population structure and dynamics, conservation, and evolutionary history. Furthermore, it establishes evidence of putative male heterogametic regions with 2 genes playing a potential role in the sex determination of the species, and it provides further support for the rapid evolution of sex-determining mechanisms in teleost fish.
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Affiliation(s)
- Xueyan Shen
- Tropical Futures Institute, James Cook University Singapore, 387380, Singapore
| | - Jie Hu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, 8820808 Santiago, Chile
| | - Giana Bastos Gomes
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| | | | | | | | - Libin Shao
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Xinyu Guo
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Yunchang Shao
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518120, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China
- Geogia Tech Shenzhen Institute (GTSI), Tianjin University, Shen Zhen 518067, China
| | - Roger Huerlimann
- Marine Climate Change Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, 904-0495, Japan
| | - Chengze Li
- Marine Climate Change Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, 904-0495, Japan
| | - Evan Goulden
- Department of Agriculture and Fisheries, Queensland Government, Bribie Island Research Centre, Woorim, QLD 4507, Australia
| | - Kelli Anderson
- Department of Agriculture and Fisheries, Queensland Government, Bribie Island Research Centre, Woorim, QLD 4507, Australia
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518120, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Jose A Domingos
- Tropical Futures Institute, James Cook University Singapore, 387380, Singapore
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville QLD 4811, Australia
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Zhang Q, Chen J, Wang W, Lin J, Guo J. Genome-wide investigation of the TGF-β superfamily in scallops. BMC Genomics 2024; 25:24. [PMID: 38166626 PMCID: PMC10763453 DOI: 10.1186/s12864-023-09942-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Transforming growth factor β (TGF-β) superfamily genes can regulate various processes, especially in embryogenesis, adult development, and homeostasis. To understand the evolution and divergence patterns of the TGF-β superfamily in scallops, genome-wide data from the Bay scallop (Argopecten irradians), the Zhikong scallop (Chlamys farreri) and the Yesso scallop (Mizuhopecten yessoensis) were systematically analysed using bioinformatics methods. RESULTS Twelve members of the TGF-β superfamily were identified for each scallop. The phylogenetic tree showed that these genes were grouped into 11 clusters, including BMPs, ADMP, NODAL, GDF, activin/inhibin and AMH. The number of exons and the conserved motif showed some differences between different clusters, while genes in the same cluster exhibited high similarity. Selective pressure analysis revealed that the TGF-β superfamily in scallops was evolutionarily conserved. The spatiotemporal expression profiles suggested that different TGF-β members have distinct functions. Several BMP-like and NODAL-like genes were highly expressed in early developmental stages, patterning the embryonic body plan. GDF8/11-like genes showed high expression in striated muscle and smooth muscle, suggesting that these genes may play a critical role in regulating muscle growth. Further analysis revealed a possible duplication of AMH, which played a key role in gonadal growth/maturation in scallops. In addition, this study found that several genes were involved in heat and hypoxia stress in scallops, providing new insights into the function of the TGF-β superfamily. CONCLUSION Characteristics of the TGF-β superfamily in scallops were identified, including sequence structure, phylogenetic relationships, and selection pressure. The expression profiles of these genes in different tissues, at different developmental stages and under different stresses were investigated. Generally, the current study lays a foundation for further study of their pleiotropic biological functions in scallops.
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Affiliation(s)
- Qian Zhang
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Bioaffiliationersity, Minjiang University, Fuzhou, 350108, China
| | - Jianming Chen
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China.
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Bioaffiliationersity, Minjiang University, Fuzhou, 350108, China.
| | - Wei Wang
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China.
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Bioaffiliationersity, Minjiang University, Fuzhou, 350108, China.
| | - Jingyu Lin
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Jiabao Guo
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
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17
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Shi R, Li X, Xu X, Chen Z, Zhu Y, Wang N. Genome-wide analysis of BMP/GDF family and DAP-seq of YY1 suggest their roles in Cynoglossus semilaevis sexual size dimorphism. Int J Biol Macromol 2023; 253:127201. [PMID: 37793513 DOI: 10.1016/j.ijbiomac.2023.127201] [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: 08/02/2023] [Revised: 09/28/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023]
Abstract
Sexual size dimorphism (SSD) characterized by different body size between females and males have been reported in various animals. Gonadectomy experiments have implied important regulatory roles of the gonad in SSD. Among multiple factors from the gonad, TGF-β superfamily (especially BMP/GDF family) attracted our interest due to its pleiotropy in growth and reproduction regulations. Thus, whether BMP/GDF family members serve as crucial regulators for SSD was studied in a typically female-biased SSD flatfish named Chinese tongue sole (Cynoglossus semilaevis). Firstly, a total of 26 BMP/GDF family members were identified. The PPI network analysis showed that they may interact with ACVR2a, ACVR2b, ACVR1, BMPR2, SMAD3, BMPR1a, and other proteins. Subsequently, DAP-seq was employed to reveal the binding sites for yin yang 1 (yy1), a transcription factor involved in gonad function and cell growth partly by regulating TGF-β superfamily. The results revealed that two yy1 homologues yy1a and yy1b in C. semilaevis could regulate Hippo signaling pathway, mTOR signaling pathway, and AMPK signaling pathway. Moreover, BMP/GDF family genes including bmp2, bmp4, bmp5, gdf6a, and gdf6b were important components of Hippo pathway. In future, the crosstalk among yy1a, yy1b, and TGF-β family would provide more insight into sexual size dimorphism in C. semilaevis.
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Affiliation(s)
- Rui Shi
- Function Laboratory for Marine Science and Food Production Process, Laoshan laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xihong Li
- Function Laboratory for Marine Science and Food Production Process, Laoshan laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiwen Xu
- Function Laboratory for Marine Science and Food Production Process, Laoshan laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Zhangfan Chen
- Function Laboratory for Marine Science and Food Production Process, Laoshan laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Ying Zhu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China.
| | - Na Wang
- Function Laboratory for Marine Science and Food Production Process, Laoshan laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China.
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18
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Kuhl H, Euclide PT, Klopp C, Cabau C, Zahm M, Roques C, Iampietro C, Kuchly C, Donnadieu C, Feron R, Parrinello H, Poncet C, Jaffrelo L, Confolent C, Wen M, Herpin A, Jouanno E, Bestin A, Haffray P, Morvezen R, de Almeida TR, Lecocq T, Schaerlinger B, Chardard D, Żarski D, Larson W, Postlethwait JH, Timirkhanov S, Kloas W, Wuertz S, Stöck M, Guiguen Y. Multi-genome comparisons reveal gain-and-loss evolution of the anti-Mullerian hormone receptor type 2 gene, an old master sex determining gene, in Percidae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566804. [PMID: 38014084 PMCID: PMC10680665 DOI: 10.1101/2023.11.13.566804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplications (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome-18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variants (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in testis than ovary. Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.
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Affiliation(s)
- Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries – IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587 Berlin, Germany
| | - Peter T Euclide
- Department of Forestry and Natural Resources | Illinois-Indiana Sea Grant, Purdue University, West Lafayette, Indiana, USA
| | - Christophe Klopp
- Sigenae, Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Cedric Cabau
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Margot Zahm
- Sigenae, Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Céline Roques
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Claire Kuchly
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hugues Parrinello
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Charles Poncet
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Lydia Jaffrelo
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Carole Confolent
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ming Wen
- INRAE, LPGP, 35000, Rennes, France
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | | | | | - Anastasia Bestin
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | - Pierrick Haffray
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | - Romain Morvezen
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | | | - Thomas Lecocq
- University of Lorraine, INRAE, UR AFPA, Nancy, France
| | | | | | - Daniel Żarski
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, ul. Tuwima 10, 10-748, Olsztyn, Poland
| | - Wes Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science Center, Auke Bay Laboratories, 17109 Point Lena Loop Road, Juneau, AK, 99801, USA
| | | | | | - Werner Kloas
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries – IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587 Berlin, Germany
| | - Sven Wuertz
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries – IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587 Berlin, Germany
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries – IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587 Berlin, Germany
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19
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Yu Y, Chen M, Shen ZG. Molecular biological, physiological, cytological, and epigenetic mechanisms of environmental sex differentiation in teleosts: A systematic review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 267:115654. [PMID: 37918334 DOI: 10.1016/j.ecoenv.2023.115654] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/04/2023]
Abstract
Human activities have been exerting widespread stress and environmental risks in aquatic ecosystems. Environmental stress, including temperature rise, acidification, hypoxia, light pollution, and crowding, had a considerable negative impact on the life histology of aquatic animals, especially on sex differentiation (SDi) and the resulting sex ratios. Understanding how the sex of fish responds to stressful environments is of great importance for understanding the origin and maintenance of sex, the dynamics of the natural population in the changing world, and the precise application of sex control in aquaculture. This review conducted an exhaustive search of the available literature on the influence of environmental stress (ES) on SDi. Evidence has shown that all types of ES can affect SDi and universally result in an increase in males or masculinization, which has been reported in 100 fish species and 121 cases. Then, this comprehensive review aimed to summarize the molecular biology, physiology, cytology, and epigenetic mechanisms through which ES contributes to male development or masculinization. The relationship between ES and fish SDi from multiple aspects was analyzed, and it was found that environmental sex differentiation (ESDi) is the result of the combined effects of genetic and epigenetic factors, self-physiological regulation, and response to environmental signals, which involves a sophisticated network of various hormones and numerous genes at multiple levels and multiple gradations in bipotential gonads. In both normal male differentiation and ES-induced masculinization, the stress pathway and epigenetic regulation play important roles; however, how they co-regulate SDi is unclear. Evidence suggests that the universal emergence or increase in males in aquatic animals is an adaptation to moderate ES. ES-induced sex reversal should be fully investigated in more fish species and extensively in the wild. The potential aquaculture applications and difficulties associated with ESDi have also been addressed. Finally, the knowledge gaps in the ESDi are presented, which will guide the priorities of future research.
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Affiliation(s)
- Yue Yu
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, PR China
| | - Min Chen
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, PR China
| | - Zhi-Gang Shen
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, PR China.
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20
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Pinto BJ, Nielsen SV, Sullivan KA, Behere A, Keating SE, van Schingen-Khan M, Nguyen TQ, Ziegler T, Pramuk J, Wilson MA, Gamble T. It's a Trap?! Escape from an ancient, ancestral sex chromosome system and implication of Foxl2 as the putative primary sex determining gene in a lizard (Anguimorpha; Shinisauridae). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547803. [PMID: 37461522 PMCID: PMC10349997 DOI: 10.1101/2023.07.05.547803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Although sex determination is ubiquitous in vertebrates, mechanisms of sex determination vary from environmentally- to genetically-influenced. In vertebrates, genetic sex determination is typically accomplished with sex chromosomes. Groups like mammals maintain conserved sex chromosome systems, while sex chromosomes in most vertebrate clades aren't conserved across similar evolutionary timescales. One group inferred to have an evolutionarily stable mode of sex determination is Anguimorpha, a clade of charismatic taxa including: monitor lizards, Gila monsters, and crocodile lizards. The common ancestor of extant anguimorphs possessed a ZW system that has been retained across the clade. However, the sex chromosome system in the endangered, monotypic family of crocodile lizards (Shinisauridae) has remained elusive. Here, we analyze genomic data to demonstrate that Shinisaurus has replaced the ancestral anguimorph ZW system on LG7 chromosome with a novel ZW system on LG3. The linkage group LG3 corresponds to chromosome 9 in chicken, and this is the first documented use of this syntenic block as a sex chromosome in amniotes. Additionally, this ~1Mb region harbors approximately 10 genes, including a duplication of the sex-determining transcription factor, Foxl2-critical for the determination and maintenance of sexual differentiation in vertebrates, and thus a putative primary sex determining gene for Shinisaurus.
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Affiliation(s)
- Brendan J. Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
| | - Stuart V. Nielsen
- Department of Biological Sciences, Museum of Life Sciences, Louisiana State University-Shreveport, Shreveport, LA USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL USA
| | - Kathryn A. Sullivan
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
- Department of Biological Sciences, Marquette University, Milwaukee WI USA
| | - Ashmika Behere
- Department of Biological Sciences, Marquette University, Milwaukee WI USA
| | - Shannon E. Keating
- Department of Biological Sciences, Marquette University, Milwaukee WI USA
| | - Mona van Schingen-Khan
- Federal Agency for Nature Conservation, CITES Scientific Authority, Konstantinstraße 110, 53179 Bonn, Germany
| | - Truong Quang Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi 10072, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10072, Vietnam
| | - Thomas Ziegler
- Cologne Zoo, Riehler Straße 173, 50735 Cologne, Germany
- Department of Biology, Institute of Zoology, University of Cologne, Zülpicher Straße 47b, 50674 Cologne, Germany
| | | | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ USA
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
- Department of Biological Sciences, Marquette University, Milwaukee WI USA
- Bell Museum of Natural History, University of Minnesota, St Paul, MN USA
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21
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Shen X, Yan H, Li W, Zhou H, Wang J, Zhang Q, Zhang L, Liu Q, Liu Y. Estrodiol-17β and aromatase inhibitor treatment induced alternations of genome-wide DNA methylation pattern in Takifugu rubripes gonads. Gene 2023; 882:147641. [PMID: 37460000 DOI: 10.1016/j.gene.2023.147641] [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: 03/27/2023] [Revised: 05/12/2023] [Accepted: 07/12/2023] [Indexed: 07/28/2023]
Abstract
Estradiol-17β (E2) and aromatase inhibitor (AI) exposure can change the phenotypic sex of fish gonads. To investigated whether alterations in DNA methylation is involved in this process, the level of genome-wide DNA methylation in Takifugu rubripes gonads was quantitatively analyzed during the E2-induced feminization and AI-induced masculinization processes in this study. The methylation levels of the total cytosine (C) in control-XX(C-XX), control-XY (C-XY), E2-treated-XY (E-XY) and AI-treated-XX (AI-XX) were 9.11%, 9.19%, 8.63% and 9.23%, respectively. In the C-XX vs C-XY comparison, 4,196 differentially methylated regions (DMRs) overlapped with the gene body of 2,497 genes and 608 DMRs overlapped with the promoter of 575 genes. In the E-XY vs C-XY comparison, 6,539 DMRs overlapped with the gene body of 3,416 genes and 856 DMRs overlapped with the promoter of 776 genes. In the AI-XX vs C-XX comparison, 2,843 DMRs overlapped with the gene body of 1,831 genes and 461 DMRs overlapped with the promoter of 421 genes. Gonadal genomic methylation mainly occurred at CG sites and the genes that overlapped with DMRs on CG context were most enriched in the signaling pathways related to gonad differentiation, such as the Wnt, TGF-β, MAPK, CAM and GnRH pathways. The DNA methylation levels of steroid synthesis genes and estrogen receptor genes promoter or gene body were negative correlated with their expression. After bisulfite sequencing verification, the DNA methylation level of the amhr2 promoter in XY was increased after E2 treatment, which consistent with the data from the genome-wide DNA methylation sequencing. In C-XY group, the expression of amhr2 was significantly higher than that in E-XY (p < 0.05). Additionally, dnmt1, which is responsible for methylation maintenance, expressed at similar level in four groups (p > 0.05). dnmt3, tet2, and setd1b, which were responsible for methylation modification, expressed at significantly higher levels in E-XY compared to the C-XY (p < 0.05). Dnmt3 and tet2 were expressed at significantly higher levels in AI-XX than that in C-XX (p < 0.05). These results indicated that E2 and AI treatment lead to the aberrant genome-wide DNA methylation level and expression level of dnmt3, tet2, and setd1b in T. rubripes gonad.
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Affiliation(s)
- Xufang Shen
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Life Sciences, Liaoning Normal University, Dalian, Liaoning 116029, China
| | - Hongwei Yan
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China.
| | - Weiyuan Li
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Marine Science and Environment Engineering, Dalian Ocean University, 116023 Dalian, Liaoning, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China
| | - Huiting Zhou
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China
| | - Jia Wang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China
| | - Qi Zhang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China
| | - Lei Zhang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Marine Science and Environment Engineering, Dalian Ocean University, 116023 Dalian, Liaoning, China
| | - Qi Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Marine Science and Environment Engineering, Dalian Ocean University, 116023 Dalian, Liaoning, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China.
| | - Ying Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China
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22
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Smith SH, Hsiung K, Böhne A. Evaluating the role of sexual antagonism in the evolution of sex chromosomes: new data from fish. Curr Opin Genet Dev 2023; 81:102078. [PMID: 37379742 DOI: 10.1016/j.gde.2023.102078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/07/2023] [Accepted: 06/07/2023] [Indexed: 06/30/2023]
Abstract
The recent increase in available molecular and genomic data for diverse taxa helps to shed new light on long-standing theories. Research into sex chromosome evolution has particularly benefited from a growing number of studies of fish, motivated by their highly diverse mechanisms of sex determination. Sexual antagonism is regularly cited as an influential force in sex chromosome emergence; however, this so far proves difficult to demonstrate. In this review, we highlight recent developments in the investigation of sexual antagonism in sex chromosome research in fish. We find strong emphasis placed on study-organism specific genomic features and patterns of recombination, rather than evidence for a comprehensive role of sexual antagonism. In this light, we discuss the alternative models of sex chromosome evolution. We conclude that fish represents a key resource for further research, provided attention is given to species-specific effects while simultaneously integrating comparative studies across taxa for a vital and comprehensive understanding of sex chromosome evolution and investigation of proposed models.
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Affiliation(s)
- Sophie Helen Smith
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113 Bonn, Germany. https://twitter.com/@shg_smith
| | - Kevin Hsiung
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113 Bonn, Germany. https://twitter.com/@KevinKHsiung
| | - Astrid Böhne
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113 Bonn, Germany.
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23
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Balogh RE, Csorbai B, Guti C, Keszte S, Urbányi B, Orbán L, Kovács B. Validation of a male-specific DNA marker confirms XX/XY-type sex determination in several Hungarian strains of African catfish (Clarias gariepinus). Theriogenology 2023; 205:106-113. [PMID: 37116410 DOI: 10.1016/j.theriogenology.2023.04.017] [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: 12/19/2022] [Revised: 03/24/2023] [Accepted: 04/15/2023] [Indexed: 04/30/2023]
Abstract
African catfish (Clarias gariepinus) is a promising food fish species with significant potential and growing mass of production in freshwater aquaculture. Male African catfish possess improved production characteristics over females, therefore the use of monosex populations could be advantageous for aquaculture production. However, our knowledge about the sex determination mechanism of this species is still limited and controversial. A previously isolated male-specific DNA marker (CgaY1) was validated using offspring groups from targeted crosses (n = 630) and it was found to predict the sex of 608 individuals correctly (96.43% accuracy). Using the proportion of recombinants, we estimated the average genetic distance between the potential sex determination locus and the sex-specific marker to be 3.57 cM. As an earlier study suggested that both XX/XY and ZZ/ZW systems coexist in this species, we tested the applicability of their putative 'moderately sex-linked loci' and found that no sex-specific amplification could be detected for any of them. In addition, temperature-induced masculinization suggested by others was also tested, but no such effect was detected in our stocks when the published parameters were used for heat treatment. Altogether, our results support an exclusive XX/XY sex determination system in our African catfish stock and indicate a good potential for the future use of this male-specific DNA marker in research and commercial production.
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Affiliation(s)
- Réka Enikő Balogh
- Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Balázs Csorbai
- Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Csaba Guti
- The Hungarian National Fishing Association, Budapest, Hungary
| | - Szilvia Keszte
- Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Béla Urbányi
- Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - László Orbán
- Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, Keszthely, Hungary.
| | - Balázs Kovács
- Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary.
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24
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Schartl M, Georges A, Marshall Graves JA. Polygenic sex determination in vertebrates - is there any such thing? Trends Genet 2023; 39:242-250. [PMID: 36669949 PMCID: PMC10148267 DOI: 10.1016/j.tig.2022.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/28/2022] [Accepted: 12/15/2022] [Indexed: 01/20/2023]
Abstract
Genetic sex determination (SD) in most vertebrates is controlled by a single master sex gene, which ensures a 1:1 sex ratio. However, more complex systems abound, and several have been ascribed to polygenic SD (PSD), in which many genes at different loci interact to produce the sexual phenotype. Here we examine claims for PSD in vertebrates, finding that most constitute transient states during sex chromosome turnover, or aberrant systems in species hybrids. To avoid confusion about terminology, we propose a consistent nomenclature for genetic SD systems.
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Affiliation(s)
- Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA; Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany.
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, ACT, 2601, Australia
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25
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Lichilín N, Salzburger W, Böhne A. No evidence for sex chromosomes in natural populations of the cichlid fish Astatotilapia burtoni. G3 (BETHESDA, MD.) 2023; 13:6989787. [PMID: 36649174 PMCID: PMC9997565 DOI: 10.1093/g3journal/jkad011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/14/2022] [Accepted: 12/16/2022] [Indexed: 01/18/2023]
Abstract
Sex determination (SD) is not conserved among teleost fishes and can even differ between populations of the same species. Across the outstandingly species-rich fish family Cichlidae, more and more SD systems are being discovered. Still, the picture of SD evolution in this group is far from being complete. Lake Tanganyika and its affluent rivers are home to Astatotilapia burtoni, which belongs to the extremely successful East African cichlid lineage Haplochromini. Previously, in different families of an A. burtoni laboratory strain, an XYW system and an XY system have been described. The latter was also found in a second laboratory strain. In a laboratory-reared family descending from a population of the species' southern distribution, a second XY system was discovered. Yet, an analysis of sex chromosomes for the whole species distribution is missing. Here, we examined the genomes of 11 natural populations of A. burtoni, encompassing a wide range of its distribution, for sex-linked regions. We did not detect signs of differentiated sex chromosomes and also not the previously described sex chromosomal systems present in laboratory lines, suggesting different SD systems in the same species under natural and (long-term) artificial conditions. We suggest that SD in A. burtoni is more labile than previously assumed and consists of a combination of non-genetic, polygenic, or poorly differentiated sex chromosomes.
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Affiliation(s)
- Nicolás Lichilín
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland.,Department of Neuroscience and Developmental Biology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Astrid Böhne
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland.,Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113 Bonn, Germany
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26
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Nacif CL, Kratochwil CF, Kautt AF, Nater A, Machado-Schiaffino G, Meyer A, Henning F. Molecular parallelism in the evolution of a master sex-determining role for the anti-Mullerian hormone receptor 2 gene (amhr2) in Midas cichlids. Mol Ecol 2023; 32:1398-1410. [PMID: 35403749 DOI: 10.1111/mec.16466] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/28/2022] [Accepted: 03/25/2022] [Indexed: 12/01/2022]
Abstract
The evolution of sex chromosomes and their differentiation from autosomes is a major event during genome evolution that happened many times in several lineages. The repeated evolution and lability of sex-determination mechanisms in fishes makes this a well-suited system to test for general patterns in evolution. According to current theory, differentiation is triggered by the suppression of recombination following the evolution of a new master sex-determining gene. However, the molecular mechanisms that establish recombination suppression are known from few examples, owing to the intrinsic difficulties of assembling sex-determining regions (SDRs). The development of forward-genetics and long-read sequencing have generated a wealth of data questioning central aspects of the current theory. Here, we demonstrate that sex in Midas cichlids is determined by an XY system, and identify and assemble the SDR by combining forward-genetics, long-read sequencing and optical mapping. We show how long-reads aid in the detection of artefacts in genotype-phenotype mapping that arise from incomplete genome assemblies. The male-specific region is restricted to a 100-kb segment on chromosome 4 that harbours transposable elements and a Y-specific duplicate of the anti-Mullerian receptor 2 gene, which has evolved master sex-determining functions repeatedly. Our data suggest that amhr2Y originated by an interchromosomal translocation from chromosome 20 to 4 pre-dating the split of Midas and Flier cichlids. In the latter, it is pseudogenized and translocated to another chromosome. Duplication of anti-Mullerian genes is a common route to establishing new sex determiners, highlighting the role of molecular parallelism in the evolution of sex determination.
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Affiliation(s)
- Camila L Nacif
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Cidade Universitária, Rio de Janeiro, Brazil
| | | | - Andreas F Kautt
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Alexander Nater
- Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Frederico Henning
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Cidade Universitária, Rio de Janeiro, Brazil.,Department of Biology, University of Konstanz, Konstanz, Germany
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27
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de la Herrán R, Hermida M, Rubiolo JA, Gómez-Garrido J, Cruz F, Robles F, Navajas-Pérez R, Blanco A, Villamayor PR, Torres D, Sánchez-Quinteiro P, Ramirez D, Rodríguez ME, Arias-Pérez A, Cross I, Duncan N, Martínez-Peña T, Riaza A, Millán A, De Rosa MC, Pirolli D, Gut M, Bouza C, Robledo D, Rebordinos L, Alioto T, Ruíz-Rejón C, Martínez P. A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex-determining gene in the flatfish Solea senegalensis. Mol Ecol Resour 2023; 23:886-904. [PMID: 36587276 DOI: 10.1111/1755-0998.13750] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023]
Abstract
Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and diversity of SD mechanisms. Here, we assembled the Solea senegalensis genome, a flatfish of great commercial value, into 82 contigs (614 Mb) combining long- and short-read sequencing, which were next scaffolded using a highly dense genetic map (28,838 markers, 21 linkage groups), representing 98.9% of the assembly. Further, we established the correspondence between the assembly and the 21 chromosomes by using BAC-FISH. Whole genome resequencing of six males and six females enabled the identification of 41 single nucleotide polymorphism variants in the follicle stimulating hormone receptor (fshr) consistent with an XX/XY SD system. The observed sex association was validated in a broader independent sample, providing a novel molecular sexing tool. The fshr gene displayed differential expression between male and female gonads from 86 days post-fertilization, when the gonad is still an undifferentiated primordium, concomitant with the activation of amh and cyp19a1a, testis and ovary marker genes, respectively, in males and females. The Y-linked fshr allele, which included 24 nonsynonymous variants and showed a highly divergent 3D protein structure, was overexpressed in males compared to the X-linked allele at all stages of gonadal differentiation. We hypothesize a mechanism hampering the action of the follicle stimulating hormone driving the undifferentiated gonad toward testis.
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Affiliation(s)
- Roberto de la Herrán
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Miguel Hermida
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Juan Andres Rubiolo
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Jèssica Gómez-Garrido
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain
| | - Fernando Cruz
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain
| | - Francisca Robles
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Rafael Navajas-Pérez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Andres Blanco
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Paula Rodriguez Villamayor
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Dorinda Torres
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Pablo Sánchez-Quinteiro
- Departamento de Anatomía, Producción Animal y Ciencias Clínicas Veterinarias Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Daniel Ramirez
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Maria Esther Rodríguez
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Alberto Arias-Pérez
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Ismael Cross
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Neil Duncan
- IRTA Sant Carles de la Rapita, Tarragona, Spain
| | | | - Ana Riaza
- Stolt Sea Farm SA, Departamento I+D, A Coruña, Spain
| | | | - M Cristina De Rosa
- Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC) - CNR c/o Catholic University of Rome, Rome, Italy
| | - Davide Pirolli
- Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC) - CNR c/o Catholic University of Rome, Rome, Italy
| | - Marta Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain
| | - Carmen Bouza
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Laureana Rebordinos
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Tyler Alioto
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carmelo Ruíz-Rejón
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Paulino Martínez
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
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28
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Meuser AV, Pyne CB, Mandeville EG. Limited evidence of a genetic basis for sex determination in the common creek chub, Semotilus atromaculatus. J Evol Biol 2022; 35:1635-1645. [PMID: 35411987 DOI: 10.1111/jeb.14006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 03/15/2022] [Indexed: 12/16/2022]
Abstract
Sexual reproduction is almost universal in vertebrates; therefore, each animal species which uses it must have a mechanism for designating sex as male or female. Fish, especially, have a wide range of sex determining systems. In the present study, we aimed to identify a genetic basis for sex determination in the common creek chub (Semotilus atromaculatus) using genotyping-by-sequencing data. No sex-associated markers were found by RADSex or a GWAS using GEMMA; however, Weir and Cockerham locus-specific FST analysis and discriminant analysis of principal components revealed genetic differentiation between the sexes at several loci. While no explicit sex determination mechanism has been yet discovered in creek chub, these loci are potential candidates for future studies. Incompatible systems are thought to increase reproductive isolation but interspecific hybridization is common among groups such as cyprinid minnows; thus, studies such as ours can provide insight into hybridization and evolutionary diversification of this clade. We also highlight technical challenges involved in studying sex determination in evolutionary groups with extremely variable mechanisms and without heteromorphic sex chromosomes.
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Affiliation(s)
- Amanda V Meuser
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Cassandre B Pyne
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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29
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Liu Z, Zhou T, Gao D. Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture. Front Genet 2022; 13:994471. [PMID: 36406125 PMCID: PMC9666392 DOI: 10.3389/fgene.2022.994471] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/20/2022] [Indexed: 11/25/2022] Open
Abstract
Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.
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Affiliation(s)
- Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States,*Correspondence: Zhanjiang Liu,
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Dongya Gao
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States
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30
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Wen M, Pan Q, Larson W, Eché C, Guiguen Y. Characterization of the sex determining region of channel catfish (Ictalurus punctatus) and development of a sex-genotyping test. Gene X 2022; 850:146933. [DOI: 10.1016/j.gene.2022.146933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/01/2022] [Accepted: 09/26/2022] [Indexed: 10/14/2022] Open
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31
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Ansai S, Montenegro J, Masengi KWA, Nagano AJ, Yamahira K, Kitano J. Diversity of sex chromosomes in Sulawesian medaka fishes. J Evol Biol 2022; 35:1751-1764. [DOI: 10.1111/jeb.14076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/30/2022] [Accepted: 07/14/2022] [Indexed: 12/16/2022]
Affiliation(s)
- Satoshi Ansai
- Graduate School of Life Sciences Tohoku University Sendai Japan
| | - Javier Montenegro
- Tropical Biosphere Research Center University of the Ryukyus Nishihara Japan
| | | | - Atsushi J. Nagano
- Faculty of Agriculture Ryukoku University Otsu Japan
- Institute for Advanced Biosciences Keio University Tsuruoka Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center University of the Ryukyus Nishihara Japan
| | - Jun Kitano
- Ecological Genetics Laboratory National Institute of Genetics Shizuoka Japan
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32
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Wen M, Pan Q, Jouanno E, Montfort J, Zahm M, Cabau C, Klopp C, Iampietro C, Roques C, Bouchez O, Castinel A, Donnadieu C, Parrinello H, Poncet C, Belmonte E, Gautier V, Avarre JC, Dugue R, Gustiano R, Hà TTT, Campet M, Sriphairoj K, Ribolli J, de Almeida FL, Desvignes T, Postlethwait JH, Bucao CF, Robinson-Rechavi M, Bobe J, Herpin A, Guiguen Y. An ancient truncated duplication of the anti-Müllerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family. Mol Ecol Resour 2022; 22:2411-2428. [PMID: 35429227 PMCID: PMC9555307 DOI: 10.1111/1755-0998.13620] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/29/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
The evolution of sex determination (SD) in teleosts is amazingly dynamic, as reflected by the variety of different master sex-determining genes identified. Pangasiids are economically important catfishes in South Asian countries, but little is known about their SD system. Here, we generated novel genomic resources for 12 Pangasiids and characterized their SD system. Based on a Pangasianodon hypophthalmus chromosome-scale genome assembly, we identified an anti-Müllerian hormone receptor type Ⅱ gene (amhr2) duplication, which was further characterized as being sex-linked in males and expressed only in testes. These results point to a Y chromosome male-specific duplication (amhr2by) of the autosomal amhr2a. Sequence annotation revealed that the P. hypophthalmus Amhr2by is truncated in its N-terminal domain, lacking the cysteine-rich extracellular part of the receptor that is crucial for ligand binding, suggesting a potential route for its neofunctionalization. Reference-guided assembly of 11 additional Pangasiids, along with sex-linkage studies, revealed that this truncated amhr2by duplication is a male-specific conserved gene in Pangasiids. Reconstructions of the amhr2 phylogeny suggested that amhr2by arose from an ancient duplication/insertion event at the root of the Siluroidei radiation that is dated to ~100 million years ago. Together these results bring multiple lines of evidence supporting that amhr2by is an ancient and conserved master sex-determining gene in Pangasiids, a finding that highlights the recurrent use of the transforming growth factor β pathway, which is often used for the recruitment of teleost master SD genes, and provides another empirical case towards firther understanding of dynamics of SD systems.
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Affiliation(s)
- Ming Wen
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
- INRAE, LPGP, Rennes, France
| | - Qiaowei Pan
- INRAE, LPGP, Rennes, France
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | | | - Margot Zahm
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAE, Castanet Tolosan, France
| | - Cédric Cabau
- SIGENAE, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Christophe Klopp
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAE, Castanet Tolosan, France
- SIGENAE, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | | | - Céline Roques
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Adrien Castinel
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Hugues Parrinello
- Montpellier GenomiX (MGX), C/O Institut de Génomique Fonctionnelle, Montpellier, France
| | - Charles Poncet
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Elodie Belmonte
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Véronique Gautier
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | | | - Remi Dugue
- ISEM, CNRS, IRD, Univ Montpellier, Montpellier, France
| | - Rudhy Gustiano
- Research Institute of Freshwater Fisheries (CRIFI-RIFF), Instalasi Penelitian Perikanan Air Tawar, Jakarta, Indonesia
| | - Trần Thị Thúy Hà
- Research Institute for Aquaculture No.1. Dinh Bang, Tu Son, Bac Ninh, Viet Nam
| | | | - Kednapat Sriphairoj
- Faculty of Natural Resources and Agro-Industry, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Josiane Ribolli
- Laboratório de Biologia e Cultivo de Peixes de Água Doce, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | | | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | | | - Christabel Floi Bucao
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Curzon AY, Shirak A, Benet-Perlberg A, Naor A, Low-Tanne SI, Sharkawi H, Ron M, Seroussi E. Absence of Figla-like Gene Is Concordant with Femaleness in Cichlids Harboring the LG1 Sex-Determination System. Int J Mol Sci 2022; 23:ijms23147636. [PMID: 35886982 PMCID: PMC9316214 DOI: 10.3390/ijms23147636] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 02/04/2023] Open
Abstract
Oreochromis niloticus has been used as a reference genome for studies of tilapia sex determination (SD) revealing segregating genetic loci on linkage groups (LGs) 1, 3, and 23. The master key regulator genes (MKR) underlying the SD regions on LGs 3 and 23 have been already found. To identify the MKR in fish that segregate for the LG1 XX/XY SD-system, we applied short variant discovery within the sequence reads of the genomic libraries of the Amherst hybrid stock, Coptodon zillii and Sarotherodon galilaeus, which were aligned to a 3-Mbp-region of the O. aureus genome. We obtained 66,372 variants of which six were concordant with the XX/XY model of SD and were conserved across these species, disclosing the male specific figla-like gene. We further validated this observation in O. mossambicus and in the Chitralada hybrid stock. Genome alignment of the 1252-bp transcript showed that the figla-like gene’s size was 2664 bp, and that its three exons were capable of encoding 99 amino acids including a 45-amino-acid basic helix–loop–helix domain that is typical of the ovary development regulator—factor-in-the-germline-alpha (FIGLA). In Amherst gonads, the figla-like gene was exclusively expressed in testes. Thus, the figla-like genomic presence determines male fate by interrupting the female developmental program. This indicates that the figla-like gene is the long-sought SD MKR on LG1.
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Affiliation(s)
- Arie Yehuda Curzon
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 75288, Israel; (A.Y.C.); (A.S.); (M.R.)
- Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Andrey Shirak
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 75288, Israel; (A.Y.C.); (A.S.); (M.R.)
| | - Ayana Benet-Perlberg
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Alon Naor
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Shay Israel Low-Tanne
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Haled Sharkawi
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Micha Ron
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 75288, Israel; (A.Y.C.); (A.S.); (M.R.)
| | - Eyal Seroussi
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 75288, Israel; (A.Y.C.); (A.S.); (M.R.)
- Correspondence:
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34
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Jeffries DL, Mee JA, Peichel CL. Identification of a candidate sex determination gene in Culaea inconstans suggests convergent recruitment of an Amh duplicate in two lineages of stickleback. J Evol Biol 2022; 35:1683-1695. [PMID: 35816592 PMCID: PMC10083969 DOI: 10.1111/jeb.14034] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/07/2022] [Accepted: 05/19/2022] [Indexed: 11/29/2022]
Abstract
Sex chromosomes vary greatly in their age and levels of differentiation across the tree of life. This variation is largely due to the rates of sex chromosome turnover in different lineages; however, we still lack an explanation for why sex chromosomes are so conserved in some lineages (e.g. mammals, birds) but so labile in others (e.g. teleosts, amphibians). To identify general mechanisms driving transitions in sex determination systems or forces which favour their conservation, we first require empirical data on sex chromosome systems from multiple lineages. Stickleback fishes are a valuable model lineage for the study of sex chromosome evolution due to variation in sex chromosome systems between closely-related species. Here, we identify the sex chromosome and a strong candidate for the master sex determination gene in the brook stickleback, Culaea inconstans. Using whole-genome sequencing of wild-caught samples and a lab cross, we identify AmhY, a male specific duplication of the gene Amh, as the candidate master sex determination gene. AmhY resides on Chromosome 20 in C. inconstans and is likely a recent duplication, as both AmhY and the sex-linked region of Chromosome 20 show little sequence divergence. Importantly, this duplicate AmhY represents the second independent duplication and recruitment of Amh as the sex determination gene in stickleback and the eighth example known across teleosts. We discuss this convergence in the context of sex chromosome turnovers and the role that the Amh/AmhrII pathway, which is crucial for sex determination, may play in the evolution of sex chromosomes in teleosts.
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Affiliation(s)
- Daniel L Jeffries
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Jonathan A Mee
- Department of Biology, Mount Royal University, Calgary, Alberta, Canada
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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35
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Zhu C, Liu H, Pan Z, Cheng L, Sun Y, Wang H, Chang G, Wu N, Ding H, Zhao H, Zhang L, Yu X. Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome. DNA Res 2022; 29:dsac028. [PMID: 35861402 PMCID: PMC9358014 DOI: 10.1093/dnares/dsac028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/20/2022] [Indexed: 12/01/2022] Open
Abstract
Pseudobagrus ussuriensis is an aquaculture catfish with significant sexual dimorphism. In this study, a chromosome-level genome with a size of 741.97 Mb was assembled for female P. ussuriensis. A total of 26 chromosome-level contigs covering 97.34% of the whole-genome assembly were obtained with an N50 of 28.53 Mb and an L50 of 11. A total of 24,075 protein-coding genes were identified, with 91.54% (22,039) genes being functionally annotated. Based on the genome assembly, four chromosome evolution clusters of catfishes were identified and the formation process of P. ussuriensis chromosomes was predicted. A total of 55 sex-related quantitative trait loci (QTLs) with a phenotypic variance explained value of 100% were located on chromosome 8 (chr08). The QTLs and other previously identified sex-specific markers were located in a sex-determining region of 16.83 Mb (from 6.90 to 23.73 Mb) on chr08, which was predicted as the X chromosome. The sex-determining region comprised 554 genes, with 135 of which being differently expressed between males and females/pseudofemales, and 16 candidate sex-determining genes were screened out. The results of this study provided a useful chromosome-level genome for genetic, genomic and evolutionary studies of P. ussuriensis, and also be useful for further studies on sex-determination mechanism analysis and sex-control breeding of this fish.
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Affiliation(s)
- Chuankun Zhu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an 223300, China
| | - Haiyang Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Zhengjun Pan
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an 223300, China
| | - Lei Cheng
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
| | - Yanhong Sun
- Wuhan Aquaculture Science Research Institute, Wuhan 430207, China
| | - Hui Wang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an 223300, China
| | - Guoliang Chang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an 223300, China
| | - Nan Wu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an 223300, China
| | - Huaiyu Ding
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an 223300, China
| | - Haitao Zhao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an 223300, China
| | - Lei Zhang
- Key Laboratory of Fishery Sustainable Development and Water Environment Protection of Huai’an City, Huai’an Sub Center of the Institute of Hydrobiology, Chinese Academy of Sciences, Huai’an 223002, China
| | - Xiangsheng Yu
- Huai’an Fisheries Technical Guidance Station, Huai’an 223001, China
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Triay C, Courcelle M, Caminade P, Bezault E, Baroiller JF, Kocher TD, D'Cotta H. Polymorphism of Sex Determination Amongst Wild Populations Suggests its Rapid Turnover Within the Nile Tilapia Species. Front Genet 2022; 13:820772. [PMID: 35656328 PMCID: PMC9152217 DOI: 10.3389/fgene.2022.820772] [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: 11/23/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Sex-determining regions have been identified in the Nile tilapia on linkage groups (LG) 1, 20 and 23, depending on the domesticated strains used. Sex determining studies on wild populations of this species are scarce. Previous work on two wild populations, from Lake Volta (Ghana) and from Lake Koka (Ethiopia), found the sex-determining region on LG23. These populations have a Y-specific tandem duplication containing two copies of the Anti-Müllerian Hormone amh gene (named amhY and amhΔY). Here, we performed a whole-genome short-reads analysis using male and female pools on a third wild population from Lake Hora (Ethiopia). We found no association of sex with LG23, and no duplication of the amh gene. Furthermore, we found no evidence of sex linkage on LG1 or on any other LGs. Long read whole genome sequencing of a male from each population confirmed the absence of a duplicated region on LG23 in the Lake Hora male. In contrast, long reads established the structure of the Y haplotype in Koka and Kpandu males and the order of the genes in the duplicated region. Phylogenies constructed on the nuclear and mitochondrial genomes, showed a closer relationship between the two Ethiopian populations compared to the Ghanaian population, implying an absence of the LG23Y sex-determination region in Lake Hora males. Our study supports the hypothesis that the amh region is not the sex-determining region in Hora males. The absence of the Y amh duplication in the Lake Hora population reflects a rapid change in sex determination within Nile tilapia populations. The genetic basis of sex determination in the Lake Hora population remains unknown.
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Affiliation(s)
- Cécile Triay
- UMR116-Institut des Sciences de l'Evolution de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International Baillarguet, Montpellier, France.,UMR-Institut des Sciences de l'Evolution de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche Pour le Développement, Ecole Pratique des Hautes Etudes, University of Montpellier, Montpellier, France
| | - Maxime Courcelle
- UMR-Institut des Sciences de l'Evolution de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche Pour le Développement, Ecole Pratique des Hautes Etudes, University of Montpellier, Montpellier, France
| | - Pierre Caminade
- UMR-Institut des Sciences de l'Evolution de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche Pour le Développement, Ecole Pratique des Hautes Etudes, University of Montpellier, Montpellier, France
| | - Etienne Bezault
- UMR BOREA, CNRS-7208/MNHN/UPMC/IRD-207/UCN/UA, Université des Antilles, Guadeloupe, France
| | - Jean-François Baroiller
- UMR116-Institut des Sciences de l'Evolution de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International Baillarguet, Montpellier, France.,UMR-Institut des Sciences de l'Evolution de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche Pour le Développement, Ecole Pratique des Hautes Etudes, University of Montpellier, Montpellier, France
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, United States
| | - Helena D'Cotta
- UMR116-Institut des Sciences de l'Evolution de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International Baillarguet, Montpellier, France.,UMR-Institut des Sciences de l'Evolution de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche Pour le Développement, Ecole Pratique des Hautes Etudes, University of Montpellier, Montpellier, France
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37
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Li XY, Mei J, Ge CT, Liu XL, Gui JF. Sex determination mechanisms and sex control approaches in aquaculture animals. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1091-1122. [PMID: 35583710 DOI: 10.1007/s11427-021-2075-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/14/2022] [Indexed: 01/21/2023]
Abstract
Aquaculture is one of the most efficient modes of animal protein production and plays an important role in global food security. Aquaculture animals exhibit extraordinarily diverse sexual phenotypes and underlying mechanisms, providing an ideal system to perform sex determination research, one of the important areas in life science. Moreover, sex is also one of the most valuable traits because sexual dimorphism in growth, size, and other economic characteristics commonly exist in aquaculture animals. Here, we synthesize current knowledge of sex determination mechanisms, sex chromosome evolution, reproduction strategies, and sexual dimorphism, and also review several approaches for sex control in aquaculture animals, including artificial gynogenesis, application of sex-specific or sex chromosome-linked markers, artificial sex reversal, as well as gene editing. We anticipate that better understanding of sex determination mechanisms and innovation of sex control approaches will facilitate sustainable development of aquaculture.
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Affiliation(s)
- Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jie Mei
- College of Fisheries, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chu-Tian Ge
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China
| | - Xiao-Li Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China.
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38
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Takács P, Bánó B, Czeglédi I, Erős T, Ferincz Á, Gál B, Bánó-Kern B, Kovács B, Nagy AA, Nyeste K, Lente V, Preiszner B, Sipos S, Staszny Á, Vitál Z, Weiperth A, Csoma E. The mixed phylogenetic origin of northern pike (Esox lucius Linnaeus 1758) populations in the Middle Danubian drainage. BMC ZOOL 2022; 7:28. [PMID: 37170181 PMCID: PMC10127386 DOI: 10.1186/s40850-022-00129-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pikes, members of genus Esox, are widespread freshwater predators of the northern hemisphere, and important sport fish also. From the Carpathian basin only one species, the northern pike (E. lucius) is noted. At the same time the pike stocks living in this area show high level of phenotypic variance (e.g. various body pattern) and its growth varies highly both among and within populations. These features usually explained by the environmental diversity of the area. Whereas we think that genetic reasons -e.g. the appearance of other/new pike species in the area- may also be responsible for these observed features. Since as no detailed information have been published from the pike populations of this area, so far; we conducted phylogenetic and morphological assay on 88 pike specimens, collected from 49 Middle Danubian sampling sites. RESULTS Our phylogenetic surveys showed that the northern pike appear in the study area solely, but all the three of its major lineages (Northern, Circumpolar, Southern) were indicated. Only six specimens represent the Northern lineage, collected from the western part of the study area. The Circumpolar and Southern lineages were common in the Carpathian basin, but the Southern lineage showed higher levels of haplotype diversity than the Circumpolar clade. Which indicates that only the Southern lineage is native in the area, while the other two groups could have appeared in the Middle Danubian system either spontaneously or by human introduction. Moreover, the different clades appeared in the same populations, suggesting the opportunity of inter-lineage hybridisation. From the studied morphologicalal features, the number of scales on the lateral line and the head length showed significant differences among the lineages. At the same time the body pattern of the studied individuals seems to be rather influenced by the ontogenic changes than phylogeny. CONCLUSIONS The high phenotypic variability of Middle Danubian northern pike populations may be due that all of its three major clades appeared and came in secondary contact in the area. In the within watershed spread of the non-native lineages the human stocking/transfer may play a considerable role.
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Affiliation(s)
- Péter Takács
- Balaton Limnological Research Institute, Klebelsberg Kuno str. 3, Tihany, 8237, Hungary.
| | - Bálint Bánó
- Balaton Limnological Research Institute, Klebelsberg Kuno str. 3, Tihany, 8237, Hungary
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly str. 1, Gödöllő, 2103, Hungary
| | - István Czeglédi
- Balaton Limnological Research Institute, Klebelsberg Kuno str. 3, Tihany, 8237, Hungary
| | - Tibor Erős
- Balaton Limnological Research Institute, Klebelsberg Kuno str. 3, Tihany, 8237, Hungary
| | - Árpád Ferincz
- Department of Freshwater Fish Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly str. 1, Gödöllő, 2103, Hungary
| | - Blanka Gál
- Balaton Limnological Research Institute, Klebelsberg Kuno str. 3, Tihany, 8237, Hungary
| | - Bernadett Bánó-Kern
- Balaton Limnological Research Institute, Klebelsberg Kuno str. 3, Tihany, 8237, Hungary
| | - Balázs Kovács
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly str. 1, Gödöllő, 2103, Hungary
| | - András Attila Nagy
- "MilvusGroup" Birdland Nature Protection Association, Crinului nr 22, 540343, Tîrgu Mureș, Romania
- Evolutionary Ecology Group, Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, University Babeş-Bolyai, Strada Clinicilor 5-7, 400006, Cluj-Napoca-Napoca, Romania
| | - Krisztián Nyeste
- Department of Hydrobiology, Faculty of Science and Technology, University of Debrecen, Egyetem sqr. 1, Debrecen, 4032, Hungary
| | - Vera Lente
- Department of Freshwater Fish Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly str. 1, Gödöllő, 2103, Hungary
| | - Bálint Preiszner
- Balaton Limnological Research Institute, Klebelsberg Kuno str. 3, Tihany, 8237, Hungary
| | - Sándor Sipos
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, 21102, Novi Sad, Serbia
| | - Ádám Staszny
- Department of Freshwater Fish Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly str. 1, Gödöllő, 2103, Hungary
| | - Zoltán Vitál
- Research Center for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agricultural and Life Sciences, Anna-liget u. 35, Szarvas, 5540, Hungary
| | - András Weiperth
- Department of Freshwater Fish Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly str. 1, Gödöllő, 2103, Hungary
| | - Eszter Csoma
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, 4032, Hungary
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Pinto BJ, Keating SE, Nielsen SV, Scantlebury DP, Daza JD, Gamble T. Chromosome-Level Genome Assembly Reveals Dynamic Sex Chromosomes in Neotropical Leaf-Litter Geckos (Sphaerodactylidae: Sphaerodactylus). J Hered 2022; 113:272-287. [PMID: 35363859 PMCID: PMC9270867 DOI: 10.1093/jhered/esac016] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 03/24/2022] [Indexed: 02/07/2023] Open
Abstract
Sex determination is a critical element of successful vertebrate development, suggesting that sex chromosome systems might be evolutionarily stable across lineages. For example, mammals and birds have maintained conserved sex chromosome systems over long evolutionary time periods. Other vertebrates, in contrast, have undergone frequent sex chromosome transitions, which is even more amazing considering we still know comparatively little across large swaths of their respective phylogenies. One reptile group in particular, the gecko lizards (infraorder Gekkota), shows an exceptional lability with regard to sex chromosome transitions and may possess the majority of transitions within squamates (lizards and snakes). However, detailed genomic and cytogenetic information about sex chromosomes is lacking for most gecko species, leaving large gaps in our understanding of the evolutionary processes at play. To address this, we assembled a chromosome-level genome for a gecko (Sphaerodactylidae: Sphaerodactylus) and used this assembly to search for sex chromosomes among six closely related species using a variety of genomic data, including whole-genome re-sequencing, RADseq, and RNAseq. Previous work has identified XY systems in two species of Sphaerodactylus geckos. We expand upon that work to identify between two and four sex chromosome cis-transitions (XY to a new XY) within the genus. Interestingly, we confirmed two different linkage groups as XY sex chromosome systems that were previously unknown to act as sex chromosomes in tetrapods (syntenic with Gallus chromosome 3 and Gallus chromosomes 18/30/33), further highlighting a unique and fascinating trend that most linkage groups have the potential to act as sex chromosomes in squamates.
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Affiliation(s)
- Brendan J Pinto
- Address correspondence to B. J. Pinto at the address above, or e-mail:
| | - Shannon E Keating
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Stuart V Nielsen
- Department of Biological Sciences, Louisiana State University in Shreveport, Shreveport, LA 71115, USA,Division of Herpetology, Florida Museum of Natural History, Gainesville, FL 32611, USA
| | | | - Juan D Daza
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77340, USA
| | - Tony Gamble
- Milwaukee Public Museum, Milwaukee, WI 53233, USA,Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA,Bell Museum of Natural History, University of Minnesota, St Paul, MN 55455, USA
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Mustapha UF, Assan D, Huang YQ, Li GL, Jiang DN. High Polymorphism in the Dmrt2a Gene Is Incompletely Sex-Linked in Spotted Scat, Scatophagus argus. Animals (Basel) 2022; 12:ani12050613. [PMID: 35268179 PMCID: PMC8909180 DOI: 10.3390/ani12050613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/14/2022] [Accepted: 02/25/2022] [Indexed: 12/10/2022] Open
Abstract
Unlike mammals and birds, many fishes have young sex chromosomes, providing excellent models to study sex chromosome differentiation at early stages. Previous studies showed that spotted scat possesses an XX-XY sex determination system. The X has a complete Dmrt3 copy (termed normal) and a truncated copy of Dmrt1 (called Dmrt1b), while the Y has the opposite (normal Dmrt1, which is male-specific, and a truncated Dmrt3 called Dmrt3△-Y). Dmrt1 is the candidate sex determination gene, while the differentiation of other sex-linked genes remains unknown. The spotted scat has proven to be a good model to study the evolution of sex chromosomes in vertebrates. Herein, we sequenced a neighbor gene of this family, Dmrt2, positioned farther from Dmrt1 and closer to Dmrt3 in the spotted scat, and analyzed its sequence variation and expression profiles. The physical locations of the three genes span across an estimated size of >40 kb. The open reading frames of Dmrt2a and its paralog Dmrt2b are 1578 bp and 1311 bp, encoding peptides of 525 and 436 amino acid residues, respectively. Dmrt2a is positioned close to Dmrt3 but farther from Dmrt1 on the same chromosome, while Dmrt2b is not. Sequence analysis revealed several mutations; insertions, and deletions (indels) on Dmrt2a non-coding regions and single-nucleotide polymorphisms (SNPs) on the Dmrt2a transcript. These indels and SNPs are sex-linked and showed high male heterogeneity but do not affect gene translation. The markers designed to span the mutation sites tested on four different populations showed varied concordance with the genetic sexes. Dmrt2a is transcribed solely in the gonads and gills, while Dmrt2b exists in the gonads, hypothalamus, gills, heart, and spleen. The Dmrt2a and Dmrt2b transcripts are profoundly expressed in the male gonads. Analyses of the transcriptome data from five other fish species (Hainan medaka (Oryzias curvinotus), silver sillago (Sillago sihama), Nile tilapia (Oreochromis niloticus), Hong Kong catfish (Clarias fuscus), and spot-fin porcupine fish (Diodon hystrix)) revealed testes-biased expression of Dmrt1 in all, similar to spotted scat. Additionally, the expression of Dmrt2a is higher in the testes than the ovaries in spotted scat and Hainan medaka. The Dmrt2a transcript was not altered in the coding regions as found in Dmrt1 and Dmrt3 in spotted scat. This could be due to the functional importance of Dmrt2a in development. Another possibility is that because Dmrt2a is positioned farther from Dmrt1 and the chromosome is still young, meaning it is only a matter of time before it differentiates. This study undeniably will aid in understanding the functional divergence of the sex-linked genes in fish.
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Ramos L, Antunes A. Decoding sex: Elucidating sex determination and how high-quality genome assemblies are untangling the evolutionary dynamics of sex chromosomes. Genomics 2022; 114:110277. [PMID: 35104609 DOI: 10.1016/j.ygeno.2022.110277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 12/22/2021] [Accepted: 01/26/2022] [Indexed: 11/28/2022]
Abstract
Sexual reproduction is a diverse and widespread process. In gonochoristic species, the differentiation of sexes occurs through diverse mechanisms, influenced by environmental and genetic factors. In most vertebrates, a master-switch gene is responsible for triggering a sex determination network. However, only a few genes have acquired master-switch functions, and this process is associated with the evolution of sex-chromosomes, which have a significant influence in evolution. Additionally, their highly repetitive regions impose challenges for high-quality sequencing, even using high-throughput, state-of-the-art techniques. Here, we review the mechanisms involved in sex determination and their role in the evolution of species, particularly vertebrates, focusing on sex chromosomes and the challenges involved in sequencing these genomic elements. We also address the improvements provided by the growth of sequencing projects, by generating a massive number of near-gapless, telomere-to-telomere, chromosome-level, phased assemblies, increasing the number and quality of sex-chromosome sequences available for further studies.
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Affiliation(s)
- Luana Ramos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
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Wang L, Sun F, Wan ZY, Yang Z, Tay YX, Lee M, Ye B, Wen Y, Meng Z, Fan B, Alfiko Y, Shen Y, Piferrer F, Meyer A, Schartl M, Yue GH. Transposon-induced epigenetic silencing in the X chromosome as a novel form of dmrt1 expression regulation during sex determination in the fighting fish. BMC Biol 2022; 20:5. [PMID: 34996452 PMCID: PMC8742447 DOI: 10.1186/s12915-021-01205-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 12/03/2021] [Indexed: 01/14/2023] Open
Abstract
Background Fishes are the one of the most diverse groups of animals with respect to their modes of sex determination, providing unique models for uncovering the evolutionary and molecular mechanisms underlying sex determination and reversal. Here, we have investigated how sex is determined in a species of both commercial and ecological importance, the Siamese fighting fish Betta splendens. Results We conducted association mapping on four commercial and two wild populations of B. splendens. In three of the four commercial populations, the master sex determining (MSD) locus was found to be located in a region of ~ 80 kb on LG2 which harbours five protein coding genes, including dmrt1, a gene involved in male sex determination in different animal taxa. In these fish, dmrt1 shows a male-biased gonadal expression from undifferentiated stages to adult organs and the knockout of this gene resulted in ovarian development in XY genotypes. Genome sequencing of XX and YY genotypes identified a transposon, drbx1, inserted into the fourth intron of the X-linked dmrt1 allele. Methylation assays revealed that epigenetic changes induced by drbx1 spread out to the promoter region of dmrt1. In addition, drbx1 being inserted between two closely linked cis-regulatory elements reduced their enhancer activities. Thus, epigenetic changes, induced by drbx1, contribute to the reduced expression of the X-linked dmrt1 allele, leading to female development. This represents a previously undescribed solution in animals relying on dmrt1 function for sex determination. Differentiation between the X and Y chromosomes is limited to a small region of ~ 200 kb surrounding the MSD gene. Recombination suppression spread slightly out of the SD locus. However, this mechanism was not found in the fourth commercial stock we studied, or in the two wild populations analysed, suggesting that it originated recently during domestication. Conclusions Taken together, our data provide novel insights into the role of epigenetic regulation of dmrt1 in sex determination and turnover of SD systems and suggest that fighting fish are a suitable model to study the initial stages of sex chromosome evolution. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01205-y.
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Affiliation(s)
- Le Wang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - Fei Sun
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - Zi Yi Wan
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - Zituo Yang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - Yi Xuan Tay
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - May Lee
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - Baoqing Ye
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - Yanfei Wen
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | - Zining Meng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Bin Fan
- Department of Food and Environmental Engineering, Yangjiang Polytechnic, Yangjiang, 529500, China
| | - Yuzer Alfiko
- Biotech Lab, Wilmar International, Jakarta, Indonesia
| | - Yubang Shen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, China
| | - Francesc Piferrer
- Institute of Marine Sciences (ICM), Spanish National Research Council (CSIC), 08003, Barcelona, Spain.
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Wuerzburg, 97074, Wuerzburg, Germany. .,The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, 78666, USA.
| | - Gen Hua Yue
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, 117604, Singapore. .,Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore. .,School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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Liu X, Dai S, Wu J, Wei X, Zhou X, Chen M, Tan D, Pu D, Li M, Wang D. Roles of anti-Müllerian hormone and its duplicates in sex determination and germ cell proliferation of Nile tilapia. Genetics 2021; 220:6486528. [PMID: 35100374 PMCID: PMC9208641 DOI: 10.1093/genetics/iyab237] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/17/2021] [Indexed: 12/30/2022] Open
Abstract
Duplicates of amh are crucial for fish sex determination and differentiation. In Nile tilapia, unlike in other teleosts, amh is located on X chromosome. The Y chromosome amh (amhΔ-y) is mutated with 5 bp insertion and 233 bp deletion in the coding sequence, and tandem duplicate of amh on Y chromosome (amhy) has been identified as the sex determiner. However, the expression of amh, amhΔ-y, and amhy, their roles in germ cell proliferation and the molecular mechanism of how amhy determines sex is still unclear. In this study, expression and functions of each duplicate were analyzed. Sex reversal occurred only when amhy was mutated as revealed by single, double, and triple mutation of the 3 duplicates in XY fish. Homozygous mutation of amhy in YY fish also resulted in sex reversal. Earlier and higher expression of amhy/Amhy was observed in XY gonads compared with amh/Amh during sex determination. Amhy could inhibit the transcription of cyp19a1a through Amhr2/Smads signaling. Loss of cyp19a1a rescued the sex reversal phenotype in XY fish with amhy mutation. Interestingly, mutation of both amh and amhy in XY fish or homozygous mutation of amhy in YY fish resulted in infertile females with significantly increased germ cell proliferation. Taken together, these results indicated that up-regulation of amhy during the critical period of sex determination makes it the sex-determining gene, and it functions through repressing cyp19a1a expression via Amhr2/Smads signaling pathway. Amh retained its function in controlling germ cell proliferation as reported in other teleosts, while amhΔ-y was nonfunctionalized.
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Affiliation(s)
- Xingyong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Shengfei Dai
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jiahong Wu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xueyan Wei
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xin Zhou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Mimi Chen
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Dejie Tan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Deyong Pu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Minghui Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China,Corresponding author: Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China. ; Corresponding author: Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China,Corresponding author: Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China. ; Corresponding author: Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
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Nakamura Y, Higuchi K, Kumon K, Yasuike M, Takashi T, Gen K, Fujiwara A. Prediction of the Sex-Associated Genomic Region in Tunas ( Thunnus Fishes). Int J Genomics 2021; 2021:7226353. [PMID: 34957293 PMCID: PMC8693018 DOI: 10.1155/2021/7226353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/28/2021] [Accepted: 11/13/2021] [Indexed: 11/17/2022] Open
Abstract
Fish species have a variety of sex determination systems. Tunas (genus Thunnus) have an XY genetic sex determination system. However, the Y chromosome or responsible locus has not yet been identified in males. In a previous study, a female genome of Pacific bluefin tuna (T. orientalis) was sequenced, and candidates for sex-associated DNA polymorphisms were identified by a genome-wide association study using resequencing data. In the present study, we sequenced a male genome of Pacific bluefin tuna by long-read and linked-read sequencing technologies and explored male-specific loci through a comparison with the female genome. As a result, we found a unique region carrying the male-specific haplotype, where a homolog of estrogen sulfotransferase gene was predicted to be encoded. The genome-wide mapping of previously resequenced data indicated that, among the functionally annotated genes, only this gene, named sult1st6y, was paternally inherited in the males of Pacific bluefin tuna. We reviewed the RNA-seq data of southern bluefin tuna (T. maccoyii) in the public database and found that sult1st6y of southern bluefin tuna was expressed in all male testes, but absent or suppressed in the female ovary. Since estrogen sulfotransferase is responsible for the inactivation of estrogens, it is reasonable to assume that the expression of sult1st6y in gonad cells may inhibit female development, thereby inducing the individuals to become males. Thus, our results raise a promising hypothesis that sult1st6y is the sex determination gene in Thunnus fishes or at least functions at a crucial point in the sex-differentiation cascade.
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Affiliation(s)
- Yoji Nakamura
- Bioinformatics and Biosciences Division, Fisheries Stock Assessment Center, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Kentaro Higuchi
- Tuna Aquaculture Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 1551-8 Taira-machi, Nagasaki 851-2213, Japan
| | - Kazunori Kumon
- Amami Field Station, Tuna Aquaculture Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 955-5 Hyousakiyamahara, Setouchi, Kagoshima 894-2414, Japan
| | - Motoshige Yasuike
- Bioinformatics and Biosciences Division, Fisheries Stock Assessment Center, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Toshinori Takashi
- Tuna Aquaculture Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 1551-8 Taira-machi, Nagasaki 851-2213, Japan
| | - Koichiro Gen
- Tuna Aquaculture Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 1551-8 Taira-machi, Nagasaki 851-2213, Japan
| | - Atushi Fujiwara
- Aquatic Breeding Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhamaura, Minami-ise, Mie 516-0193, Japan
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Tao W, Cao J, Xiao H, Zhu X, Dong J, Kocher TD, Lu M, Wang D. A Chromosome-Level Genome Assembly of Mozambique Tilapia ( Oreochromis mossambicus) Reveals the Structure of Sex Determining Regions. Front Genet 2021; 12:796211. [PMID: 34956335 PMCID: PMC8692795 DOI: 10.3389/fgene.2021.796211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
The Mozambique tilapia (Oreochromis mossambicus) is a fascinating taxon for evolutionary and ecological research. It is an important food fish and one of the most widely distributed tilapias. Because males grow faster than females, genetically male tilapia are preferred in aquaculture. However, studies of sex determination and sex control in O. mossambicus have been hindered by the limited characterization of the genome. To address this gap, we assembled a high-quality genome of O. mossambicus, using a combination of high coverage of Illumina and Nanopore reads, coupled with Hi-C and RNA-Seq data. Our genome assembly spans 1,007 Mb with a scaffold N50 of 11.38 Mb. We successfully anchored and oriented 98.6% of the genome on 22 linkage groups (LGs). Based on re-sequencing data for male and female fishes from three families, O. mossambicus segregates both an XY system on LG14 and a ZW system on LG3. The sex-patterned SNPs shared by two XY families narrowed the sex determining regions to ∼3 Mb on LG14. The shared sex-patterned SNPs included two deleterious missense mutations in ahnak and rhbdd1, indicating the possible roles of these two genes in sex determination. This annotated chromosome-level genome assembly and identification of sex determining regions represents a valuable resource to help understand the evolution of genetic sex determination in tilapias.
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Affiliation(s)
- Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Jianmeng Cao
- Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Science, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Guangzhou, China
| | - Hesheng Xiao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Xi Zhu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Junjian Dong
- Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Science, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Guangzhou, China
| | - Thomas D. Kocher
- Department of Biology, University of Maryland, College Park, Rockville, MD, United States
| | - Maixin Lu
- Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Science, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Guangzhou, China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
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Holborn MK, Einfeldt AL, Kess T, Duffy SJ, Messmer AM, Langille BL, Gauthier J, Bentzen P, Knutsen TM, Kent M, Boyce D, Bradbury IR. Reference genome of Lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway. Mol Ecol Resour 2021; 22:1427-1439. [PMID: 34859595 DOI: 10.1111/1755-0998.13565] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 11/15/2021] [Accepted: 11/23/2021] [Indexed: 11/30/2022]
Abstract
Teleosts exhibit extensive diversity of sex determination (SD) systems and mechanisms, providing the opportunity to study the evolution of sex determination and sex chromosomes. Here we sequenced the genome of the Common Lumpfish (Cyclopterus lumpus Linnaeus), a species of increasing importance to aquaculture, and identified the SD region and master SD locus using a 70K SNP array and tissue-specific expression data. The chromosome-level assembly identified 25 diploid chromosomes with a total size of 572.89 Mb, a scaffold N50 of 23.86 Mb, and genome annotation predicted 21,480 protein-coding genes. Genome wide association analysis located a highly sex-associated region on chromosome 13, suggesting that anti-Müllerian hormone (AMH) is the putative SD factor. Linkage disequilibrium and heterozygosity across chromosome 13 support a proto-XX/XY system, with an absence of widespread chromosome divergence between sexes. We identified three copies of AMH in the Lumpfish primary and alternate haplotype assemblies localized in the SD region. Comparison to sequences from other teleosts suggested a monophyletic relationship and conservation within the Cottioidei. One AMH copy showed similarity to AMH/AMHY in a related species and was also the only copy with expression in testis tissue, suggesting this copy may be the functional copy of AMH in Lumpfish. The two other copies arranged in tandem inverted duplication were highly similar, suggesting a recent duplication event. This study provides a resource for the study of early sex chromosome evolution and novel genomic resources that benefits Lumpfish conservation management and aquaculture.
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Affiliation(s)
- Melissa K Holborn
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, NL, A1C 5X1, Canada
| | - Anthony L Einfeldt
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Tony Kess
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, NL, A1C 5X1, Canada
| | - Steve J Duffy
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, NL, A1C 5X1, Canada
| | - Amber M Messmer
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, NL, A1C 5X1, Canada
| | - Barbara L Langille
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, NL, A1C 5X1, Canada
| | - Johanne Gauthier
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, Mont-Joli, QC, G5H 3Z4, Canada
| | - Paul Bentzen
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | | | - Matthew Kent
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Danny Boyce
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Ian R Bradbury
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, NL, A1C 5X1, Canada
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Fan B, Xie D, Li Y, Wang X, Qi X, Li S, Meng Z, Chen X, Peng J, Yang Y, Li Y, Wang L. A single intronic single nucleotide polymorphism in splicing site of steroidogenic enzyme hsd17b1 is associated with phenotypic sex in oyster pompano, Trachinotus anak. Proc Biol Sci 2021; 288:20212245. [PMID: 34784765 DOI: 10.1098/rspb.2021.2245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Teleosts show varied master sex determining (MSD) genes and sex determination (SD) mechanisms, with frequent turnovers of sex chromosomes. Tracing the origins of MSD genes and turnovers of sex chromosomes in a taxonomic group is of particular interest in evolutionary biology. Oyster pompano (Trachinotus anak), a marine fish, belongs to the family Carangidae, in which 17b-hydroxysteroid dehydrogenase 1 (hsd17b1) has repeatedly evolved to an MSD gene. Whole-genome resequencing identified a single nucleotide polymorphism (SNP) at chromosome 24 to be strictly associated with phenotypic sex, with females being the heterozygous sex. This SNP is located in a splicing site at the first exon/intron boundary of hsd17b1. The Z-linked SNP results in malfunction of all spliced isoforms, whereas the W-linked isoforms were predicted to have open reading frames that are conserved among vertebrates, suggesting that hsd17b1 is a female-determining gene. The differential alternative splicing patterns of ZZ and ZW genotypes were consistently observed both in undifferentiated stages and differentiated gonads. We observed elevated recombination around the SD locus and no differentiation between Z and W chromosomes. The extreme diversity of mutational mechanisms that hsd17b1 evolves to an MSD gene highlights frequent in situ turnovers between sex chromosomes in the Carangidae.
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Affiliation(s)
- Bin Fan
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, People's Republic of China.,Yangjiang Haina Fisheries Co., Ltd., Yangjiang 529500, People's Republic of China.,Yangjiang Polytechnic, Yangjiang 529500, People's Republic of China
| | - Dizhi Xie
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Yanwei Li
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Xulei Wang
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao 266003, People's Republic of China
| | - Xin Qi
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao 266003, People's Republic of China
| | - Shuisheng Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Xinghan Chen
- Yangjiang Polytechnic, Yangjiang 529500, People's Republic of China
| | - Junyao Peng
- Yangjiang Hongyun Marine Fish Seed Breeding Co., Ltd., Yangjiang 529500, People's Republic of China
| | - Yongjian Yang
- Yangjiang Haina Fisheries Co., Ltd., Yangjiang 529500, People's Republic of China
| | - Yuanyou Li
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Le Wang
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore
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Sex Chromosomes and Master Sex-Determining Genes in Turtles and Other Reptiles. Genes (Basel) 2021; 12:genes12111822. [PMID: 34828428 PMCID: PMC8622242 DOI: 10.3390/genes12111822] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022] Open
Abstract
Among tetrapods, the well differentiated heteromorphic sex chromosomes of birds and mammals have been highly investigated and their master sex-determining (MSD) gene, Dmrt1 and SRY, respectively, have been identified. The homomorphic sex chromosomes of reptiles have been the least studied, but the gap with birds and mammals has begun to fill. This review describes our current knowledge of reptilian sex chromosomes at the cytogenetic and molecular level. Most of it arose recently from various studies comparing male to female gene content. This includes restriction site-associated DNA sequencing (RAD-Seq) experiments in several male and female samples, RNA sequencing and identification of Z- or X-linked genes by male/female comparative transcriptome coverage, and male/female transcriptomic or transcriptome/genome substraction approaches allowing the identification of Y- or W-linked transcripts. A few putative master sex-determining (MSD) genes have been proposed, but none has been demonstrated yet. Lastly, future directions in the field of reptilian sex chromosomes and their MSD gene studies are considered.
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Ferchaud AL, Mérot C, Normandeau E, Ragoussis J, Babin C, Djambazian H, Bérubé P, Audet C, Treble M, Walkusz W, Bernatchez L. Chromosome-level assembly reveals a putative Y-autosomal fusion in the sex determination system of the Greenland Halibut (Reinhardtius hippoglossoides). G3-GENES GENOMES GENETICS 2021; 12:6428537. [PMID: 34791178 DOI: 10.1093/g3journal/jkab376] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022]
Abstract
Despite the commercial importance of Greenland Halibut (Reinhardtius hippoglossoides), important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. Here, we combined single-molecule sequencing of long reads (Pacific Sciences) with chromatin conformation capture sequencing (Hi-C) data to assemble the first chromosome-level reference genome for this species. The high-quality assembly encompassed more than 598 Megabases (Mb) assigned to 1 594 scaffolds (scaffold N50 = 25 Mb) with 96% of its total length distributed among 24 chromosomes. Investigation of the syntenic relationship with other economically important flatfish species revealed a high conservation of synteny blocks among members of this phylogenetic clade. Sex determination analysis revealed that, similar to other teleost fishes, flatfishes also exhibit a high level of plasticity and turnover in sex-determination mechanisms. A low-coverage whole-genome sequence analysis of 198 individuals revealed that Greenland Halibut possesses a male heterogametic XY system and several putative candidate genes implied in the sex determination of this species. Our study also suggests for the first time in flatfishes that a putative Y-autosomal fusion could be associated with a reduction of recombination typical of the early steps of sex chromosome evolution.
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Affiliation(s)
- Anne-Laure Ferchaud
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Claire Mérot
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Charles Babin
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Haig Djambazian
- McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Pierre Bérubé
- McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Céline Audet
- Institut des sciences de la mer de Rimouski, Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, QC G5L 3A1, Canada
| | - Margaret Treble
- Fisheries and Oceans Canada, Winnipeg Department, Arctic Aquatic Research Division, Freshwater Institute Winnipeg, Manitoba, R3T2N6, Canada
| | - Wocjciech Walkusz
- Fisheries and Oceans Canada, Winnipeg Department, Arctic Aquatic Research Division, Freshwater Institute Winnipeg, Manitoba, R3T2N6, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
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A supernumerary "B-sex" chromosome drives male sex determination in the Pachón cavefish, Astyanax mexicanus. Curr Biol 2021; 31:4800-4809.e9. [PMID: 34496222 DOI: 10.1016/j.cub.2021.08.030] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/30/2021] [Accepted: 08/09/2021] [Indexed: 01/30/2023]
Abstract
Sex chromosomes are generally derived from a pair of classical type-A chromosomes, and relatively few alternative models have been proposed up to now.1,2 B chromosomes (Bs) are supernumerary and dispensable chromosomes with non-Mendelian inheritance found in many plant and animal species3,4 that have often been considered as selfish genetic elements that behave as genome parasites.5,6 The observation that in some species Bs can be either restricted or predominant in one sex7-14 raised the interesting hypothesis that Bs could play a role in sex determination.15 The characterization of putative B master sex-determining (MSD) genes, however, has not yet been provided to support this hypothesis. Here, in Astyanax mexicanus cavefish originating from Pachón cave, we show that Bs are strongly male predominant. Based on a high-quality genome assembly of a B-carrying male, we characterized the Pachón cavefish B sequence and found that it contains two duplicated loci of the putative MSD gene growth differentiation factor 6b (gdf6b). Supporting its role as an MSD gene, we found that the Pachón cavefish gdf6b gene is expressed specifically in differentiating male gonads, and that its knockout induces male-to-female sex reversal in B-carrying males. This demonstrates that gdf6b is necessary for triggering male sex determination in Pachón cavefish. Altogether these results bring multiple and independent lines of evidence supporting the conclusion that the Pachón cavefish B is a "B-sex" chromosome that contains duplicated copies of the gdf6b gene, which can promote male sex determination in this species.
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