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Xu XD, Zhou Y, Wang CQ, Huang X, Zhang K, Xu XW, He LW, Zhang XY, Fu XZ, Ma M, Qin QB, Liu SJ. Identification and effective regulation of scarb1 gene involved in pigmentation change in autotetraploid Carassius auratus. Zool Res 2024; 45:381-397. [PMID: 38485507 PMCID: PMC11017083 DOI: 10.24272/j.issn.2095-8137.2023.293] [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: 11/24/2023] [Accepted: 12/25/2023] [Indexed: 03/19/2024] Open
Abstract
The autotetraploid Carassius auratus (4nRR, 4 n=200, RRRR) is derived from whole-genome duplication of Carassius auratus red var. (RCC, 2 n=100, RR). In the current study, we demonstrated that chromatophores and pigment changes directly caused the coloration and variation of 4nRR skin (red in RCC, brownish-yellow in 4nRR). To further explore the molecular mechanisms underlying coloration formation and variation in 4nRR, we performed transcriptome profiling and molecular functional verification in RCC and 4nRR. Results revealed that scarb1, associated with carotenoid metabolism, underwent significant down-regulation in 4nRR. Efficient editing of this candidate pigment gene provided clear evidence of its significant role in RCC coloration. Subsequently, we identified four divergent scarb1 homeologs in 4nRR: two original scarb1 homeologs from RCC and two duplicated ones. Notably, three of these homeologs possessed two highly conserved alleles, exhibiting biased and allele-specific expression in the skin. Remarkably, after precise editing of both the original and duplicated scarb1 homeologs and/or alleles, 4nRR individuals, whether singly or multiply mutated, displayed a transition from brownish-yellow skin to a cyan-gray phenotype. Concurrently, the proportional areas of the cyan-gray regions displayed a gene-dose correlation. These findings illustrate the subfunctionalization of duplicated scarb1, with all scarb1 genes synergistically and equally contributing to the pigmentation of 4nRR. This is the first report concerning the functional differentiation of duplicated homeologs in an autopolyploid fish, substantially enriching our understanding of coloration formation and change within this group of organisms.
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Affiliation(s)
- Xi-Dan Xu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
- College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
| | - Yue Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Chong-Qing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Xu Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Kun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Xiao-Wei Xu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Li-Wen He
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Xin-Yue Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Xin-Zhu Fu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Ming Ma
- College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
| | - Qin-Bo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, Guangdong 511458, China
- Hunan Yuelu Mountain Science and Technology Co. Ltd. for Aquatic Breeding, Changsha, Hunan 410081, China. E-mail:
| | - Shao-Jun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China. E-mail:
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Zhang E, Li Z, Lv T, Fu J, Dong L, Feng Y, Sun G, Xu X, Cui C, Wang W, Yang J. Transcriptome profiling explores the immune defence mechanism of triploid Pacific oyster (Crassostrea gigas) blood against Vibrio alginolyticus based on protein interaction networks. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 143:104677. [PMID: 36870582 DOI: 10.1016/j.dci.2023.104677] [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: 12/20/2022] [Revised: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Triploid oysters have provided the oyster industry with many benefits, such as fast growth rates, meat quality improvement, and increased oyster production and economic benefits, since the first report on triploid oysters was published. The development of polyploid technology has remarkably increased the output of triploid oysters to meet the increasing demand of consumers for Crassostrea gigas in the past decades. At present, research on triploid oyster has mainly focused on breeding and growth, but studies on the immunity of triploid oysters are limited. According to recent reports, Vibrio alginolyticus is a highly virulent strain that can cause disease and death in shellfish, shrimp, as well as serious economic losses. V. alginolyticus may be a reason why oysters die during summer. Therefore, using V. alginolyticus to explore the resistance and immune defense mechanisms of triploid oysters against pathogens presents practical significance. Transcriptome analysis of gene expression was performed in triploid C. gigas at 12 and 48 h after infection with V. alginolyticus, and the respective 2257 and 191 differentially expressed genes (DEGs) were identified. The results of GO and KEGG enrichment analyses showed that multiple significantly enriched GO terms and KEGG signaling pathways are associated with immunity. A protein-protein interaction network was constructed to investigate the interaction relationship of immune-related genes. Finally, we verified the expression situation of 16 key genes using quantitative RT-PCR. This study is the first to use the PPI network in exploring the immune defense mechanism of triploid C. gigas blood to fill the gap in the immune mechanism of triploid oysters and other mollusks, and provide valuable reference for future triploid farming and pathogen prevention and control.
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Affiliation(s)
- Enshuo Zhang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Zan Li
- School of Agriculture, Ludong University, Yantai, 264025, China.
| | - Tingjin Lv
- Yantai Institute of Marine Economy, Yantai, 264003, China
| | - Jingjing Fu
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Luyao Dong
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Yanwei Feng
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Guohua Sun
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiaohui Xu
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Cuiju Cui
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Weijun Wang
- School of Agriculture, Ludong University, Yantai, 264025, China.
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai, 264025, China
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Wang L, Dong X, Wu Y, Zhou Q, Xu R, Ren L, Zhang C, Tao M, Luo K, Zeng Y, Liu S. Proteomics-based molecular and functional characteristic profiling of muscle tissue in Triploid crucian carp. Mol Omics 2022; 18:967-976. [PMID: 36349986 DOI: 10.1039/d2mo00215a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Triploid crucian carp (TCC) is a kind of artificially bred fish with huge economic value to China. It has several excellent characteristics, such as fast growth, strong disease resistance and delicious taste. However, as a regionally specific fish, the underlying molecular mechanisms of these characteristics are largely unknown. In this study, we performed quantitative proteomics on the muscle tissues of TCC and its parents, allotetraploid (♂), red crucian carp (♀) and common carp. Combined with multiple bioinformatic analysis, we found that the taste of TCC can be mainly attributed to umami amino acid-enriched proteins such as PURBA, PVALBI and ATP5F1B, and that its rapid growth can be mainly ascribed to the high expression and regulation of metabolism-related proteins such as NDUFS1, ENO1A and CS. These play significant roles in substrate and energy metabolism, as well as in bias transformation. Subsequently, we identified several proteins, including MDH1AA, GOT1 and DLAT, that may serve as potential regulators of innate immunity by regulating the biosynthesis and transformation of significant antibiotics and antimicrobial peptides. In conclusion, this study can serve as a significant reference for similar investigations and shed light on the molecular and biological functions of individual proteins in TCC muscle tissue.
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Affiliation(s)
- Lingxiang Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China. .,National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Xiaoping Dong
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China. .,National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Yun Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China. .,National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Qian Zhou
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Rongfang Xu
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China.
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China.
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China.
| | - Kaikun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China.
| | - Yong Zeng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China. .,National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China.
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McElroy KE, Bankers L, Soper D, Hehman G, Boore JL, Logsdon JM, Neiman M. Patterns of gene expression in ovaries of sexual vs. asexual lineages of a freshwater snail. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.845640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Why sexual reproduction is so common when asexual reproduction should be much more efficient and less costly remains an open question in evolutionary biology. Comparisons between otherwise similar sexual and asexual taxa allow us to characterize the genetic architecture underlying asexuality, which can, in turn, illuminate how this reproductive mode transition occurred and the mechanisms by which it is maintained or disrupted. Here, we used transcriptome sequencing to compare patterns of ovarian gene expression between actively reproducing obligately sexual and obligately asexual females from multiple lineages of Potamopyrgus antipodarum, a freshwater New Zealand snail characterized by frequent separate transitions to asexuality and coexistence of otherwise similar sexual and asexual lineages. We also used these sequence data to evaluate whether population history accounts for variation in patterns of gene expression. We found that source population was a major source of gene expression variation, and likely more influential than reproductive mode. This outcome for these common garden-raised snails is strikingly similar to earlier results from field-collected snails. While we did not identify a likely set of candidate genes from expression profiles that could plausibly explain how transitions to asexuality occurred, we identified around 1,000 genes with evidence of differential expression between sexual and asexual reproductive modes, and 21 genes that appear to exhibit consistent expression differences between sexuals and asexuals across genetic backgrounds. This second smaller set of genes provides a good starting point for further exploration regarding a potential role in the transition to asexual reproduction. These results mark the first effort to characterize the causes of asexuality in P. antipodarum, demonstrate the apparently high heritability of gene expression patterns in this species, and hint that for P. antipodarum, transitions to asexuality might not necessarily be strongly associated with broad changes in gene expression.
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5
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Ren L, Zhang H, Luo M, Gao X, Cui J, Zhang X, Liu S. Heterosis of growth trait regulated by DNA methylation and miRNA in allotriploid fish. Epigenetics Chromatin 2022; 15:19. [PMID: 35597966 PMCID: PMC9123727 DOI: 10.1186/s13072-022-00455-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/04/2022] [Indexed: 11/26/2022] Open
Abstract
Background Heterosis of growth traits in allotriploid fish has benefited the production of aquaculture for many years, yet its genetic and molecular basis has remained obscure. Now, an allotriploid complex, including two triploids and their diploid inbred parents, has provided an excellent model for investigating the potential regulatory mechanisms of heterosis. Results Here, we performed a series of analyses on DNA methylation modification and miRNA expression in combination with gene expression in the allotriploid complex. We first established a model of cis- and trans-regulation related to DNA methylation and miRNA in allotriploids. Then, comparative analyses showed that DNA methylation contributed to the emergence of a dosage compensation effect, which reduced gene expression levels in the triploid to the diploid state. We detected 31 genes regulated by DNA methylation in the subgenomes of the allotriploids. Finally, the patterns of coevolution between small RNAs and their homoeologous targets were classified and used to predict the regulation of miRNA expression in the allotriploids. Conclusions Our results uncovered the regulatory network between DNA methylation and miRNAs in allotriploids, which not only helps us understand the regulatory mechanisms of heterosis of growth traits but also benefits the study and application of epigenetics in aquaculture. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00455-6.
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Affiliation(s)
- Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Hong Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Mengxue Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Xin Gao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Jialin Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Xueyin Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China. .,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
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Xu D, Yoshino T, de Bello Cioffi M, Yoshikawa H, Ino Y, Yazawa R, Dos Santos Nassif Lacerda SM, Takeuchi Y. Production of donor-derived eggs after ovarian germ cell transplantation into the gonads of adult, germ cell-less, triploid hybrid fish†. Biol Reprod 2020; 103:1289-1299. [PMID: 32940693 DOI: 10.1093/biolre/ioaa168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 08/05/2020] [Accepted: 09/15/2020] [Indexed: 12/13/2022] Open
Abstract
In animals, spermatogonial transplantation in sterile adult males is widely developed; however, despite its utility, ovarian germ cell transplantation is not well developed. We previously showed that the interspecific hybrid offspring of sciaenid was a suitable model for germ cell transplantation studies as they have germ cell-less gonads. However, all these gonads have testis-like characteristics. Here, we tested whether triploidization in hybrid embryos could result in germ cell-less ovary development. Gonadal structure dimorphism and sex-specific gene expression patterns were examined in 6-month-old triploid hybrids (3nHybs). Thirty-one percent of 3nHybs had germ cell-less gonads with an ovarian cavity. cyp19a1a and foxl2, ovarian differentiation-related genes, were expressed in these gonads, whereas dmrt1 and vasa were not expressed, suggesting ovary-like germ cell-less gonad development. Some (26%) 3nHybs had testis-like germ cell-less gonads. Ovarian germ cells collected from homozygous green fluorescent protein (GFP) transgenic blue drum (BD) (Nibea mitsukurii) were transplanted into 6-month-old 3nHybs gonads via the urogenital papilla or oviduct. After 9 months, the recipients were crossed with wild type BD. Among the six 3nHyb recipients that survived, one female and one male produced fertile eggs and motile sperm carrying gfp-specific DNA sequences. Progeny tests revealed that all F1 offspring possessed gfp-specific DNA sequences, suggesting that these recipients produced only donor-derived eggs or sperm. Histological observation confirmed donor-derived gametogenesis in the 3nHyb recipients' gonads. Overall, triploidization reduces male-biased sex differentiation in germ cell-less gonads. We report, for the first time, donor-derived egg production in an animal via direct ovarian germ cell transplantation into a germ cell-less ovary.
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Affiliation(s)
- Dongdong Xu
- Marine Fisheries Institute of Zhejiang Province, Zhoushan, P.R. China.,Department of Aquatic Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Tasuku Yoshino
- Department of Aquatic Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | | | | | - Yasuko Ino
- National Fisheries University, Shimonoseki, Japan
| | - Ryosuke Yazawa
- Department of Aquatic Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | | | - Yutaka Takeuchi
- Noto Center for Fisheries Science and Technology, Faculty of Biological Science and Technology, Kanazawa University, Ishikawa, Japan
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Fujita MK, Singhal S, Brunes TO, Maldonado JA. Evolutionary Dynamics and Consequences of Parthenogenesis in Vertebrates. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-114900] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Parthenogenesis is asexual reproduction without any required participation from males and, as such, is a null model for sexual reproduction. In a comparative context, we can expand our understanding of the evolution and ecology of sex by investigating the consequences of parthenogenesis. In this review, we examine the theoretical predictions of and empirical results on the evolution of asexual reproduction in vertebrates, focusing on recent studies addressing the origins and geographic spread of parthenogenetic lineages and the genomic consequences of an asexual life history. With advances in computational methods and genome technologies, researchers are poised to make rapid and significant progress in studying the origin and evolution of parthenogenesis in vertebrates, thus providing an important perspective on understanding biodiversity patterns of both asexual and sexual populations.
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Affiliation(s)
- Matthew K. Fujita
- Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, California 90747, USA
| | - Tuliana O. Brunes
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Jose A. Maldonado
- Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
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Transcriptome sequencing and histology reveal dosage compensation in the liver of triploid pre-smolt Atlantic salmon. Sci Rep 2020; 10:16836. [PMID: 33033342 PMCID: PMC7544907 DOI: 10.1038/s41598-020-73814-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/03/2020] [Indexed: 02/04/2023] Open
Abstract
Triploid Atlantic salmon (Salmo salar L.) is seen as one of the best solutions to solve key issues in the salmon farming industry, such as the impact of escapees on wild stocks and pre-harvest sexual maturation. However, the effects of triploidy on salmon smoltification are poorly understood at the molecular level, even though smoltification is a very sensitive period that has a major influence on survival rate and performance of farmed salmon. In this study, we have compared the liver transcriptomes of diploid and triploid Atlantic salmon at three ontogeny stages: fry, parr and smolt. In diploid fish, a total of 2,655 genes were differentially expressed between fry and parr, whereas 506 genes had significantly different transcript levels between parr and smolts. In triploids, 1,507 and 974 genes were differentially expressed between fry and parr, and between parr and smolts, respectively. Most of these genes were down-regulated and 34 genes were differentially expressed between ploidies at the same stage. In both ploidy groups, the top differentially expressed genes with ontogeny stage belonged to common functional categories that can be related to smoltification. Nucleotide and energy metabolism were significantly down-regulated in fry when compared to parr, while immune system processes were significantly down-regulated in parr when compared to smolts. The close resemblance of enriched biological processes and pathways between ploidy groups suggests that triploidy is regulated by genome dosage compensation in Atlantic salmon. Histological analysis revealed that areas of vacuolization (steatosis) were present only in fry and parr stages, in contrast to a compact cellular histology with glycogen granules after smoltification. There was no significant difference in vacuolization between ploidy groups at the fry stage but the liver of diploid parr had a 33.5% higher vacuolization area compared to their triploid counterparts. Taken together, our data provide novel insights into the changes that occur at the molecular and histological level in the liver of both diploid and triploid Atlantic salmon prior to and during smoltification.
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Bartoš O, Röslein J, Kotusz J, Paces J, Pekárik L, Petrtýl M, Halačka K, Štefková Kašparová E, Mendel J, Boroń A, Juchno D, Leska A, Jablonska O, Benes V, Šídová M, Janko K. The Legacy of Sexual Ancestors in Phenotypic Variability, Gene Expression, and Homoeolog Regulation of Asexual Hybrids and Polyploids. Mol Biol Evol 2020; 36:1902-1920. [PMID: 31077330 PMCID: PMC6735777 DOI: 10.1093/molbev/msz114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hybridization and polyploidization are important evolutionary processes whose impacts range from the alteration of gene expression and phenotypic variation to the triggering of asexual reproduction. We investigated fishes of the Cobitis taenia-elongatoides hybrid complex, which allowed us to disentangle the direct effects of both processes, due to the co-occurrence of parental species with their diploid and triploid hybrids. Employing morphological, ecological, and RNAseq approaches, we investigated the molecular determinants of hybrid and polyploid forms. In contrast with other studies, hybridization and polyploidy induced relatively very little transgressivity. Instead, Cobitis hybrids appeared intermediate with a clear effect of genomic dosing when triploids expressed higher similarity to the parent contributing two genome sets. This dosage effect was symmetric in the germline (oocyte gene expression), interestingly though, we observed an overall bias toward C. taenia in somatic tissues and traits. At the level of individual genes, expression-level dominance vastly prevailed over additivity or transgressivity. Also, trans-regulation of gene expression was less efficient in diploid hybrids than in triploids, where the expression modulation of homoeologs derived from the "haploid" parent was stronger than those derived from the "diploid" parent. Our findings suggest that the apparent intermediacy of hybrid phenotypes results from the combination of individual genes with dominant expression rather than from simple additivity. The efficiency of cross-talk between trans-regulatory elements further appears dosage dependent. Important effects of polyploidization may thus stem from changes in relative concentrations of trans-regulatory elements and their binding sites between hybridizing genomes. Links between gene regulation and asexuality are discussed.
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Affiliation(s)
- Oldřich Bartoš
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Röslein
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Kotusz
- Museum of Natural History, University of Wroclaw, Wroclaw, Poland
| | - Jan Paces
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Institute of Molecular Genetics, Laboratory of Genomics and Bioinformatics, The Czech Academy of Sciences, Prague, Czech Republic
| | - Ladislav Pekárik
- Plant Science and Biodiversity Center, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia.,Faculty of Education, Trnava University, Trnava, Slovakia
| | - Miloslav Petrtýl
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Karel Halačka
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Eva Štefková Kašparová
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
| | - Jan Mendel
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Alicja Boroń
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Dorota Juchno
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anna Leska
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Olga Jablonska
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Monika Šídová
- Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Vestec, Czech Republic
| | - Karel Janko
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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10
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Ren L, Yan X, Cao L, Li J, Zhang X, Gao X, Liu J, Cui J, Liu S. Combined effects of dosage compensation and incomplete dominance on gene expression in triploid cyprinids. DNA Res 2019; 26:485-494. [PMID: 31883002 PMCID: PMC6993813 DOI: 10.1093/dnares/dsz026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 12/24/2019] [Indexed: 11/12/2022] Open
Abstract
Hybridization and polyploidy are pervasive evolutionary features of flowering plants and frequent among some animal groups, such as fish. These processes always lead to novel genotypes and various phenotypes, including growth heterosis. However, its genetic basis in lower vertebrate is still poorly understood. Here, we conducted transcriptome-level analyses of the allopolyploid complex of Carassius auratus red var. (R) (♀) × Cyprinus carpio L. (C) (♂), including the allodiploid and allotetraploid with symmetric subgenomes, and the two allotriploids with asymmetric subgenomes. The gradual changes of gene silencing and novel gene expression suggested the weakening of the constraint of polymorphic expression in genotypic changes. Then, analyses of the direction and magnitude of homoeolog expression exhibited various asymmetric expression patterns, which supported that R incomplete dominance and dosage compensation were co-regulated in the two triploids. Under these effects, various magnitudes of R-homoeolog expression bias were observed in growth-regulated genes, suggesting that they might contribute to growth heterosis in the two triploids. The determination of R incomplete dominance and dosage compensation, which might be led by asymmetric subgenomes and multiple sets of homologous chromosomes, explained why various expression patterns were shaped and their potential contribution to growth heterosis in the two triploids.
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Affiliation(s)
- Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Xiaojing Yan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Liu Cao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Jiaming Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Xueyin Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Xin Gao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Jia Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Jialin Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan 410081, P.R. China
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, P.R. China
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11
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Wan Z, Tang J, Ren L, Xiao Y, Liu S. Optimization Techniques to Deeply Mine the Transcriptomic Profile of the Sub-Genomes in Hybrid Fish Lineage. Front Genet 2019; 10:911. [PMID: 31737028 PMCID: PMC6833921 DOI: 10.3389/fgene.2019.00911] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 08/29/2019] [Indexed: 11/13/2022] Open
Abstract
It has been shown that reciprocal cross allodiploid lineage with sub-genomes derived from the cross of Megalobrama amblycephala (BSB) × Culter alburnus (TC) generates the variations in phenotypes and genotypes, but it is still a challenge to deeply mine biological information in the transcriptomic profile of this lineage owing to its genomic complexity and lack of efficient data mining methods. In this paper, we establish an optimization model by non-negative matrix factorization approach for deeply mining the transcriptomic profile of the sub-genomes in hybrid fish lineage. A new so-called spectral conjugate gradient algorithm is developed to solve a sequence of large-scale subproblems such that the original complicated model can be efficiently solved. It is shown that the proposed method can provide a satisfactory result of taxonomy for the hybrid fish lineage such that their genetic characteristics are revealed, even for the samples with larger detection errors. Particularly, highly expressed shared genes are found for each class of the fish. The hybrid progeny of TC and BSB displays significant hybrid characteristics. The third generation of TC-BSB hybrid progeny (BTF3 and TBF3) shows larger trait separation.
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Affiliation(s)
- Zhong Wan
- School of Mathematics and Statistics, Central South University, Changsha, China
| | - Jiayi Tang
- School of Mathematics and Statistics, Central South University, Changsha, China
| | - Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
| | - Yamei Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
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12
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Wang Z, Miao H, Liu J, Xu B, Yao X, Xu C, Zhao S, Fang X, Jia C, Wang J, Zhang J, Li J, Xu Y, Wang J, Ma W, Wu Z, Yu L, Yang Y, Liu C, Guo Y, Sun S, Baurens FC, Martin G, Salmon F, Garsmeur O, Yahiaoui N, Hervouet C, Rouard M, Laboureau N, Habas R, Ricci S, Peng M, Guo A, Xie J, Li Y, Ding Z, Yan Y, Tie W, D'Hont A, Hu W, Jin Z. Musa balbisiana genome reveals subgenome evolution and functional divergence. NATURE PLANTS 2019; 5:810-821. [PMID: 31308504 PMCID: PMC6784884 DOI: 10.1038/s41477-019-0452-6] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 05/20/2019] [Indexed: 05/19/2023]
Abstract
Banana cultivars (Musa ssp.) are diploid, triploid and tetraploid hybrids derived from Musa acuminata and Musa balbisiana. We presented a high-quality draft genome assembly of M. balbisiana with 430 Mb (87%) assembled into 11 chromosomes. We identified that the recent divergence of M. acuminata (A-genome) and M. balbisiana (B-genome) occurred after lineage-specific whole-genome duplication, and that the B-genome may be more sensitive to the fractionation process compared to the A-genome. Homoeologous exchanges occurred frequently between A- and B-subgenomes in allopolyploids. Genomic variation within progenitors resulted in functional divergence of subgenomes. Global homoeologue expression dominance occurred between subgenomes of the allotriploid. Gene families related to ethylene biosynthesis and starch metabolism exhibited significant expansion at the pathway level and wide homoeologue expression dominance in the B-subgenome of the allotriploid. The independent origin of 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) homoeologue gene pairs and tandem duplication-driven expansion of ACO genes in the B-subgenome contributed to rapid and major ethylene production post-harvest in allotriploid banana fruits. The findings of this study provide greater context for understanding fruit biology, and aid the development of tools for breeding optimal banana cultivars.
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Affiliation(s)
- Zhuo Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Hongxia Miao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Juhua Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China
| | - Biyu Xu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | | | - Chunyan Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shancen Zhao
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | | | - Caihong Jia
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jingyi Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jianbin Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jingyang Li
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yi Xu
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jiashui Wang
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China
| | - Weihong Ma
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China
| | | | - Lili Yu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yulan Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Chun Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yu Guo
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Silong Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Frederic Salmon
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, Guadeloupe, France
| | - Olivier Garsmeur
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Nathalie Laboureau
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Remy Habas
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Sebastien Ricci
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, Guadeloupe, France
| | - Ming Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Anping Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jianghui Xie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yin Li
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Montpellier, France.
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
| | - Zhiqiang Jin
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China.
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13
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Sriswasdi S, Takashima M, Manabe RI, Ohkuma M, Iwasaki W. Genome and transcriptome evolve separately in recently hybridized Trichosporon fungi. Commun Biol 2019; 2:263. [PMID: 31341962 PMCID: PMC6642101 DOI: 10.1038/s42003-019-0515-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/25/2019] [Indexed: 11/28/2022] Open
Abstract
Genome hybridization is an important evolutionary event that gives rise to species with novel capabilities. However, the merging of distinct genomes also brings together incompatible regulatory networks that must be resolved during the course of evolution. Understanding of the early stages of post-hybridization evolution is particularly important because changes in these stages have long-term evolutionary consequences. Here, via comparative transcriptomic analyses of two closely related, recently hybridized Trichosporon fungi, T. coremiiforme and T. ovoides, and three extant relatives, we show that early post-hybridization evolutionary processes occur separately at the gene sequence and gene expression levels but together contribute to the stabilization of hybrid genome and transcriptome. Our findings also highlight lineage-specific consequences of genome hybridization, revealing that the transcriptional regulatory dynamics in these hybrids responded completely differently to gene loss events: one involving both subgenomes and another that is strictly subgenome-specific.
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Affiliation(s)
- Sira Sriswasdi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 Japan
- Research Affairs, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathum Wan, Bangkok 10330 Thailand
- Computational Molecular Biology Group, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathum Wan, Bangkok 10330 Thailand
| | - Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1, Koyadai, Tsukuba-shi, Ibaraki 305-0074 Japan
- Department of Microbiology, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 Japan
| | - Ri-ichiroh Manabe
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1, Koyadai, Tsukuba-shi, Ibaraki 305-0074 Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8568 Japan
- Atmosphere and Ocean Research Institute, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8564 Japan
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14
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Zhou Y, Zhang X, Xu Q, Yan J, Yu F, Wang F, Xiao J, Luo Y, Zhong H. Nonadditive and allele-specific expression of insulin-like growth factor 1 in Nile tilapia (Oreochromis niloticus, ♀) × blue tilapia (O. aureus, ♂) hybrids. Comp Biochem Physiol B Biochem Mol Biol 2019; 232:93-100. [PMID: 30898546 DOI: 10.1016/j.cbpb.2019.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/04/2019] [Accepted: 03/07/2019] [Indexed: 11/18/2022]
Abstract
Hybrid Nile tilapia (Oreochromis niloticus, ♀) × blue tilapia (O. aureus, ♂) is a widely cultured tilapia variety due to its growth vigor compared to the parent species. As a peptide hormone, insulin-like growth factor 1 (IGF-1) plays a critical role in regulating somatic growth. The present study focuses on the expression characteristics of IGF-1 in hybrid tilapia. The cloned complete open reading frame of IGF-1 in hybrid tilapia is 549 bp in length, encoding a protein of 182 amino acids. The deduced protein is highly similar to that of Nile tilapia and blue tilapia. IGF-1 was found to be primarily expressed in the liver and muscle in the hybrid; lower expression levels were found in other tissues such as the intestine, spleen, and head-kidney. Increased mRNA expression was observed in the liver and muscle of the hybrid compared to Nile tilapia and blue tilapia, indicating a nonadditive expression pattern in the hybrid. An IGF-1 SNP site (397 site: C in Nile tilapia, G in blue tilapia) for differentiating the Nile tilapia or blue tilapia subgenome in hybrids was identified. Pyrosequencing analysis of the liver transcriptome indicated that most of the hybrids (9 of 10 individuals) predominantly expressed the G allele, demonstrating bias of the blue tilapia subgenome. The present study provides novel data indicating, for the first time, overall gene expression of IGF-1 and allele-specific expression in hybrid tilapia.
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Affiliation(s)
- Yi Zhou
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi 530021, China
| | - Xiaojin Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi 530021, China; Key Laboratory of Aquatic Genetic Resources and Utilization, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
| | - Qian Xu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China
| | - Jinpeng Yan
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China
| | - Fan Yu
- Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Fenghua Wang
- Sports Biochemistry Laboratory, Institute of Physical Education, Xinjiang Normal University, Urumqi 830054, China
| | - Jun Xiao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi 530021, China
| | - Yongju Luo
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi 530021, China; Key Laboratory of Aquatic Genetic Resources and Utilization, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
| | - Huan Zhong
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi 530021, China.
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15
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Establishment and application of distant hybridization technology in fish. SCIENCE CHINA-LIFE SCIENCES 2018; 62:22-45. [DOI: 10.1007/s11427-018-9408-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 09/19/2018] [Indexed: 12/11/2022]
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16
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Xiao L, Wang D, Guo Y, Tang Z, Liu Q, Li S, Zhang Y, Lin H. Comparative transcriptome analysis of diploid and triploid hybrid groupers (Epinephelus coioides♀ × E. lanceolatus♂) reveals the mechanism of abnormal gonadal development in triploid hybrids. Genomics 2018; 111:251-259. [PMID: 30453060 DOI: 10.1016/j.ygeno.2018.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 10/10/2018] [Accepted: 11/10/2018] [Indexed: 10/27/2022]
Abstract
In our previous studies, diploid and triploid hybrids have been detected from the hybridization of Epinephelus coioides♀ × E. lanceolatus♂. The triploid groupers have been found to be delayed in gonadal development, but the mechanism remains poorly understood. In this study, we examined the gonadal development, assayed the serum steroid hormone levels, and compared the BP (brain and pituitary) and G (gonad) transcriptomes of 18-month-old diploid and triploid hybrids. The results showed that levels of serum estradiol-17β and testosterone were significantly higher in triploid groupers. The RNA-seq data revealed that 1518 and 14,963 differentially expressed genes were identified in the BP and G transcriptome, respectively. Further analysis revealed that the expression levels of genes involved in the sexual differentiation pathway and sex steroid synthesis pathway are significantly higher in triploid hybrids. Our findings provided a comprehensive insight into a better understanding of the regulatory mechanisms of sterility in triploid hybrid fish.
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Affiliation(s)
- Ling Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Dengdong Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Yin Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Zhujing Tang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Qiongyu Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Shuisheng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China.
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; Marine Fisheries Development Center of Guangdong Province, Huizhou 516081, People's Republic of China.
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; College of Ocean, Hainan University, Haikou 570228, People's Republic of China
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17
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Chalmers L, Vera LM, Taylor JF, Adams A, Migaud H. Comparative ploidy response to experimental hydrogen peroxide exposure in Atlantic salmon (Salmo salar). FISH & SHELLFISH IMMUNOLOGY 2018; 81:354-367. [PMID: 30012493 PMCID: PMC6115329 DOI: 10.1016/j.fsi.2018.07.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/04/2018] [Accepted: 07/10/2018] [Indexed: 05/05/2023]
Abstract
While research into the growth, survival, nutrition and, more recently, disease susceptibility of triploid Atlantic salmon has expanded, there remains an overall lack of studies assessing the response of triploids to chemical treatments. It is essential that the response of triploids to disease treatments be characterised to validate their suitability for commercial production. This study aimed to investigate and compare the stress and immune responses of triploid and diploid Atlantic salmon following an experimental treatment with hydrogen peroxide (H2O2). A dose response test was first undertaken to determine a suitable test dose for both diploid and triploid Atlantic salmon. Following this, diploids and triploids were exposed to H2O2 (1800 ppm) for 20 min, as per commercial practices, after which blood glucose and lactate, and plasma cortisol and lysozyme were measured, along with the expression of oxidative stress and immune-related genes. In the first 6 h post-exposure to H2O2, comparable mortalities occurred in both diploid and triploid Atlantic salmon. Cortisol, glucose and lactate were not significantly influenced by ploidy suggesting that, physiologically, triploid Atlantic salmon are able to cope with the stress associated with H2O2 exposure as well as their diploid counterparts. Exposure to H2O2 significantly elevated the expression of cat and sod2 in diploid livers and gr, il1β and crp/sap1b in diploid gills, while it significantly decreased the expression of saa5 and crp/sap1a in diploid gills. In triploids, the expression levels of cat, hsp70, sod1, saa5, crp/sap1a and crp/sap1b in liver was significantly higher in fish exposed to H2O2 compared to control fish. The expression of gr, sod1 and il1β in triploid gills was also elevated in response to H2O2 exposure. This study represents the first experimental evidence of the effects of H2O2 exposure on triploid Atlantic salmon and continues to support their application into commercial production.
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Affiliation(s)
- Lynn Chalmers
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Luisa M Vera
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - John F Taylor
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Alexandra Adams
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Herve Migaud
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK.
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Li W, Liu J, Tan H, Luo L, Cui J, Hu J, Wang S, Liu Q, Hu F, Tang C, Ren L, Yang C, Zhao R, Tao M, Zhang C, Qin Q, Liu S. Asymmetric expression patterns reveal a strong maternal effect and dosage compensation in polyploid hybrid fish. BMC Genomics 2018; 19:517. [PMID: 29969984 PMCID: PMC6030793 DOI: 10.1186/s12864-018-4883-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/19/2018] [Indexed: 03/05/2023] Open
Abstract
Background Hybridization and polyploidization are regarded as the major driving forces in plant speciation, diversification, and ecological adaptation. Our knowledge regarding the mechanisms of duplicated-gene regulation following genomic merging or doubling is primarily derived from plants and is sparse for vertebrates. Results We successfully obtained an F1 generation (including allodiploid hybrids and triploid hybrids) from female Megalobrama amblycephala Yih (BSB, 2n = 48) × male Xenocypri davidi Bleeker (YB, 2n = 48). The duplicated-gene expression patterns of the two types of hybrids were explored using RNA-Seq data. In total, 5.44 × 108 (69.32 GB) clean reads and 499,631 assembled unigenes were obtained from the testis transcriptomes. The sequence similarity analysis of 4265 orthologs revealed that the merged genomes were dominantly expressed in different ploidy hybrids. The differentially expressed genes in the two types of hybrids were asymmetric compared with those in both parents. Furthermore, the genome-wide expression level dominance (ELD) was biased toward the maternal BSB genome in both the allodiploid and triploid hybrids. In addition, the dosage-compensation mechanisms that reduced the triploid expression levels to the diploid state were determined in the triploid hybrids. Conclusions Our results indicate that divergent genomes undergo strong interactions and domination in allopolyploid offspring. Genomic merger has a greater effect on the gene-expression patterns than genomic doubling. The various expression mechanisms (including maternal effect and dosage compensation) in different ploidy hybrids suggest that the initial genomic merger and doubling play important roles in polyploidy adaptation and evolution. Electronic supplementary material The online version of this article (10.1186/s12864-018-4883-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wuhui Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Junmei Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Hui Tan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Lingling Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Jialin Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Jie Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Qingfeng Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Conghui Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal university, Changsha, 410081, Hunan, People's Republic of China. .,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
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Dosage compensation in the process of inactivation/reactivation during both germ cell development and early embryogenesis in mouse. Sci Rep 2017. [PMID: 28623283 PMCID: PMC5473838 DOI: 10.1038/s41598-017-03829-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ohno proposed that dosage compensation in mammals evolved as a two-step mechanism involving X-inactivation and X-upregulation. While X-inactivation is well characterized, it remains to further analysis whether upregulation of the single activated X chromosome in mammals occurs. We obtained RNA-seq data, including single-cell RNA-seq data, from cells undergoing inactivation/reactivation in both germ cell development and early embryogenesis stages in mouse and calculated the X: A ratio from the gene expression. Our results showed that the X: A ratio is always 1, regardless of the number of X chromosomes being transcribed for expressed genes. Furthermore, the single-cell RNA-seq data across individual cells of mouse preimplantation embryos of mixed backgrounds indicated that strain-specific SNPs could be used to distinguish transcription from maternal and paternal chromosomes and further showed that when the paternal was inactivated, the average gene dosage of the active maternal X chromosome was increased to restore the balance between the X chromosome and autosomes. In conclusion, our analysis of RNA-seq data (particularly single-cell RNA-seq) from cells undergoing the process of inactivation/reactivation provides direct evidence that the average gene dosage of the single active X chromosome is upregulated to achieve a similar level to that of two active X chromosomes and autosomes present in two copies.
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