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Chen Q, Wu B, Li C, Ding L, Huang S, Wang J, Zhao J. Deciphering male influence in gynogenetic Pengze crucian carp ( Carassius auratus var. pengsenensis): insights from Nanopore sequencing of structural variations. Front Genet 2024; 15:1392110. [PMID: 38784042 PMCID: PMC11111978 DOI: 10.3389/fgene.2024.1392110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/11/2024] [Indexed: 05/25/2024] Open
Abstract
In this study, we investigate gynogenetic reproduction in Pengze Crucian Carp (Carassius auratus var. pengsenensis) using third-generation Nanopore sequencing to uncover structural variations (SVs) in offspring. Our objective was to understand the role of male genetic material in gynogenesis by examining the genomes of both parents and their offspring. We discovered a notable number of male-specific structural variations (MSSVs): 1,195 to 1,709 MSSVs in homologous offspring, accounting for approximately 0.52%-0.60% of their detected SVs, and 236 to 350 MSSVs in heterologous offspring, making up about 0.10%-0.13%. These results highlight the significant influence of male genetic material on the genetic composition of offspring, particularly in homologous pairs, challenging the traditional view of asexual reproduction. The gene annotation of MSSVs revealed their presence in critical gene regions, indicating potential functional impacts. Specifically, we found 5 MSSVs in the exonic regions of protein-coding genes in homologous offspring, suggesting possible direct effects on protein structure and function. Validation of an MSSV in the exonic region of the polyunsaturated fatty acid 5-lipoxygenase gene confirmed male genetic material transmission in some offspring. This study underscores the importance of further research on the genetic diversity and gynogenesis mechanisms, providing valuable insights for reproductive biology, aquaculture, and fostering innovation in biological research and aquaculture practices.
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Affiliation(s)
- Qianhui Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Biyu Wu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Chao Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Liyun Ding
- Jiangxi Fisheries Research Institute, Nanchang, China
| | - Shiting Huang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Junjie Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jun Zhao
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
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Currey MC, Walker C, Bassham S, Healey HM, Beck EA, Cresko WA. Genome-wide analysis facilitates estimation of the amount of male contribution in meiotic gynogenetic three-spined stickleback (Gasterosteus aculeatus). JOURNAL OF FISH BIOLOGY 2023; 102:844-855. [PMID: 36647901 DOI: 10.1111/jfb.15321] [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: 07/15/2022] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
Gynogenetic embryos - those inheriting only maternal DNA - can be experimentally created by fertilizing eggs with radiation-treated sperm containing inactivated paternal chromosomes. Diploidy in the zygotes can be maintained through prevention of the second meiosis or restored by preventing the first mitosis after the maternal chromosome complement has been replicated. These gynogenetic organisms are useful in many fields including aquaculture, evolutionary biology and genomics. Although gynogenetic organisms have been created in numerous species, the completeness of uni-parental inheritance has often been assumed rather than thoroughly quantified across the genome. Instead, when tests of uni-parental inheritance occur, they typically rely on well-studied genetically determined phenotypes that represent a very small sub-set of the genome. Only assessing small genomic regions for paternal inheritance leaves the question of whether some paternal contributions to offspring might still have occurred. In this study, the authors quantify the efficacy of creating gynogenetic diploid three-spined stickleback fish (Gasterosteus aculeatus). To this end, the authors mirrored previous assessments of paternal contribution using well-studied genetically determined phenotypes including sex and genetically dominant morphological traits but expanded on previous studies using dense restriction site-associated DNA sequencing (RAD-seq) markers in parents and offspring to assess paternal inheritance genome-wide. In the gynogenetic diploids, the authors found no male genotypes underlying their phenotypes of interest - sex and dominant phenotypic traits. Using genome-wide assessments of paternal contribution, nevertheless, the authors found evidence of a small, yet potentially important, amount of paternally "leaked" genetic material. The application of this genome-wide approach identifies the need for more widespread assessment of paternal contributions to gynogenetic animals and promises benefits for many aspects of aquaculture, evolutionary biology and genomics.
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Affiliation(s)
- Mark C Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Charline Walker
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Hope M Healey
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Emily A Beck
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
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Sun Z, Gong C, Ren J, Zhang X, Wang G, Liu Y, Ren Y, Zhao Y, Yu Q, Wang Y, Hou J. Toxicity of nickel and cobalt in Japanese flounder. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114516. [PMID: 32283401 DOI: 10.1016/j.envpol.2020.114516] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 03/28/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
Nickel and cobalt are essential elements that become toxic at high concentrations. Little is known about nickel and cobalt toxicity in aquatic animals. This study aimed to investigate acute and chronic toxicity of nickel and cobalt in Japanese flounder (Paralichthys olivaceous), with emphasis on oxidative stress reactions, histopathological changes, and differences in gene expression. The lethal concentration for 50% mortality (LC50) in 3 and 8 cm Japanese flounder exposed to nickel for 96 h was found to be 86.2 ± 0.018 and 151.3 ± 0.039 mg/L; for cobalt exposure, LC50 was 47.5 ± 0.015 and 180.4 ± 0.034 mg/L, respectively. Chronic nickel and cobalt exposure caused different degrees of oxidative enzyme activity changes in gill, liver, and muscle tissues. Erythrocyte deformations were detected after acute or chronic exposure to nickel and cobalt. the nickel and cobalt exposure also caused pathological changes such as spherical swelling over other gill patches, rod-like proliferations in the gill patch epithelial cell layer, and disorder in hepatocyte arrangement, cell swelling, and cytoplasm loosening. RNA-Seq indicated that there were 184 upregulated and 185 downregulated genes in the liver of Japanese flounder exposed to 15 mg/L nickel for 28 d. For cobalt, 920 upregulated and 457 downregulated genes were detected. Among these differentially expressed genes, 162 were shared by both nickel and cobalt exposure. In both nickel and cobalt, pathways including fatty acid elongation, steroid biosynthesis, unsaturated fatty acid biosynthesis, fatty acid metabolism, PPAR signaling, and ferroptosis were significantly enriched. Taken together, these results aided our understanding of the toxicity of nickel and cobalt in aquatic animals.
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Affiliation(s)
- Zhaohui Sun
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, Beijing, 100141, China; Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Chunguang Gong
- Ocean Collage, Agricultural University of Hebei, Qinhuangdao, 066009, China
| | - Jiangong Ren
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Xiaoyan Zhang
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Guixing Wang
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Yufeng Liu
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Yuqin Ren
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Yaxian Zhao
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Qinghai Yu
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Yufen Wang
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Jilun Hou
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, Beijing, 100141, China; Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China.
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Ji-Lun H, Xiao-Yan Z, Gui-Xing W, Zhao-Hui S, Wei D, Ya-Xian Z, Fei S, Li-Yan W, Xin-Hui X, Yu-Fen W. Novel breeding approach for Japanese flounder using atmosphere and room temperature plasma mutagenesis tool. BMC Genomics 2019; 20:323. [PMID: 31035925 PMCID: PMC6489211 DOI: 10.1186/s12864-019-5681-6] [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: 10/16/2018] [Accepted: 04/09/2019] [Indexed: 11/20/2022] Open
Abstract
Background Artificial induction of mutagenesis is effective for genetic resource innovation and breeding. However, the traditional mutation methods for fish breeding are not convenient or safe for daily use. Hence, development of a simple, safe and effective mutagenesis method with a high mutation rate and applicability to multiple fish species, is needed. Results We reported the first successful mutagenesis in a marine aquaculture fish species, Japanese flounder, Paralichthys olivaceus, using a novel atmosphere and room temperature plasma (ARTP) mutagenesis tool. ARTP treatment time was optimized for the fertilized eggs and sperm, respectively. Eggs fertilized for 60 min were treated by ARTP with a radio-frequency power input of 120 W, and the ARTP treatment time was 25 min. Under an ARTP radio-frequency power input of 200 W, the optimal treatment time for sperm diluted with Ringer’s solution by 1:40 v/v was 10 min. The ARTP-treated group presented differences in morphological traits such as body height, total length among individuals at day 90 after hatching. Whole-genome sequencing was used to reveal the mutation features of ARTP-treated individuals collected at day 120 after hatching. In total, 69.25Gb clean data were obtained from three controls and eight randomly selected ARTP-treated individuals, revealing 240,722 to 322,978 SNPs and 82,149 to 86,798 InDels located in 17,394~18,457 and 12,907~13,333 genes, respectively. The average mutation rate reached 0.064% at the genome level. Gene ontology clustering indicated that genes associated with cell components, binding function, catalytic activity, cellular process, metabolic process and biological regulation processes had higher mutation rates. Conclusions ARTP mutagenesis is a useful method for breeding of fish species to accelerate the selection of economically important traits that would benefit the aquaculture industry, given the variety of mutations detected.
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Affiliation(s)
- Hou Ji-Lun
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, Beijing, China.,Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, China
| | - Zhang Xiao-Yan
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, China
| | - Wang Gui-Xing
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, China
| | - Sun Zhao-Hui
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, China
| | - Du Wei
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, China
| | - Zhao Ya-Xian
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, China
| | - Si Fei
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, China
| | - Wang Li-Yan
- TmaxTree Biotechnology Company, Luoyang, China
| | - Xing Xin-Hui
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China. .,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China.
| | - Wang Yu-Fen
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, China.
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Jagiełło K, Dobosz S, Zalewski T, Polonis M, Ocalewicz K. Developmental competence of eggs produced by rainbow trout Doubled Haploids (DHs) and generation of the clonal lines. Reprod Domest Anim 2018; 53:1176-1183. [PMID: 29956409 DOI: 10.1111/rda.13223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/23/2018] [Accepted: 05/10/2018] [Indexed: 11/27/2022]
Abstract
Poor quality eggs produced by the fully homozygous doubled haploids (DHs) may impair generation of clonal lines in fish species. In the present research, gynogenetic development of rainbow trout (Oncorhynchus mykiss) was induced in eggs originated from the DH females. Eggs were activated with the UV-irradiated grayling (Thymallus thymallus) spermatozoa and subjected to the high hydrostatic pressure (HHP) shock to provide diploid clonal individuals. Only two of four DH females produced eggs that were successfully activated by the irradiated spermatozoa and subsequently developed into the gynogenetic embryos. Survival rates of rainbow trout from the clonal lines equalled 21.5% and 19.8% during embryogenesis and decreased after hatching to 18.6% and 14.9%, respectively. Some of the dead rainbow trout clones collected between hatching and swim-up stage were emaciated and exhibited spinal deformities including scoliosis. Provided results confirmed limited developmental competences of eggs produced by rainbow trout DH females. Clonal rainbow trout developing in such eggs exhibited reduced survival and increased frequency of the body abnormalities.
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Affiliation(s)
- Krzysztof Jagiełło
- Faculty of Oceanography and Geography, Department of Marine Biology and Ecology, Institute of Oceanography, University of Gdansk, Gdynia, Poland
| | - Stefan Dobosz
- Department of Salmonid Research, Inland Fisheries Institute in Olsztyn, Żukowo, Poland
| | - Tomasz Zalewski
- Department of Salmonid Research, Inland Fisheries Institute in Olsztyn, Żukowo, Poland
| | - Marcin Polonis
- Faculty of Oceanography and Geography, Department of Marine Biology and Ecology, Institute of Oceanography, University of Gdansk, Gdynia, Poland
| | - Konrad Ocalewicz
- Faculty of Oceanography and Geography, Department of Marine Biology and Ecology, Institute of Oceanography, University of Gdansk, Gdynia, Poland
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Sundaram A, Tengs T, Grimholt U. Issues with RNA-seq analysis in non-model organisms: A salmonid example. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:38-47. [PMID: 28223254 DOI: 10.1016/j.dci.2017.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 02/02/2017] [Accepted: 02/14/2017] [Indexed: 06/06/2023]
Abstract
High throughput sequencing (HTS) is useful for many purposes as exemplified by the other topics included in this special issue. The purpose of this paper is to look into the unique challenges of using this technology in non-model organisms where resources such as genomes, functional genome annotations or genome complexity provide obstacles not met in model organisms. To describe these challenges, we narrow our scope to RNA sequencing used to study differential gene expression in response to pathogen challenge. As a demonstration species we chose Atlantic salmon, which has a sequenced genome with poor annotation and an added complexity due to many duplicated genes. We find that our RNA-seq analysis pipeline deciphers between duplicates despite high sequence identity. However, annotation issues provide problems in linking differentially expressed genes to pathways. Also, comparing results between approaches and species are complicated due to lack of standardized annotation.
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Affiliation(s)
- Arvind Sundaram
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0407 Oslo, Norway
| | - Torstein Tengs
- Norwegian Veterinary Institute, Department of Virology, P.O. Box 750 Sentrum, 0106 Oslo, Norway
| | - Unni Grimholt
- Norwegian Veterinary Institute, Department of Virology, P.O. Box 750 Sentrum, 0106 Oslo, Norway.
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