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Lisachov A, Dedukh D, Simanovsky S, Panthum T, Singchat W, Srikulnath K. Spaghetti Connections: Synaptonemal Complexes as a Tool to Explore Chromosome Structure, Evolution, and Meiotic Behavior in Fish. Cytogenet Genome Res 2024; 164:1-15. [PMID: 38452741 DOI: 10.1159/000538238] [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: 01/14/2024] [Accepted: 03/05/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND The synaptonemal complex (SC) is a protein axis formed along chromosomes during meiotic prophase to ensure proper pairing and crossing over. SC analysis has been widely used to study the chromosomes of mammals and less frequently of birds, reptiles, and fish. It is a promising method to investigate the evolution of fish genomes and chromosomes as a part of complex approach. SUMMARY Compared with conventional metaphase chromosomes, pachytene chromosomes are less condensed and exhibit pairing between homologous chromosomes. These features of SCs facilitate the study of the small chromosomes that are typical in fish. Moreover, it allows the study of heteromorphisms in sex chromosomes and supernumerary chromosomes. In addition, it enables the investigation of the pairing between orthologous chromosomes in hybrids, which is crucial for uncovering the causes of hybrid sterility and asexual reproduction, such as gynogenesis or hybridogenesis. However, the application of SC analysis to fish chromosomes is limited by the associated complications. First, in most fish, meiosis does not occur during every season and life stage. Second, different SC preparation methods are optimal for different fish species. Third, commercial antibodies targeting meiotic proteins have been primarily developed against mammalian antigens, and not all of them are suitable for fish chromosomes. KEY MESSAGES In the present review, we provide an overview of the methods for preparing fish SCs and highlight important studies using SC analysis in fish. This study will be valuable for planning and designing research that applies SC analysis to fish cytogenetics and genomics.
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Affiliation(s)
- Artem Lisachov
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russian Federation
| | - Dmitrij Dedukh
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Libechov, Czechia
| | - Sergey Simanovsky
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russian Federation
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
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Zhang Y, Lv M, Jiang H, Li H, Li R, Yang C, Huang Y, Zhou H, Mei Y, Gao J, Cao X. Mitotic defects lead to unreduced sperm formation in cdk1 -/- mutants. Int J Biol Macromol 2023:125171. [PMID: 37271265 DOI: 10.1016/j.ijbiomac.2023.125171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/03/2023] [Accepted: 05/23/2023] [Indexed: 06/06/2023]
Abstract
Unreduced gametes, that are important for species evolution and agricultural development, are generally believed to be formed by meiotic defects. However, we found that male diploid loach (Misgurnus anguillicaudatus) could produce not only haploid sperms, but also unreduced sperms, after cyclin-dependent kinase 1 gene (cdk1, one of the most important kinases in regulating cell mitosis) deletion. Observations on synaptonemal complexes of spermatocyte in prophase of meiosis and spermatogonia suggested that the number of chromosomes in some spermatogonia of cdk1-/- loach doubled, leading to unreduced diploid sperm production. Then, transcriptome analysis revealed aberrant expressions of some cell cycle-related genes (such as ppp1c and gadd45) in spermatogonia of cdk1-/- loach relative to wild-type loach. An in vitro and in vivo experiment further validated that Cdk1 deletion in diploid loach resulted in mitotic defects, leading to unreduced diploid sperm formation. In addition, we found that cdk1-/- zebrafish could also produce unreduced diploid sperms. This study provides important information on revealing the molecular mechanisms behind unreduced gamete formation through mitotic defects, and lays the foundation for a novel strategy for fish polyploidy creation by using cdk1 mutants to produce unreduced sperms, which can then be used to obtain polyploidy, proposed to benefit aquaculture.
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Affiliation(s)
- Yunbang Zhang
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, China
| | - Meiqi Lv
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Hanjun Jiang
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Hui Li
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Rongyun Li
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Chuang Yang
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuwei Huang
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - He Zhou
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Yihui Mei
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian Gao
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, China.
| | - Xiaojuan Cao
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, China.
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Li B, Huang Y, Guo D, Liu Y, Liu Z, Han JC, Zhao J, Zhu X, Huang Y, Wang Z, Xing B. Environmental risks of disposable face masks during the pandemic of COVID-19: Challenges and management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:153880. [PMID: 35189225 PMCID: PMC8855619 DOI: 10.1016/j.scitotenv.2022.153880] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/07/2022] [Accepted: 02/10/2022] [Indexed: 05/10/2023]
Abstract
Since the COVID-19 outbreak in early 2020, face mask (FM) has been recognized as an effective measure to reduce the infection, increasing its consumption across the world. However, the large amount of at-home FM usage changed traditional medical waste management practices, lack of improper management. Currently, few studies estimate FM consumption at a global scale, not to say a comprehensive investigation on the environmental risks of FM from a life cycle perspective. Therefore, global FM consumption and its associated environmental risks are clarified in the present study. Our result shows that 449.5 billion FMs were consumed from January 2020 to March 2021, with an average of 59.4 FMs per person worldwide. This review also provides a basis to understand the environmental risk of randomly disposed of FM and highlights the urgent requirement for the attention of FMs waste management to prevent pollution in the near future.
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Affiliation(s)
- Bing Li
- Water Research Center, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Department of Hydraulic Engineering, Tsinghua University, Beijing, PR China
| | - Yuxiong Huang
- Water Research Center, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Dengting Guo
- Water Research Center, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Chemical and Materials Engineering, The University of Auckland, New Zealand
| | - Yuzhi Liu
- Water Research Center, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Ziyi Liu
- Water Research Center, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Jing-Cheng Han
- Water Science and Environmental Engineering Research Centre, College of Chemical and Environmental Engineering, Shenzhen University, Shenzhen, PR China
| | - Jian Zhao
- School of Environmental Science and Engineering, Ocean University of China, Qingdao 214122, PR China
| | - Xiaoshan Zhu
- Water Research Center, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China.
| | - Yuefei Huang
- Water Research Center, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Department of Hydraulic Engineering, Tsinghua University, Beijing, PR China
| | - Zhenyu Wang
- Institute of Environmental Process and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, PR China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, USA.
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Shivaramu S, Lebeda I, Vuong DT, Rodina M, Gela D, Flajšhans M. Ploidy Levels and Fitness-Related Traits in Purebreds and Hybrids Originating from Sterlet ( Acipenser ruthenus) and Unusual Ploidy Levels of Siberian Sturgeon ( A. baerii). Genes (Basel) 2020; 11:E1164. [PMID: 33023081 PMCID: PMC7600540 DOI: 10.3390/genes11101164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/24/2020] [Accepted: 09/30/2020] [Indexed: 11/20/2022] Open
Abstract
The present study aimed to investigate and compare fitness-related traits and ploidy levels of purebreds and hybrids produced from sturgeon broodstock with both normal and abnormal ploidy levels. We used diploid Acipenser ruthenus and tetraploid A. baerii males and females to produce purebreds and reciprocal hybrids of normal ploidy levels. Likewise, we used diploid A. ruthenus and tetraploid A. baerii females mated to pentaploid and hexaploid A. baerii males to produce hybrids of abnormal ploidy levels. Fertilization of ova of A. ruthenus and A. baerii of normal ploidy with the sperm of pentaploid and hexaploid A. baerii produced fully viable progeny with ploidy levels that were intermediate between those of the parents as was also found in crosses of purebreds and reciprocal hybrids of normal ploidy levels. The A. ruthenus × pentaploid A. baerii and A. ruthenus × hexaploid A. baerii hybrids did not survive after 22 days post-hatch (dph). Mean body weight and cumulative survival were periodically checked at seven-time intervals. The recorded values of mean body weight were significantly higher in A. baerii × pentaploid A. baerii hybrids than other groups at three sampling points (160, 252 and 330 dph). In contrast, the highest cumulative survival was observed in A. baerii × A. ruthenus hybrids at all sampling points (14.47 ± 5.70 at 497 dph). Overall, most of the studied sturgeon hybrids displayed higher mean BW and cumulative survival compared to the purebreds. The utilization of sturgeon hybrids should be restricted to aquaculture purposes because they can pose a significant genetic threat to native populations through ecological interactions.
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Affiliation(s)
- Sahana Shivaramu
- South Bohemian Research Center for Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25 Vodňany, Czech Republic; (I.L.); (D.T.V.); (M.R.); (D.G.); (M.F.)
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Endoh M, Shima F, Havelka M, Asanuma R, Yamaha E, Fujimoto T, Arai K. Hybrid between Danio rerio female and Danio nigrofasciatus male produces aneuploid sperm with limited fertilization capacity. PLoS One 2020; 15:e0233885. [PMID: 32470029 PMCID: PMC7259755 DOI: 10.1371/journal.pone.0233885] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/14/2020] [Indexed: 12/23/2022] Open
Abstract
In the Danio species, interspecific hybridization has been conducted in several combinations. Among them, only the hybrid between a zebrafish (D. rerio) female and a spotted danio (D. nigrofasciatus) male was reported to be fertile. However, beyond these investigations, by means of reproductive biology, gametes of the hybrid have also not been investigated genetically. For this study, we induced a hybrid of the D. rerio female and D. nigrofasciatus male in order to study its developmental capacity, reproductive performance and gametic characteristics. Its hybrid nature was genetically verified by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the rhodopsin gene. Almost all the hybrids (36/37) were males, and only one was female. Developing oocytes were observed in the hybrid female, but ovulated eggs have not been obtained thus far. Microscopic observation revealed various head sizes of sperm in the hybrid males. Flow cytometry showed that the hybrid males generated aneuploid sperm with various ploidy levels up to diploidy. In backcrosses between D. rerio females and hybrid males, fertilization rates were significantly lower than the control D. rerio, and most resultant progeny with abnormal appearance exhibited various kinds of aneuploidies ranging from haploidy to triploidy, but only one viable progeny, which survived more than four months, was triploid. This suggested the contribution of fertile diploid sperm of the hybrid male to successful fertilization and development.
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Affiliation(s)
- Mitsuru Endoh
- Laboratory of Aquaculture Genetics and Genomics, Division of Marine Life Science, Faculty and Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
- Research Fellow of Japan Society for the Promotion of Science, Tokyo, Japan
- * E-mail:
| | - Fumika Shima
- Laboratory of Aquaculture Genetics and Genomics, Division of Marine Life Science, Faculty and Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Miloš Havelka
- Laboratory of Aquaculture Genetics and Genomics, Division of Marine Life Science, Faculty and Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Rei Asanuma
- Laboratory of Aquaculture Genetics and Genomics, Division of Marine Life Science, Faculty and Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Etsuro Yamaha
- Nanae Fresh-Water Station, Field Science Center for Northern Biosphere, Hokkaido University, Nanae, Hokkaido, Japan
| | - Takafumi Fujimoto
- Laboratory of Aquaculture Genetics and Genomics, Division of Marine Life Science, Faculty and Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Katsutoshi Arai
- Laboratory of Aquaculture Genetics and Genomics, Division of Marine Life Science, Faculty and Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
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Kuroda M, Fujimoto T, Murakami M, Yamaha E, Arai K. Aberrant Meiotic Configurations Cause Sterility in Clone-Origin Triploid and Inter-Group Hybrid Males of the Dojo Loach, Misgurnus anguillicaudatus. Cytogenet Genome Res 2019; 158:46-54. [DOI: 10.1159/000500303] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2019] [Indexed: 11/19/2022] Open
Abstract
Gonochoristic wild-type dojo loaches (Misgurnus anguillicaudatus) are diploid (2n = 50) and reproduce bisexually. However, sympatric clonal diploids generate unreduced diploid isogenic eggs that develop gynogenetically. Clone-origin triploidy arises following the incorporation of a haploid wild-type sperm nucleus into the diploid egg. Triploid females produce fertile haploid eggs by meiotic hybridogenesis, while triploid males are sterile. Clonal loaches arose from past hybridization event(s) between genetically diverse groups, A and B. Artificial hybrid females between the 2 groups produce unreduced and/or aneuploid eggs, but the hybrid males are sterile. In this study using FISH, we analyzed chromosome pairing in meiotic cells of clone-origin triploid and inter-group hybrid males to clarify the cytogenetic mechanisms underlying the male-specific sterility. We used a repetitive sequence probe to identify group B-derived chromosomes and a 5.8S + 28S rDNA probe to identify pairs of homologous chromosomes. We found that asynapsis and irregular synapsis occur in triploid and hybrid males containing 2 different genomes and that this may cause the formation of sterile germ cells. These results will help us to understand hybrid sterility from the viewpoint of synapsis behavior.
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Zhong J, Yi S, Ma L, Wang W. Evolution and phylogeography analysis of diploid and polyploid Misgurnus anguillicaudatus populations across China. Proc Biol Sci 2019; 286:20190076. [PMID: 31014220 PMCID: PMC6501937 DOI: 10.1098/rspb.2019.0076] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/03/2019] [Indexed: 12/14/2022] Open
Abstract
The origin and evolution of polyploid organisms have been extensively studied in plants, but this topic remains only partially understood in vertebrates, where polyploidy is relatively rare. In this study, we used Misgurnus anguillicaudatus, a fish that comprises five ploidy levels in nature, as a model animal to improve our understanding of biogeographic history and evolution of polyploid vertebrates. After collecting samples from different geographical populations in China, their ploidy levels were determined using flow cytometry. Two mitochondrial markers ( cytochrome b and control region) were then used for phylogeographic analyses to unravel the possible origins of diploids and tetraploids in China. The results showed that diploids have wider geographical distribution than tetraploids and triploids. There was no clear allopatric geographical range or boundary to divide diploid and polyploid populations. Rather, the analysis of mitochondrial DNA sequences indicated that tetraploids were autopolyploids, with lower genetic diversity than diploids. This suggests that tetraploids originated from sympatric diploids via multiple independent polyploidization events. Genetic structure patterns were similar between diploids and tetraploids, whereas complex genetic differentiation was found among different regions. The potential origin of M. anguillicaudatus was deduced to be in the Pearl River basin, which exhibited the highest nucleotide diversity and genetic differentiation. These findings provide insights into the evolution of polyploidy in vertebrates.
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Affiliation(s)
| | | | | | - Weimin Wang
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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Kuroda M, Fujimoto T, Murakami M, Yamaha E, Arai K. Clonal reproduction assured by sister chromosome pairing in dojo loach, a teleost fish. Chromosome Res 2018; 26:243-253. [DOI: 10.1007/s10577-018-9581-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/12/2018] [Accepted: 05/15/2018] [Indexed: 01/13/2023]
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Zhou H, Xu QZ, Zhang R, Zhuang ZX, Ma YQ, Wang W, Ma TY, Sui Y, Liu Y, Cao X. Gonadal transcriptome analysis of hybrid triploid loaches (Misgurnus anguillicaudatus) and their diploid and tetraploid parents. PLoS One 2018; 13:e0198179. [PMID: 29795681 PMCID: PMC5967825 DOI: 10.1371/journal.pone.0198179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 05/15/2018] [Indexed: 11/18/2022] Open
Abstract
Hybrid triploid loaches (Misgurnus anguillicaudatus) were generated from natural tetraploid and diploid loaches. We studied the gonads of parents and offspring from direct and reciprocal crosses through histological and transcriptome analyses. The triploid offspring had inferior ability to form sperm and egg cells compared with diploid forms. After sequencing the transcriptomes, 655,109,158 clean reads were obtained, and 62,821 unigenes and 178,962 transcripts were assembled. Of these unigenes, 23,189 were annotated in the GO database, 18,525 in the KEGG database and 24,661 in the KOG database. 36 fertility-related genes were found to be differentially expressed between the direct cross (2n × 4n) progenies and their parents, while 53 fertility-related genes between the reciprocal cross (4n × 2n) progenies and their parents. Following protein-protein interaction network analyses, 54 differentially expressed genes, including PLCB4, cyp17a1 and Pla2g4d, were mined, yielding candidate genes involved in the poor fertility of hybrid triploid loaches. This is the first report of transcriptomes of gonads of hybrid triploid loaches and their parents, offering a substantial contribution to sequence resources for this species and providing a deep insight into the molecular mechanism controlling the fertility of hybrid triploid fish.
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Affiliation(s)
- He Zhou
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Qi-Zheng Xu
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Rui Zhang
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Zi-Xin Zhuang
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | | | - Wei Wang
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Tian-Yu Ma
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Yi Sui
- Ma'anshan Municipal Agriculture Commission, Anhui, China
| | - Yang Liu
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Xiaojuan Cao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail:
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Feng B, Yi SV, Zhang M, Zhou X. Development of novel EST-SSR markers for ploidy identification based on de novo transcriptome assembly for Misgurnus anguillicaudatus. PLoS One 2018; 13:e0195829. [PMID: 29649332 PMCID: PMC5896994 DOI: 10.1371/journal.pone.0195829] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/01/2018] [Indexed: 11/19/2022] Open
Abstract
The co-existence of several ploidy types in natural populations makes the cyprinid loach Misgurnus anguillicaudatus an exciting model system to study the genetic and phenotypic consequences of ploidy variations. A first step in such effort is to identify the specific ploidy of an individual. Currently popular methods of karyotyping via cytological preparation or flow cytometry require a large amount of tissue (such as blood) samples, which can be damaging or fatal to the fishes. Here, we developed novel microsatellite markers (SSR markers) from M. anguillicaudatus and show that they can effectively discriminate ploidy using samples collected in a minimally invasive way. Specifically, we generated whole genome transcriptomes from multiple M. anguillicaudatus using the Illumina paired-end sequencing. Approximately 150 million raw reads were assembled into 76,544 non-redundant unigenes. A total of 8,194 potential SSR markers were identified. We selected 98 pairs with more than five tandem repeats for further assays. Out of 45 putative EST-SSR markers that successfully amplified and harbored polymorphism in diploids, 11 markers displayed high variability in tetraploids. We further demonstrate that a set of five EST-SSR markers selected from these are sufficient to distinguish ploidy levels, by first validating them on 69 reference specimens with known ploidy levels and then subsequently using fresh-collected 96 ploidy-unknown specimens. The results from EST-SSR markers are highly concordant with those from independent flow cytometry analysis. The novel EST-SSR markers developed here should facilitate genetic studies of polyploidy in the emerging model system M. anguillicaudatus.
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Affiliation(s)
- Bing Feng
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, P. R. China
| | - Soojin V. Yi
- School of Biology, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Manman Zhang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, P. R. China
| | - Xiaoyun Zhou
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, P. R. China
- * E-mail:
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Yi S, Li Y, Wang W. Selection shapes the patterns of codon usage in three closely related species of genus Misgurnus. Genomics 2017; 110:134-142. [PMID: 28911975 DOI: 10.1016/j.ygeno.2017.09.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/29/2017] [Accepted: 09/07/2017] [Indexed: 11/17/2022]
Abstract
Neutrality plots revealed that selection probably dominates codon bias, whereas mutation plays only a minor role, in shaping the codon bias in three loaches, Misgurnus anguillicaudatus, M. mohoity, and M. bipartitus. These three species also clearly showed similar tendencies in the preferential usage of codons. Nineteen, nine, and 14 preferred codon pairs and 179, 182, and 173 avoided codon pairs were also detected in M. anguillicaudatus, M. bipartitus, and M. mohoity, respectively, and the most frequently avoided type of cP3-cA1 dinucleotide in these species was nnUAnn. The expression-linked patterns of codon usage revealed that higher expression was associated with higher GC3, lower ENC, and a smaller proportion of amino acids with high size/complexity (S/C) scores in these three species. These results elucidate selectively driven codon bias in Misgurnus species, and reveal the potential importance of expression-mediated selection in shaping the genome evolution of fish.
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Affiliation(s)
- Shaokui Yi
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanhe Li
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Weimin Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
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Juchno D, Pecio A, Boroń A, Leska A, Jablonska O, Cejko BI, Kowalski RK, Judycka S, Przybylski M. Evidence of the sterility of allotetraploidCobitisloaches (Teleostei, Cobitidae) using testes ultrastructure. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2017; 327:66-74. [DOI: 10.1002/jez.2071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Dorota Juchno
- Department of Zoology; University of Warmia and Mazury in Olsztyn; Poland
| | - Anna Pecio
- Department of Comparative Anatomy; Institute of Zoology; Jagiellonian University; Krakow Poland
| | - Alicja Boroń
- Department of Zoology; University of Warmia and Mazury in Olsztyn; Poland
| | - Anna Leska
- Department of Zoology; University of Warmia and Mazury in Olsztyn; Poland
| | - Olga Jablonska
- Department of Zoology; University of Warmia and Mazury in Olsztyn; Poland
| | - Beata Irena Cejko
- Department of Gamete and Embryo Biology; Institute of Animal Reproduction and Food Research; Polish Academy of Sciences; Olsztyn Poland
| | - Radosław Kajetan Kowalski
- Department of Gamete and Embryo Biology; Institute of Animal Reproduction and Food Research; Polish Academy of Sciences; Olsztyn Poland
| | - Sylwia Judycka
- Department of Gamete and Embryo Biology; Institute of Animal Reproduction and Food Research; Polish Academy of Sciences; Olsztyn Poland
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Li YJ, Gao YC, Zhou H, Ma HY, Lin ZQ, Ma TY, Sui Y, Arai K. Aneuploid progenies of triploid hybrids between diploid and tetraploid loach Misgurnus anguillicaudatus in China. Genetica 2016; 144:601-609. [DOI: 10.1007/s10709-016-9928-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 09/19/2016] [Indexed: 11/29/2022]
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Analysis of Different Ploidy and Parent-Offspring Genomic DNA Methylation in the Loach Misgurnus anguillicaudatus. Int J Mol Sci 2016; 17:ijms17081299. [PMID: 27556458 PMCID: PMC5000696 DOI: 10.3390/ijms17081299] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/21/2016] [Accepted: 07/26/2016] [Indexed: 01/07/2023] Open
Abstract
In this study, we selected natural polyploidy loach (diploid, triploid and tetraploid) and hybrid F1 generation obverse cross (4 × 2) and inverse cross (2 × 4) by diploids and tetraploids as the research model. The MSAP (methylation-sensitive amplified polymorphism) reaction system was established by our laboratory to explore methylation levels and pattern diversification features at the whole genome level of the polyploidy loach. The results showed that the total methylation and full methylation rates decreased on increased ploidy individuals; moreover, the hemimethylation rate showed no consistent pattern. Compared with diploid loach, the methylation patterns of tetraploid sites changed 68.17%, and the methylation patterns of triploid sites changed 73.05%. The proportion of hypermethylation genes is significantly higher than the proportion of demethylation genes. The methylation level of reciprocal cross F1 generation is lower than the male diploid and higher than the female tetraploid. The hemimethylation and total methylation rate of the cross hybrid F1 generation is significantly higher than the orthogonal F1 generation (p < 0.01). After readjusting, the methylation pattern of genome DNA of reciprocal hybrids changed 69.59% and 72.83%, respectively.
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Huang S, Cao X, Tian X, Luo W, Wang W. Production of Tetraploid Gynogenetic Loach Using Diploid Eggs of Natural Tetraploid Loach, Misgurnus anguillicaudatus, Fertilized with UV-Irradiated Sperm of Megalobrama amblycephala without Treatments for Chromosome Doubling. Cytogenet Genome Res 2016; 147:260-7. [PMID: 26966904 DOI: 10.1159/000444384] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2015] [Indexed: 11/19/2022] Open
Abstract
The gynogenesis phenomenon in nature mainly appears in the reproduction of fish and invertebrates. So far, gynogenesis has been successfully induced in many fish species with the aid of some physical or chemical methods for chromosome doubling. However, few fish can produce gynogenetic progenies, genetically identical or similar to the somatic cells of the mothers, without a treatment for the doubling of chromosomes, which may be related to apomixis, premeiotic endoreduplication, or premeiotic endomitosis. At present, no studies are available about fish with normal ovarian structures producing gynogenetic progenies that could spontaneously double their chromosomes. According to the analyses of flow cytometry, chromosome number, and microsatellites, we found that, with the use of UV-irradiated sperm of blunt snout bream Megalobrama amblycephala, tetraploid loach Misgurnus anguillicaudatus produced tetraploid gynogenetic progenies without any treatments for the doubling of chromosomes. To determine the genetic relationships of gynogenetic progenies and their maternal parent, microsatellite genotyping was conducted. The results indicated that the reason for spontaneous chromosome duplication in gynogenetic progenies may be cytokinesis or inhibition of the extrusion of the second polar body. This is the first report on fish with normal ovarian structures that can produce gynogenetic progenies which spontaneously double their chromosomes and which are genetically identical or similar to the somatic cells of the mothers.
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Affiliation(s)
- Songqian Huang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, PR China
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Asem A, Eimanifar A, Sun SC. Genetic variation and evolutionary origins of parthenogeneticArtemia(Crustacea: Anostraca) with different ploidies. ZOOL SCR 2016. [DOI: 10.1111/zsc.12162] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Alireza Asem
- Institute of Evolution & Marine Biodiversity; Ocean University of China; 5 Yushan Road Qingdao 266003 China
| | - Amin Eimanifar
- Honey Bee Research and Extension Laboratory (HBREL); Department of Entomology and Nematology; University of Florida; Steinmetz Hall, Natural Area Dr., P.O. Box 110620 Gainesville FL 32611 USA
| | - Shi-Chun Sun
- Institute of Evolution & Marine Biodiversity; Ocean University of China; 5 Yushan Road Qingdao 266003 China
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Li YJ, Gao YC, Zhou H, Ma HY, Li JQ, Arai K. Meiotic chromosome configurations in triploid progeny from reciprocal crosses between wild-type diploid and natural tetraploid loach Misgurnus anguillicaudatus in China. Genetica 2015; 143:555-62. [DOI: 10.1007/s10709-015-9853-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 06/21/2015] [Indexed: 12/01/2022]
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18
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Martin KJ, Holland PWH. Enigmatic orthology relationships between Hox clusters of the African butterfly fish and other teleosts following ancient whole-genome duplication. Mol Biol Evol 2014; 31:2592-611. [PMID: 24974377 PMCID: PMC4166920 DOI: 10.1093/molbev/msu202] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2014] [Indexed: 12/13/2022] Open
Abstract
Numerous ancient whole-genome duplications (WGD) have occurred during eukaryote evolution. In vertebrates, duplicated developmental genes and their functional divergence have had important consequences for morphological evolution. Although two vertebrate WGD events (1R/2R) occurred over 525 Ma, we have focused on the more recent 3R or TGD (teleost genome duplication) event which occurred approximately 350 Ma in a common ancestor of over 26,000 species of teleost fishes. Through a combination of whole genome and bacterial artificial chromosome clone sequencing we characterized all Hox gene clusters of Pantodon buchholzi, a member of the early branching teleost subdivision Osteoglossomorpha. We find 45 Hox genes organized in only five clusters indicating that Pantodon has suffered more Hox cluster loss than other known species. Despite strong evidence for homology of the five Pantodon clusters to the four canonical pre-TGD vertebrate clusters (one HoxA, two HoxB, one HoxC, and one HoxD), we were unable to confidently resolve 1:1 orthology relationships between four of the Pantodon clusters and the eight post-TGD clusters of other teleosts. Phylogenetic analysis revealed that many Pantodon genes segregate outside the conventional "a" and "b" post-TGD orthology groups, that extensive topological incongruence exists between genes physically linked on a single cluster, and that signal divergence causes ambivalence in assigning 1:1 orthology in concatenated Hox cluster analyses. Out of several possible explanations for this phenomenon we favor a model which keeps with the prevailing view of a single TGD prior to teleost radiation, but which also considers the timing of diploidization after duplication, relative to speciation events. We suggest that although the duplicated hoxa clusters diploidized prior to divergence of osteoglossomorphs, the duplicated hoxb, hoxc, and hoxd clusters concluded diploidization independently in osteoglossomorphs and other teleosts. We use the term "tetralogy" to describe the homology relationship which exists between duplicated sequences which originate through a shared WGD, but which diploidize into distinct paralogs from a common allelic pool independently in two lineages following speciation.
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Affiliation(s)
- Kyle J Martin
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Zhao Y, Saito T, Pšenička M, Fujimoto T, Arai K. Comparison of spermatozoa parameters, fine structures, and energy-related factors among tetraploid, hyper-tetraploid, and hyper-triploid loaches (Misgurnus anguillicaudatus). ACTA ACUST UNITED AC 2014; 321:198-206. [DOI: 10.1002/jez.1851] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 11/26/2013] [Accepted: 12/16/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Yan Zhao
- Faculty and Graduate School of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido Japan
| | - Taiju Saito
- Faculty of Fisheries and Protection of Waters; South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses; University of South Bohemia in České Budějovice; Vodňany Czech Republic
| | - Martin Pšenička
- Faculty of Fisheries and Protection of Waters; South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses; University of South Bohemia in České Budějovice; Vodňany Czech Republic
| | - Takafumi Fujimoto
- Faculty and Graduate School of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido Japan
| | - Katsutoshi Arai
- Faculty and Graduate School of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido Japan
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Arai K, Fujimoto T. Genomic Constitution and Atypical Reproduction in Polyploid and Unisexual Lineages of the Misgurnus Loach, a Teleost Fish. Cytogenet Genome Res 2013; 140:226-40. [DOI: 10.1159/000353301] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Collares-Pereira M, Matos I, Morgado-Santos M, Coelho M. Natural Pathways towards Polyploidy in Animals: TheSqualius alburnoidesFish Complex as a Model System to Study Genome Size and Genome Reorganization in Polyploids. Cytogenet Genome Res 2013; 140:97-116. [DOI: 10.1159/000351729] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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