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Small CD, Benfey TJ, Crawford BD. Tissue-specific compensatory mechanisms maintain tissue architecture and body size independent of cell size in polyploid zebrafish. Dev Biol 2024; 509:85-96. [PMID: 38387487 DOI: 10.1016/j.ydbio.2024.02.005] [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: 11/12/2022] [Revised: 01/01/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
Genome duplications and ploidy transitions have occurred in nearly every major taxon of eukaryotes, but they are far more common in plants than in animals. Due to the conservation of the nuclear:cytoplasmic volume ratio increased DNA content results in larger cells. In plants, polyploid organisms are larger than diploids as cell number remains relatively constant. Conversely, vertebrate body size does not correlate with cell size and ploidy as vertebrates compensate for increased cell size to maintain tissue architecture and body size. This has historically been explained by a simple reduction in cell number that matches the increase in cell size maintaining body size as ploidy increases, but here we show that the compensatory mechanisms that maintain body size in triploid zebrafish are tissue-specific: A) erythrocytes respond in the classical pattern with a reduced number of larger erythrocytes in circulation, B) muscle, a tissue comprised of polynucleated muscle fibers, compensates by reducing the number of larger nuclei such that myofiber and myotome size in unaffected by ploidy, and C) vascular tissue compensates by thickening blood vessel walls, possibly at the expense of luminal diameter. Understanding the physiological implications of ploidy on tissue function requires a detailed description of the specific mechanisms of morphological compensation occurring in each tissue to understand how ploidy changes affect development and physiology.
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Affiliation(s)
- C D Small
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | - T J Benfey
- Biology Department, University of New Brunswick, Fredericton, NB, Canada
| | - B D Crawford
- Biology Department, University of New Brunswick, Fredericton, NB, Canada.
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2
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Guo M, Addy GA, Yang N, Asare E, Wu H, Saleh AA, Shi S, Gao B, Song C. PiggyBac Transposon Mining in the Small Genomes of Animals. BIOLOGY 2023; 13:24. [PMID: 38248455 PMCID: PMC10813416 DOI: 10.3390/biology13010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024]
Abstract
TEs, including DNA transposons, are major contributors of genome expansions, and have played a very significant role in shaping the evolution of animal genomes, due to their capacity to jump from one genomic position to the other. In this study, we investigated the evolution landscapes of PB transposons, including their distribution, diversity, activity and structure organization in 79 species of small (compact) genomes of animals comprising both vertebrate and invertebrates. Overall, 212 PB transposon types were detected from almost half (37) of the total number of the small genome species (79) investigated. The detected PB transposon types, which were unevenly distributed in various genera and phyla, have been classified into seven distinct clades or families with good bootstrap support (>80%). The PB transposon types that were identified have a length ranging from 1.23 kb to 9.51 kb. They encode transposases of approximately ≥500 amino acids in length, and possess terminal inverted repeats (TIRs) ranging from 4 bp to 24 bp. Though some of the transposon types have long TIRs (528 bp), they still maintain the consistent and reliable 4 bp target site duplication (TSD) of TTAA. However, PiggyBac-2_Cvir transposon originating from the Crassostrea virginica species exhibits a unique TSD of TATG. The TIRs of the transposons in all the seven families display high divergence, with a highly conserved 5' end motif. The core transposase domains (DDD) were better conserved among the seven different families compared to the other protein domains, which were less prevalent in the vertebrate genome. The divergent evolution dynamics analysis also indicated that the majority of the PB transposon types identified in this study are either relatively young or old, with some being active. Additionally, numerous invasions of PB transposons were found in the genomes of both vertebrate and invertebrate animals. The data reveals that the PB superfamily is widely distributed in these species. PB transposons exhibit high diversity and activity in the small genomes of animals, and might play a crucial role in shaping the evolution of these small genomes of animals.
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Affiliation(s)
- Mengke Guo
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - George A. Addy
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Naisu Yang
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Emmanuel Asare
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Han Wu
- Department of Immunology, School of Medicine, Shenzhen University, Shenzhen 518060, China;
| | - Ahmed A. Saleh
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
- Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria City 11865, Egypt
| | - Shasha Shi
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
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3
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Kushwaha B, Nagpure NS, Srivastava S, Pandey M, Kumar R, Raizada S, Agarwal S, Singh M, Basheer VS, Kumar RG, Das P, Das SP, Patnaik S, Bit A, Srivastava SK, Vishwakarma AL, Joshi CG, Kumar D, Jena JK. Genome size estimation and its associations with body length, chromosome number and evolution in teleost fishes. Gene 2023; 864:147294. [PMID: 36858189 DOI: 10.1016/j.gene.2023.147294] [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: 09/29/2022] [Revised: 02/07/2023] [Accepted: 02/15/2023] [Indexed: 03/02/2023]
Abstract
Precise estimation of genome size (GS) is vital for various genomic studies, such as deciding genome sequencing depth, genome assembly, biodiversity documentation, evolution, genetic disorders studies, duplication events etc. Animal Genome Size Database provides GS of over 2050 fish species, which ranges from 0.35 pg in pufferfish (Tetraodon nigroviridis) to 132.83 pg in marbled lungfish (Protopterus aethiopicus). The GS of majority of the fishes inhabiting waters of Indian subcontinent are still missing. In present study, we estimated GS of 51 freshwater teleost (31 commercially important, 7 vulnerable and 13 ornamental species) that ranged from 0.58 pg in banded gourami (Trichogaster fasciata) to 1.92 pg in scribbled goby (Awaous grammepomus). Substantial variation in GS was observed within the same fish orders (0.64-1.45 pg in cypriniformes, 0.70-1.41 pg in siluriformes and 0.58-1.92 pg in perciformes). We examined the relationship between the GS, chromosome number and body length across all the fishes. Body length was found to be associated with GS, whereas no relationship was noticed between the GS and the chromosome number. The analysis using ancestral information revealed haploid chromosome number 25, 27 and 24 for the most recent common ancestor of cypriniformes, siluriformes and perciformes, respectively. The study led to generation of new records on GS of 43 fish species and revalidated records for 8 species. The finding is valuable resource for further research in the areas of fish genomics, molecular ecology and evolutionary conservation genetics.
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Affiliation(s)
- Basdeo Kushwaha
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India.
| | - Naresh S Nagpure
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India
| | - Shreya Srivastava
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India
| | - Manmohan Pandey
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India
| | - Ravindra Kumar
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India.
| | - Sudhir Raizada
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India
| | - Suyash Agarwal
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India
| | - Mahender Singh
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India
| | - Valaparamail S Basheer
- PMFGR Division, ICAR-National Bureau of Fish Genetic Resources, CMFRI Campus, Ernakulam North, P.O. Kochi, 682 018 Kerala, India
| | - Rahul G Kumar
- PMFGR Division, ICAR-National Bureau of Fish Genetic Resources, CMFRI Campus, Ernakulam North, P.O. Kochi, 682 018 Kerala, India
| | - Paramananda Das
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyanga, Bhubaneswar, 751 002 Odisha, India
| | - Sofia P Das
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyanga, Bhubaneswar, 751 002 Odisha, India
| | - Siddhi Patnaik
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyanga, Bhubaneswar, 751 002 Odisha, India
| | - Amrita Bit
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyanga, Bhubaneswar, 751 002 Odisha, India
| | - Satish Kumar Srivastava
- Experimental Field Centre, ICAR-Directorate of Coldwater Fisheries Research, Champawat, 262 523 Uttarakhand, India
| | - Achchhe L Vishwakarma
- Flow Cytometry Lab, SAIF Division, CSIR-Central Drug Research Institute, Lucknow, 226 031 Uttar Pradesh, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat 388 001, India
| | - Dinesh Kumar
- Centre for Agricultural Bio-informatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110 012, India
| | - Joy K Jena
- ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002 Uttar Pradesh, India
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Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp. Nat Commun 2022; 13:4092. [PMID: 35835759 PMCID: PMC9283417 DOI: 10.1038/s41467-022-31515-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 06/21/2022] [Indexed: 11/08/2022] Open
Abstract
Understanding genome evolution of polyploids requires dissection of their often highly similar subgenomes and haplotypes. Polyploid animal genome assemblies so far restricted homologous chromosomes to a ‘collapsed’ representation. Here, we sequenced the genome of the asexual Prussian carp, which is a close relative of the goldfish, and present a haplotype-resolved chromosome-scale assembly of a hexaploid animal. Genome-wide comparisons of the 150 chromosomes with those of two ancestral diploid cyprinids and the allotetraploid goldfish and common carp revealed the genomic structure, phylogeny and genome duplication history of its genome. It consists of 25 syntenic, homeologous chromosome groups and evolved by a recent autoploid addition to an allotetraploid ancestor. We show that de-polyploidization of the alloploid subgenomes on the individual gene level occurred in an equilibrated fashion. Analysis of the highly conserved actinopterygian gene set uncovered a subgenome dominance in duplicate gene loss of one ancestral chromosome set. The haplotype-resolved assembly of the asexual invasive Prussian carp shows six genome copies (AAABBB), evolved from two ancestral species by a recent self-addition (AB) to its hybrid-tetraploid (AABB) goldfish ancestor. Equilibrated gene loss led to subgenome dominance.
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Wanzenböck J, Hopfinger M, Wanzenböck S, Fuxjäger L, Rund H, Lamatsch DK. First successful hybridization experiment between native European weatherfish (Misgurnus fossilis) and non-native Oriental weatherfish (M. anguillicaudatus) reveals no evidence for postzygotic barriers. NEOBIOTA 2021. [DOI: 10.3897/neobiota.69.67708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The European weatherfish Misgurnus fossilis (Linnaeus, 1758) is a threatened freshwater species in large parts of Europe and might come under pressure from currently establishing exotic weatherfish species. Additional threats might arise if those species hybridize which has been questioned in previous research. Regarding the hybridization of M. fossilis × M. anguillicaudatus (Cantor, 1842), we demonstrate that despite the considerable genetic distance between parental species, the estimated long divergence time and different ploidy levels do not represent a postzygotic barrier for hybridization of the European and Oriental weatherfish. The paternal species can be easily differentiated based on external pigment patterns with hybrids showing intermediate patterns. No difference in standard metabolic rate, indicating a lack of hybrid vigour, renders predictions of potential threats to the European weatherfish from hybridization with the Oriental weatherfish difficult. Therefore, the genetic and physiological basis of invasiveness via hybridization remains elusive in Misgurnus species and requires further research. The existence of prezygotic reproductive isolation mechanisms and the fertility of F1 hybrids remains to be tested to predict the potential threats of globally invasive Oriental weatherfish species.
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Lehmann R, Kovařík A, Ocalewicz K, Kirtiklis L, Zuccolo A, Tegner JN, Wanzenböck J, Bernatchez L, Lamatsch DK, Symonová R. DNA Transposon Expansion is Associated with Genome Size Increase in Mudminnows. Genome Biol Evol 2021; 13:6380143. [PMID: 34599322 PMCID: PMC8557787 DOI: 10.1093/gbe/evab228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2021] [Indexed: 12/20/2022] Open
Abstract
Genome sizes of eukaryotic organisms vary substantially, with whole-genome duplications (WGD) and transposable element expansion acting as main drivers for rapid genome size increase. The two North American mudminnows, Umbra limi and Umbra pygmaea, feature genomes about twice the size of their sister lineage Esocidae (e.g., pikes and pickerels). However, it is unknown whether all Umbra species share this genome expansion and which causal mechanisms drive this expansion. Using flow cytometry, we find that the genome of the European mudminnow is expanded similarly to both North American species, ranging between 4.5 and 5.4 pg per diploid nucleus. Observed blocks of interstitially located telomeric repeats in U. limi suggest frequent Robertsonian rearrangements in its history. Comparative analyses of transcriptome and genome assemblies show that the genome expansion in Umbra is driven by the expansion of DNA transposon and unclassified repeat sequences without WGD. Furthermore, we find a substantial ongoing expansion of repeat sequences in the Alaska blackfish Dallia pectoralis, the closest relative to the family Umbridae, which might mark the beginning of a similar genome expansion. Our study suggests that the genome expansion in mudminnows, driven mainly by transposon expansion, but not WGD, occurred before the separation into the American and European lineage.
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Affiliation(s)
- Robert Lehmann
- Division of Biological and Environmental Sciences & Engineering, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Aleš Kovařík
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Science, Brno, Czech Republic
| | - Konrad Ocalewicz
- Department of Marine Biology and Ecology, Institute of Oceanography, Faculty of Oceanography and Geography, University of Gdansk, Gdansk, Poland
| | - Lech Kirtiklis
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury, Olsztyn, Poland
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.,Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Jesper N Tegner
- Division of Biological and Environmental Sciences & Engineering, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Josef Wanzenböck
- Research Department for Limnology Mondsee, University of Innsbruck, Mondsee, Austria
| | - Louis Bernatchez
- Department of Biology, IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, QC, Canada
| | - Dunja K Lamatsch
- Research Department for Limnology Mondsee, University of Innsbruck, Mondsee, Austria
| | - Radka Symonová
- Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technische Universität München, Freising, Germany.,Department of Biology, Faculty of Biology, University of Hradec Kralove, Czech Republic
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Stöck M, Dedukh D, Reifová R, Lamatsch DK, Starostová Z, Janko K. Sex chromosomes in meiotic, hemiclonal, clonal and polyploid hybrid vertebrates: along the 'extended speciation continuum'. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200103. [PMID: 34304588 PMCID: PMC8310718 DOI: 10.1098/rstb.2020.0103] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 12/15/2022] Open
Abstract
We review knowledge about the roles of sex chromosomes in vertebrate hybridization and speciation, exploring a gradient of divergences with increasing reproductive isolation (speciation continuum). Under early divergence, well-differentiated sex chromosomes in meiotic hybrids may cause Haldane-effects and introgress less easily than autosomes. Undifferentiated sex chromosomes are more susceptible to introgression and form multiple (or new) sex chromosome systems with hardly predictable dominance hierarchies. Under increased divergence, most vertebrates reach complete intrinsic reproductive isolation. Slightly earlier, some hybrids (linked in 'the extended speciation continuum') exhibit aberrant gametogenesis, leading towards female clonality. This facilitates the evolution of various allodiploid and allopolyploid clonal ('asexual') hybrid vertebrates, where 'asexuality' might be a form of intrinsic reproductive isolation. A comprehensive list of 'asexual' hybrid vertebrates shows that they all evolved from parents with divergences that were greater than at the intraspecific level (K2P-distances of greater than 5-22% based on mtDNA). These 'asexual' taxa inherited genetic sex determination by mostly undifferentiated sex chromosomes. Among the few known sex-determining systems in hybrid 'asexuals', female heterogamety (ZW) occurred about twice as often as male heterogamety (XY). We hypothesize that pre-/meiotic aberrations in all-female ZW-hybrids present Haldane-effects promoting their evolution. Understanding the preconditions to produce various clonal or meiotic allopolyploids appears crucial for insights into the evolution of sex, 'asexuality' and polyploidy. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Dmitrij Dedukh
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, 277 21 Libechov, Czech Republic
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Dunja K. Lamatsch
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Zuzana Starostová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Karel Janko
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, 277 21 Libechov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 03 Ostrava, Czech Republic
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Hubálek M, Flajšhans M. Simple Field Storage of Fish Samples for Measurement of DNA Content by Flow Cytometry. Cytometry A 2021; 99:743-752. [PMID: 33215865 PMCID: PMC8359303 DOI: 10.1002/cyto.a.24271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/28/2020] [Accepted: 11/16/2020] [Indexed: 11/14/2022]
Abstract
Flow cytometry is an effective and widely used tool for determination of ploidy in fish, but it is not always possible to access the fresh samples for analysis. We investigated the potential for extended storage of fish tissue with sterlet and tench as representative species of Chondrostei and Teleostei, using blood and fin of subadult/adult specimens and tail of larvae. Thirteen procedures for extending storage, selected for rapidity and simplicity in both field and laboratory conditions, were tested for each tissue sample. Flow cytometry was applied to fresh tissue immediately after sampling and to tissue subjected to experimental protocols, always along with species-specific standard, after 1, 5, and 10 days storage at 0-4°C or freezing at -80°C. The fluorochrome 4',6-diamidine-2'-phenylindole dihydrochloride was used with excitation/emission maximum 358/461 nm. Based on the measurability of stored samples, evaluation of directly measured coefficients of variation of their DNA peaks and the changes in fluorescence intensity compared to fresh tissue, optimal procedures for extended storage of the selected tissue types of the model species are suggested. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Martin Hubálek
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of HydrocenosesZátiší 728/II, 389 25VodňanyCzech Republic
| | - Martin Flajšhans
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of HydrocenosesZátiší 728/II, 389 25VodňanyCzech Republic
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10
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Bayona-Vásquez NJ, Glenn TC, Kieran TJ, Pierson TW, Hoffberg SL, Scott PA, Bentley KE, Finger JW, Louha S, Troendle N, Diaz-Jaimes P, Mauricio R, Faircloth BC. Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD). PeerJ 2019; 7:e7724. [PMID: 31616583 PMCID: PMC6791345 DOI: 10.7717/peerj.7724] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/22/2019] [Indexed: 11/24/2022] Open
Abstract
Molecular ecologists frequently use genome reduction strategies that rely upon restriction enzyme digestion of genomic DNA to sample consistent portions of the genome from many individuals (e.g., RADseq, GBS). However, researchers often find the existing methods expensive to initiate and/or difficult to implement consistently, especially because it is difficult to multiplex sufficient numbers of samples to fill entire sequencing lanes. Here, we introduce a low-cost and highly robust approach for the construction of dual-digest RADseq libraries that build on adapters and primers designed in Adapterama I. Major features of our method include: (1) minimizing the number of processing steps; (2) focusing on a single strand of sample DNA for library construction, allowing the use of a non-phosphorylated adapter on one end; (3) ligating adapters in the presence of active restriction enzymes, thereby reducing chimeras; (4) including an optional third restriction enzyme to cut apart adapter-dimers formed by the phosphorylated adapter, thus increasing the efficiency of adapter ligation to sample DNA, which is particularly effective when only low quantity/quality DNA samples are available; (5) interchangeable adapter designs; (6) incorporating variable-length internal indexes within the adapters to increase the scope of sample indexing, facilitate pooling, and increase sequence diversity; (7) maintaining compatibility with universal dual-indexed primers and thus, Illumina sequencing reagents and libraries; and, (8) easy modification for the identification of PCR duplicates. We present eight adapter designs that work with 72 restriction enzyme combinations. We demonstrate the efficiency of our approach by comparing it with existing methods, and we validate its utility through the discovery of many variable loci in a variety of non-model organisms. Our 2RAD/3RAD method is easy to perform, has low startup costs, has increased utility with low-concentration input DNA, and produces libraries that can be highly-multiplexed and pooled with other Illumina libraries.
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Affiliation(s)
- Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
| | - Todd W. Pierson
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
| | - Sandra L. Hoffberg
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States of America
| | - Peter A. Scott
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States of America
- Current affiliation: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States of America
| | - Kerin E. Bentley
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: LeafWorks Inc., Sebastopol, CA, United States of America
| | - John W. Finger
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| | - Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Nicholas Troendle
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Natural, Health, and Mathematical Sciences, MidAmerica Nazarene University, Olathe, KS, United States of America
| | - Pindaro Diaz-Jaimes
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rodney Mauricio
- Department of Genetics, University of Georgia, Athens, GA, United States of America
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, United States of America
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Morgado-Santos M, Magalhães MF, Vicente L, Collares-Pereira MJ. Mate choice driven by genome in an allopolyploid fish complex. Behav Ecol 2018. [DOI: 10.1093/beheco/ary117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- M Morgado-Santos
- Centro de Ecologia, Evolução e Alterações Climáticas (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - M F Magalhães
- Centro de Ecologia, Evolução e Alterações Climáticas (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - L Vicente
- Centro de Filosofia das Ciências da Universidade de Lisboa (CFCUL), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - M J Collares-Pereira
- Centro de Ecologia, Evolução e Alterações Climáticas (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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12
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Hoffberg SL, Troendle NJ, Glenn TC, Mahmud O, Louha S, Chalopin D, Bennetzen JL, Mauricio R. A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library. G3 (BETHESDA, MD.) 2018; 8:1855-1861. [PMID: 29703783 PMCID: PMC5982815 DOI: 10.1534/g3.118.200101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/19/2018] [Indexed: 11/18/2022]
Abstract
The western mosquitofish, Gambusia affinis, is a freshwater poecilid fish native to the southeastern United States but with a global distribution due to widespread human introduction. Gambusia affinis has been used as a model species for a broad range of evolutionary and ecological studies. We sequenced the genome of a male G. affinis to facilitate genetic studies in diverse fields including invasion biology and comparative genetics. We generated Illumina short read data from paired-end libraries and in vitro proximity-ligation libraries. We obtained 54.9× coverage, N50 contig length of 17.6 kb, and N50 scaffold length of 6.65 Mb. Compared to two other species in the Poeciliidae family, G. affinis has slightly fewer genes that have shorter total, exon, and intron length on average. Using a set of universal single-copy orthologs in fish genomes, we found 95.5% of these genes were complete in the G. affinis assembly. The number of transposable elements in the G. affinis assembly is similar to those of closely related species. The high-quality genome sequence and annotations we report will be valuable resources for scientists to map the genetic architecture of traits of interest in this species.
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Affiliation(s)
| | | | - Travis C Glenn
- Department of Genetics
- Department of Environmental Health Science
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602
| | - Ousman Mahmud
- Department of Genetics
- Department of Computational Biology
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105
| | - Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602
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Morgado-Santos M, Carona S, Vicente L, Collares-Pereira MJ. First empirical evidence of naturally occurring androgenesis in vertebrates. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170200. [PMID: 28573029 PMCID: PMC5451830 DOI: 10.1098/rsos.170200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
Androgenesis among vertebrates is considered a rare phenomenon, with some cases reported so far, but linked to experiments involving gamete manipulation (artificial androgenesis). Herein, we report the first empirical evidence of the natural occurrence of spontaneous androgenesis in a vertebrate, the Squalius alburnoides allopolyploid complex. A genetically screened random sample of a natural population was allowed to reproduce in an isolated pond without any human interference, and the viable offspring obtained was later analysed for paternity. Both nuclear and mitochondrial markers showed that the only allodiploid fish found among all the allotriploid offspring was androgenetically produced by an allodiploid male. This specimen had no female nuclear genomic input, and the sequence of the mitochondrial fragment examined differed from that of the male progenitor, matching one of the parental females available in the pond, probably the mother. The possible role of androgenesis in the reproductive dynamics of this highly successful vertebrate complex is discussed.
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Affiliation(s)
- Miguel Morgado-Santos
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Sara Carona
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Luís Vicente
- Centro de Filosofia das Ciências da Universidade de Lisboa (CFCUL), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Maria João Collares-Pereira
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Universidade de Lisboa, 1749-016 Lisboa, Portugal
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14
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Morgado-Santos M, Carona S, Magalhães MF, Vicente L, Collares-Pereira MJ. Reproductive dynamics shapes genomotype composition in an allopolyploid complex. Proc Biol Sci 2016; 283:20153009. [PMID: 27226473 PMCID: PMC4892787 DOI: 10.1098/rspb.2015.3009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/27/2016] [Indexed: 11/12/2022] Open
Abstract
Hybrid complexes are composed of organisms with multiple combinations of parental genomes (genomotypes) that interconnect through nets of crosses. Although several such complexes are well established without speciation or extinction, mechanisms shaping their dynamics remain poorly understood. In this study, we quantified the reproductive success of the allopolyploid Iberian fish Squalius alburnoides in experimental free-access and directional crosses involving the most common genomotypes. Specifically, we analysed the paternity of the offspring produced when females had free access to male genomotypes and quantified variations in egg allocation, fertilization rate, and offspring survival among crosses involving each male genomotype. The composition of the offspring produced from free-access crosses varied significantly from that expected from random mating, suggesting that offspring production and viability are not independent of parental male genomotype. Moreover, directional crosses producing the genomotype most commonly found in wild populations appeared to be the most successful, with females laying more eggs, and fertilization rate and offspring survival being the highest. These results suggest that reproductive dynamics plays a relevant role in structuring the genomotype composition of populations and opens a path to future research on the ecology and evolutionary biology of allopolyploids and their multiplicity of possible evolutionary pathways.
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Affiliation(s)
- M Morgado-Santos
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - S Carona
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - M F Magalhães
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - L Vicente
- Centro de Filosofia das Ciências da Universidade de Lisboa (CFCUL), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - M J Collares-Pereira
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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15
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Morgado-Santos M, Pereira HM, Vicente L, Collares-Pereira MJ. Mate Choice Drives Evolutionary Stability in a Hybrid Complex. PLoS One 2015; 10:e0132760. [PMID: 26181664 PMCID: PMC4504517 DOI: 10.1371/journal.pone.0132760] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 06/17/2015] [Indexed: 01/09/2023] Open
Abstract
Previous studies have shown that assortative mating acts as a driver of speciation by countering hybridization between two populations of the same species (pre-zygotic isolation) or through mate choice among the hybrids (hybrid speciation). In both speciation types, assortative mating promotes speciation over a transient hybridization stage. We studied mate choice in a hybrid vertebrate complex, the allopolyploid fish Squalius alburnoides. This complex is composed by several genomotypes connected by an intricate reproductive dynamics. We developed a model that predicts the hybrid complex can persist when females exhibit particular mate choice patterns. Our model is able to reproduce the diversity of population dynamic outcomes found in nature, namely the dominance of the triploids and the dominance of the tetraploids, depending on female mate choice patterns and frequency of the parental species. Experimental mate choice trials showed that females exhibit the preferences predicted by the model. Thus, despite the known role of assortative mating in driving speciation, our findings suggest that certain mate choice patterns can instead hinder speciation and support the persistence of hybrids over time without speciation or extinction.
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Affiliation(s)
- Miguel Morgado-Santos
- CE3C: Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, 1749–016, Lisboa, Portugal
- CESAM-Lisboa: Centro de Estudos do Ambiente e do Mar–Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, 1749–016, Lisboa, Portugal
- * E-mail:
| | - Henrique Miguel Pereira
- CE3C: Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, 1749–016, Lisboa, Portugal
- iDiv: German Centre for Integrative Biodiversity Research, Halle-Jena-Leipzig, Germany
| | - Luís Vicente
- CESAM-Lisboa: Centro de Estudos do Ambiente e do Mar–Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, 1749–016, Lisboa, Portugal
- CFCUL: Centro de Filosofia das Ciências da Universidade de Lisboa, Faculdade de Ciências da Universidade de Lisboa, 1749–016, Lisboa, Portugal
| | - Maria João Collares-Pereira
- CE3C: Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, 1749–016, Lisboa, Portugal
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García G, Gutiérrez V, Ríos N, Turner B, Santiñaque F, López-Carro B, Folle G. Burst speciation processes and genomic expansion in the neotropical annual killifish genus Austrolebias (Cyprinodontiformes, Rivulidae). Genetica 2014; 142:87-98. [DOI: 10.1007/s10709-014-9756-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 01/10/2014] [Indexed: 10/25/2022]
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17
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Zhu D, Song W, Yang K, Cao X, Gul Y, Wang W. Flow cytometric determination of genome size for eight commercially important fish species in China. In Vitro Cell Dev Biol Anim 2012; 48:507-17. [PMID: 22956044 DOI: 10.1007/s11626-012-9543-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Accepted: 08/03/2012] [Indexed: 11/30/2022]
Abstract
The genome size (C value) of eight commercially important fish species in China was measured using flow cytometry. Chicken (Gallus domesticus) erythrocytes were used as reference cells. When using propidium iodide (PI) as the fluorescent dye, genome sizes were 1.09 ± 0.08, 2.75 ± 0.12, 1.05 ± 0.05, 1.35 ± 0.11, 0.99 ± 0.05, 0.90 ± 0.08, 0.90 ± 0.07, and 0.88 ± 0.07 pg for Japanese eel (Anguilla japonica), mullet (Myxocyprinus asiaticus), yellowcheek carp (Elopichthys bambusa), blunt snout bream (Megalobrama amblycephala), yellow catfish (Pelteobagrus fulvidraco), ricefield eel (Monopterus albus), mandarin fish (Siniperca chuatsi), and snakehead (Ophicephalus argus), respectively. However, genome sizes were 1.25 ± 0.00, 3.08 ± 0.02, 1.25 ± 0.00, 1.57 ± 0.01, 0.96 ± 0.01, 1.00 ± 0.01, 0.91 ± 0.01, and 0.89 ± 0.01 pg for these fishes, respectively, when 4', 6-diamidino-2-phenylindole (DAPI) was used as the fluorescent dye. Regardless of the dye used, the more evolutionarily advanced species had a smaller genome size than those with a lower evolutionary status. For each species, we also measured the size of erythrocytes and their nucleus and evaluated the relationships between erythrocyte size, nucleus size, chromosome number, and genome size. Genome size was positively correlated with erythrocyte nucleus size and chromosome number when using PI as the fluorescent dye, but it was only correlated with erythrocyte nucleus size when DAPI was used.
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Affiliation(s)
- Dongmei Zhu
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430-070, China
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18
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Liu S, Hui TH, Tan SL, Hong Y. Chromosome evolution and genome miniaturization in minifish. PLoS One 2012; 7:e37305. [PMID: 22615970 PMCID: PMC3353929 DOI: 10.1371/journal.pone.0037305] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 04/19/2012] [Indexed: 11/18/2022] Open
Abstract
Background Paedocypris is a newly established genus of fish in Southeast Asia. Paedocypris is characterized by several unique features, including a tiny adult size (thus named miniature fish or minifish), fragmentary habitats of acidic peat blackwater swamps, an unusual reproduction mode and truncated development. These peculiarities lend themselves excellent for studying chromosome evolution and rapid speciation in vertebrates but also make them highly controversial for the phylogenetic position. Methodology and Principal Findings We have established an organ procedure to prepare chromosome spreads from tiny organs of minifish and performed a cytogenetic study on two species of the genus Paedocypris, namely P. carbunculus (Pc) and P. sp. “Singkep” (Ps). We found 30 and 34 chromosomes in diploid cells of Pc and Ps, respectively, which are unusual in teleost fishes. The diploid metaphase has 5 pairs of metacentrics and 7 pairs of subtelocentrics in Pc compared to 3 pairs of metacentrics and 11 pairs of subtelocentrics in Ps, whereas the haploid metaphase contains 5 metacentrics and 7 subtelocentrics in Pc compared to 3 metacentrics and 11 subtelocentrics Ps. Chromosome behavior in first meiosis revealed the presence of a chromosomal ring consisting of 2 metacentrics in Pc, suggesting that centric fusion rather than fission was responsible for the karyotypic evolution from Ps to Pc. Flow cytometry revealed that Pc had a 45% nuclear staining intensity relative to medaka whose genome is 700 Mb in size and contains 0.81 pg DNA. The Pc genome should have 315 Mb in length and 0.36 pg of DNA, which represent one of the smallest values in vertebrates, suggesting genome miniaturization in this organism. Conclusions Our data demonstrate that gross chromosome rearrangements and genome miniaturization have accompanied the evolution of Paedocypris fishes. Our data also place Paedocypris outside currently described taxa of the Cypriniformes.
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Affiliation(s)
- Shaojun Liu
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Tan Heok Hui
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Sze Ley Tan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yunhan Hong
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, China
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- * E-mail:
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19
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Deguchi T, Fujimori KE, Kawasaki T, Maruyama K, Yuba S. In vivo visualization of the lymphatic vessels in pFLT4-EGFP transgenic medaka. Genesis 2012; 50:625-34. [PMID: 22334443 DOI: 10.1002/dvg.22018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 01/18/2012] [Accepted: 02/06/2012] [Indexed: 12/30/2022]
Abstract
Feline McDonough Sarcoma (FMS)-like tyrosine kinase 4 (FLT4) is a marker for lymphatic vessels and some high endothelial venules in human adult tissues. We generated a transgenic medaka fish in which the lymphatic vessels and some blood vessels are visible in vivo by transferring the promoter of medaka flt4 driving the expression of enhanced green fluorescent protein (EGFP) using a see-through medaka line. To do this, we identified and cloned medaka flt4 and generated a construct in which the promoter was the 4-kb region upstream of the translation initiation site. The fluorescent signal of EGFP could be observed with little background, and the expression pattern correlated well with that of flt4 determined by whole-mount RNA in situ hybridization. Because a see-through medaka line is transparent until adult, the model is useful for visualizing the lymphatic vessels not only in embryo and fry but also in adult. This model will be a useful tool for analyzing lymphatic development.
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Affiliation(s)
- Tomonori Deguchi
- Health Research Institute (HRI), National Institute of Advanced Industrial Science and Technology (AIST), Amagasaki, Hyogo, Japan.
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20
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Filipiak M, Tylko G, Kilarski W. Flow cytometric determination of genome size in European sunbleak Leucaspius delineatus (Heckel, 1843). FISH PHYSIOLOGY AND BIOCHEMISTRY 2012; 38:355-362. [PMID: 21614549 PMCID: PMC3309147 DOI: 10.1007/s10695-011-9512-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 05/13/2011] [Indexed: 05/30/2023]
Abstract
The aim of this study was to compare DNA content in hepatocyte and erythrocyte nuclei of the European sunbleak, Leucaspius delineatus, in relation to nuclear and cell size by means of flow cytometry and fluorescence microscopy. The DNA standards, chicken and rainbow trout erythrocytes, were prepared in parallel with both cell types, with initial separation of liver cells in pepsin solution followed by cell filtering. Standards and investigated cells were stained with a mixture of propidium iodide, citric acid, and Nonidet P40 in the presence of RNAse, and fluorescence of at least 50,000 nuclei was analyzed by flow cytometry. Average cell size was determined by flow cytometry, using fresh cell suspension in relation to latex beads of known diameter. The size of nuclei was examined on the basis of digital micrographs obtained by fluorescence microscopy after nuclei staining with DAPI. The sunbleak's erythrocyte nuclei contain 2.25 ± 0.06 pg of DNA, whereas the hepatocyte nuclei contain 2.46 ± 0.06 pg of DNA. This difference in DNA content was determined spectroscopically using isolated DNA from the two cell types. The modal diameters of the erythrocytes and hepatocytes were estimated to be 5.1 ± 0.2 and 22.3 ± 5.0 μm, respectively, and the corresponding modal dimensions of their nuclei (measured as surface area) were 15.2 and 21.4 μm(2), respectively. The nucleoplasmic index, as calculated from diameters estimated from surface area of nuclear profiles, was 2.51 for the erythrocytes compared with 0.08 for hepatocytes.
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Affiliation(s)
- Marta Filipiak
- Department of Cytology and Histology, Institute of Zoology, Jagiellonian University, 6 Ingardena, 30-060 Krakow, Poland
| | - Grzegorz Tylko
- Department of Cytology and Histology, Institute of Zoology, Jagiellonian University, 6 Ingardena, 30-060 Krakow, Poland
| | - Wincenty Kilarski
- Department of Cytology and Histology, Institute of Zoology, Jagiellonian University, 6 Ingardena, 30-060 Krakow, Poland
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Lamatsch DK, Trifonov V, Schories S, Epplen JT, Schmid M, Schartl M. Isolation of a cancer-associated microchromosome in the sperm-dependent parthenogen Poecilia formosa. Cytogenet Genome Res 2011; 135:135-42. [PMID: 21952475 DOI: 10.1159/000331271] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2011] [Indexed: 11/19/2022] Open
Abstract
In the asexual all-female fish species Poecilia formosa, the Amazon molly, supernumerary chromosomes have frequently been found in both laboratory-reared and wild-caught individuals. While wild-caught individuals with B chromosomes are phenotypically indifferent from conspecifics, individuals carrying B chromosomes from recent introgression events in the laboratory show phenotypic changes. Former analyses showed that the expression of a pigment cell locus is associated with the presence of these B chromosomes. In addition, they contain a so far unidentified locus that confers a higher susceptibility to tumor formation in the presence of pigmentation pattern. Isolation by microdissection and hybridization to metaphase chromosomes revealed that they contain one or several sequences with similarity to a highly repetitive pericentromeric and subtelomeric sequence in A chromosomes. Isolation of one particular sequence by AFLP showed that the B chromosomes contain at least 1 copy of an A-chromosomal region which is highly conserved in the whole genus Poecilia, i.e. more than 5 million years old. We propose it to be a single copy sequence.
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Affiliation(s)
- D K Lamatsch
- Physiological Chemistry I, Biocenter, University of Würzburg, Würzburg, Germany
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22
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Lamatsch DK, Stöck M, Fuchs R, Döbler M, Wacker R, Parzefall J, Schlupp I, Schartl M. Morphology, testes development and behaviour of unusual triploid males in microchromosome-carrying clones of Poecilia formosa. JOURNAL OF FISH BIOLOGY 2010; 77:1459-1487. [PMID: 21078013 DOI: 10.1111/j.1095-8649.2010.02766.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In a microchromosome-carrying laboratory stock of the normally all-female Amazon molly Poecilia formosa triploid individuals were obtained, all of which spontaneously developed into males. A comparison of morphology of the external and internal insemination apparatus and the gonads, sperm ploidy and behaviour, to laboratory-bred F(1) hybrids revealed that the triploid P. formosa males, though producing mostly aneuploid sperm, are partly functional males that differ mainly in sperm maturation and sexual motivation from gonochoristic P. formosa males.
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Affiliation(s)
- D K Lamatsch
- Lehrstuhl für Physiologische Chemie I, Theodor-Boveri-Institute, Biozentrum, Am Hubland, D-97074 Würzburg, Germany.
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23
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STÖCK MATTHIAS, LAMPERT KATHRINP, MÖLLER DIRK, SCHLUPP INGO, SCHARTL MANFRED. Monophyletic origin of multiple clonal lineages in an asexual fish (Poecilia formosa). Mol Ecol 2010; 19:5204-15. [DOI: 10.1111/j.1365-294x.2010.04869.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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24
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Juchno D, Lackowska B, Boron A, Kilarski W. DNA content of hepatocyte and erythrocyte nuclei of the spined loach (Cobitis taenia L.) and its polyploid forms. FISH PHYSIOLOGY AND BIOCHEMISTRY 2010; 36:523-529. [PMID: 19377846 DOI: 10.1007/s10695-009-9322-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 03/24/2009] [Indexed: 05/27/2023]
Abstract
We analyzed the DNA content of hepatocyte and erythrocyte nuclei of the spined loach Cobitis taenia (diploid) and its allopolyploid forms. Twenty triploid females and one tetraploid were used. At least 20,000 hepatocyte and erythrocyte nuclei were acquired and analyzed by flow cytometry. C. taenia erythrocyte nuclei contain 3.15 +/- 0.21 pg of DNA and the hepatocyte nuclei 4.45 +/- 0.46 pg of DNA. Triploid Cobitis have 5.08 +/- 0.41 pg of DNA in erythrocyte nuclei and 6.11 +/- 0.40 pg of DNA in hepatocyte nuclei, whereas the tetraploid erythrocyte and hepatocyte nuclei contained 6.60 and 7.40 pg of DNA, respectively. In general, the DNA contents correlate positively with the ploidy level of the fish investigated. The DNA content variation in the hepatocyte and erythrocyte nuclei may be due to differences in extent of chromatin condensation, which is more pronounced in the erythrocyte than hepatocyte nuclei, or to the several orders of ploidy that occur in the parenchymal liver cells.
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Affiliation(s)
- Dorota Juchno
- Department of Zoology, University of Warmia and Mazury, 5 Oczapowskiego st, 10-718, Olsztyn, Poland
| | - Bozena Lackowska
- Department of Cancer Pathology, Oncology Center, 11 Garncarska st, 31-115, Krakow, Poland
| | - Alicja Boron
- Department of Zoology, University of Warmia and Mazury, 5 Oczapowskiego st, 10-718, Olsztyn, Poland
| | - Wincenty Kilarski
- Department of Cytology and Histology, Institute of Zoology, Jagiellonian University, 6 Ingardena st, 30-060, Krakow, Poland.
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Stöck M, Ustinova J, Lamatsch DK, Schartl M, Perrin N, Moritz C. A VERTEBRATE REPRODUCTIVE SYSTEM INVOLVING THREE PLOIDY LEVELS: HYBRID ORIGIN OF TRIPLOIDS IN A CONTACT ZONE OF DIPLOID AND TETRAPLOID PALEARCTIC GREEN TOADS (BUFO VIRIDIS SUBGROUP)*. Evolution 2009; 64:944-59. [DOI: 10.1111/j.1558-5646.2009.00876.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Tripathi N, Hoffmann M, Willing EM, Lanz C, Weigel D, Dreyer C. Genetic linkage map of the guppy, Poecilia reticulata, and quantitative trait loci analysis of male size and colour variation. Proc Biol Sci 2009; 276:2195-208. [PMID: 19324769 DOI: 10.1098/rspb.2008.1930] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report construction of a genetic linkage map of the guppy genome using 790 single nucleotide polymorphism markers, integrated from six mapping crosses. The markers define 23 linkage groups (LGs), corresponding to the known haploid number of guppy chromosomes. The map, which spans a genetic length of 899 cM, includes 276 markers linked to expressed genes (expressed sequence tag), which have been used to derive broad syntenic relationships of guppy LGs with medaka chromosomes. This combined linkage map should facilitate the advancement of genetic studies for a wide variety of complex adaptive phenotypes relevant to natural and sexual selection in this species. We have used the linkage data to predict quantitative trait loci for a set of variable male traits including size and colour pattern. Contributing loci map to the sex LG for many of these traits.
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Affiliation(s)
- Namita Tripathi
- Department of Molecular Biology, Max Plank Institute for Developmental Biology, 72076 Tübingen, Germany
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27
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Reichwald K, Lauber C, Nanda I, Kirschner J, Hartmann N, Schories S, Gausmann U, Taudien S, Schilhabel MB, Szafranski K, Glöckner G, Schmid M, Cellerino A, Schartl M, Englert C, Platzer M. High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research. Genome Biol 2009; 10:R16. [PMID: 19210790 PMCID: PMC2688266 DOI: 10.1186/gb-2009-10-2-r16] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Revised: 01/26/2009] [Accepted: 02/11/2009] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The annual fish Nothobranchius furzeri is the vertebrate with the shortest known life span in captivity. Fish of the GRZ strain live only three to four months under optimal laboratory conditions, show explosive growth, early sexual maturation and age-dependent physiological and behavioral decline, and express aging related biomarkers. Treatment with resveratrol and low temperature significantly extends the maximum life span. These features make N. furzeri a promising new vertebrate model for age research. RESULTS To contribute to establishing N. furzeri as a new model organism, we provide a first insight into its genome and a comparison to medaka, stickleback, tetraodon and zebrafish. The N. furzeri genome contains 19 chromosomes (2n = 38). Its genome of between 1.6 and 1.9 Gb is the largest among the analyzed fish species and has, at 45%, the highest repeat content. Remarkably, tandem repeats comprise 21%, which is 4-12 times more than in the other four fish species. In addition, G+C-rich tandem repeats preferentially localize to centromeric regions. Phylogenetic analysis based on coding sequences identifies medaka as the closest relative. Genotyping of an initial set of 27 markers and multi-locus fingerprinting of one microsatellite provides the first molecular evidence that the GRZ strain is highly inbred. CONCLUSIONS Our work presents a first basis for systematic genomic and genetic analyses aimed at understanding the mechanisms of life span determination in N. furzeri.
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Affiliation(s)
- Kathrin Reichwald
- Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr,, 07745 Jena, Germany.
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28
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Koga A, Cheah FSH, Hamaguchi S, Yeo GH, Chong SS. Germline transgenesis of zebrafish using the medaka Tol1 transposon system. Dev Dyn 2009; 237:2466-74. [PMID: 18729212 DOI: 10.1002/dvdy.21688] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Tol1 is a DNA-based transposable element first identified from an albino mutant medaka fish. It has been demonstrated to function as an efficient gene transfer vector in mammalian cells. We now demonstrate Tol1 germline transgenesis in zebrafish. A construct containing the green fluorescence protein (GFP) reporter gene inserted between the Tol1 arms was microinjected together with Tol1 transposase mRNA into fertilized eggs. Sustained GFP expression was observed in 88% of 1-month-old fish, suggesting efficient transposon integration into somatic cells. Eleven of 24 adult GFP-positive fish yielded GFP-positive progeny. Sequencing analysis of Tol1 insertion sites in GFP-positive progeny confirmed Tol1 transposition-mediated integrations into zebrafish chromosomes. We also observed functional independence of the Tol1 transposase-substrate system from that of Tol2, another medaka-derived transposon. Coupled with its previously demonstrated maximal cargo capacity of >20 kb, Tol1 could serve as a useful addition to the zebrafish genetic engineering toolbox.
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Affiliation(s)
- Akihiko Koga
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
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29
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Schlupp I. Chapter 5 Behavior of Fishes in the Sexual/Unisexual Mating System of the Amazon Molly (Poecilia formosa). ADVANCES IN THE STUDY OF BEHAVIOR 2009. [DOI: 10.1016/s0065-3454(09)39005-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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30
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PARENTI LYNNER. A phylogenetic analysis and taxonomic revision of ricefishes, Oryzias and relatives (Beloniformes, Adrianichthyidae). Zool J Linn Soc 2008. [DOI: 10.1111/j.1096-3642.2008.00417.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Choleva L, Apostolou A, Rab P, Janko K. Making it on their own: sperm-dependent hybrid fishes (Cobitis) switch the sexual hosts and expand beyond the ranges of their original sperm donors. Philos Trans R Soc Lond B Biol Sci 2008; 363:2911-9. [PMID: 18508748 DOI: 10.1098/rstb.2008.0059] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Interspecific hybridization may result in asexual hybrid lineages that reproduce via parthenogenesis. Contrary to true parthenogens, sperm-dependent asexuals (gynogens and hybridogens) are restricted to the range of bisexual species, generally the parental taxa, by their need for a sperm donor. It has been documented that asexual lineages may rarely use sperm from a non-parental species or even switch a host. The available literature reports do not allow distinguishing, between whether such host switches arise by the expansion of asexuals out of their parental's range (and into that of another's) or by the local extinction of a parental population followed by a host switch. The present study combines new and previously collected data on the distribution and history of gynogenetic spined loaches (Cobitis) of hybrid origin. We identified at least three clonal lineages that have independently switched their sperm dependency to different non-parental Cobitis species, and in cases incorporated their genomes. Our current knowledge of European Cobitis species and their hybrids suggests that this pattern most probably results from the expansion of gynogenetic lineages into new areas. Such expansion was independent of the original parental species. This suggests that sperm dependence is not as restrictive to geographical expansion when compared with true parthenogenesis as previously thought.
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Affiliation(s)
- Lukás Choleva
- Department of Vertebrate Evolutionary Biology and Genetics, Institute of Animal Physiology and Genetics, AS CR, v.v.i., Libechov 277 21, Czech Republic.
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32
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Diploid Amazon mollies (Poecilia formosa) show a higher fitness than triploids in clonal competition experiments. Evol Ecol 2008. [DOI: 10.1007/s10682-008-9264-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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33
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Loewe L, Lamatsch DK. Quantifying the threat of extinction from Muller's ratchet in the diploid Amazon molly (Poecilia formosa). BMC Evol Biol 2008; 8:88. [PMID: 18366680 PMCID: PMC2292145 DOI: 10.1186/1471-2148-8-88] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Accepted: 03/19/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Amazon molly (Poecilia formosa) is a small unisexual fish that has been suspected of being threatened by extinction from the stochastic accumulation of slightly deleterious mutations that is caused by Muller's ratchet in non-recombining populations. However, no detailed quantification of the extent of this threat is available. RESULTS Here we quantify genomic decay in this fish by using a simple model of Muller's ratchet with the most realistic parameter combinations available employing the evolution@home global computing system. We also describe simple extensions of the standard model of Muller's ratchet that allow us to deal with selfing diploids, triploids and mitotic recombination. We show that Muller's ratchet creates a threat of extinction for the Amazon molly for many biologically realistic parameter combinations. In most cases, extinction is expected to occur within a time frame that is less than previous estimates of the age of the species, leading to a genomic decay paradox. CONCLUSION How then does the Amazon molly survive? Several biological processes could individually or in combination solve this genomic decay paradox, including paternal leakage of undamaged DNA from sexual sister species, compensatory mutations and many others. More research is needed to quantify the contribution of these potential solutions towards the survival of the Amazon molly and other (ancient) asexual species.
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Affiliation(s)
- Laurence Loewe
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, King's Buildings, Edinburgh EH9 3JT, UK
- Centre for Systems Biology Edinburgh, School of Biological Sciences, University of Edinburgh, Darwin Building, King's Buildings, Edinburgh EH9 3JU, UK
| | - Dunja K Lamatsch
- Universität Würzburg, Institute of Physiological Chemistry I, Biocenter, Würzburg, 97074 Würzburg, Germany
- Freshwater Biology, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B – 1000 Brussels, Belgium
- University of Sheffield, Department of Animal and Plant Sciences, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK
- Austrian Academy of Sciences, Institute for Limnology, Mondseestrasse 9, 5310 Mondsee, Austria
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34
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Lampert KP, Lamatsch DK, Fischer P, Schartl M. A Tetraploid Amazon Molly, Poecilia formosa. J Hered 2008; 99:223-6. [DOI: 10.1093/jhered/esm102] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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35
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Lampert K, Steinlein C, Schmid M, Fischer P, Schartl M. A haploid-diploid-triploid mosaic of the Amazon molly, Poecilia formosa. Cytogenet Genome Res 2007; 119:131-4. [DOI: 10.1159/000109629] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2007] [Accepted: 06/29/2007] [Indexed: 11/19/2022] Open
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36
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Ahsan B, Kobayashi D, Yamada T, Kasahara M, Sasaki S, Saito TL, Nagayasu Y, Doi K, Nakatani Y, Qu W, Jindo T, Shimada A, Naruse K, Toyoda A, Kuroki Y, Fujiyama A, Sasaki T, Shimizu A, Asakawa S, Shimizu N, Hashimoto SI, Yang J, Lee Y, Matsushima K, Sugano S, Sakaizumi M, Narita T, Ohishi K, Haga S, Ohta F, Nomoto H, Nogata K, Morishita T, Endo T, Shin-I T, Takeda H, Kohara Y, Morishita S. UTGB/medaka: genomic resource database for medaka biology. Nucleic Acids Res 2007; 36:D747-52. [PMID: 17932069 PMCID: PMC2238888 DOI: 10.1093/nar/gkm765] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Medaka (Oryzias latipes) is a small egg-laying freshwater teleost native to East Asia that has become an excellent model system for developmental genetics and evolutionary biology. The draft medaka genome sequence (700 Mb) was reported in June 2007, and its substantial genomic resources have been opened to the public through the University of Tokyo Genome Browser Medaka (UTGB/medaka) database. This database provides basic genomic information, such as predicted genes, expressed sequence tags (ESTs), guanine/cytosine (GC) content, repeats and comparative genomics, as well as unique data resources including (i) 2473 genetic markers and experimentally confirmed PCR primers that amplify these markers, (ii) 142,414 bacterial artificial chromosome (BAC) and 217,344 fosmid end sequences that amount to 15.0- and 11.1-fold clone coverage of the entire genome, respectively, and were used for draft genome assembly, (iii) 16,519,460 single nucleotide polymorphisms (SNPs), and 2 859 905 insertions/deletions detected between two medaka inbred strain genomes and (iv) 841 235 5'-end serial analyses of gene-expression (SAGE) tags that identified 344 266 transcription start sites on the genome. UTGB/medaka is available at: http://medaka.utgenome.org/.
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Affiliation(s)
- Budrul Ahsan
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan
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37
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Definition of the zebrafish genome using flow cytometry and cytogenetic mapping. BMC Genomics 2007; 8:195. [PMID: 17597531 PMCID: PMC1925092 DOI: 10.1186/1471-2164-8-195] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Accepted: 06/27/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The zebrafish (Danio rerio) is an important vertebrate model organism system for biomedical research. The syntenic conservation between the zebrafish and human genome allows one to investigate the function of human genes using the zebrafish model. To facilitate analysis of the zebrafish genome, genetic maps have been constructed and sequence annotation of a reference zebrafish genome is ongoing. However, the duplicative nature of teleost genomes, including the zebrafish, complicates accurate assembly and annotation of a representative genome sequence. Cytogenetic approaches provide "anchors" that can be integrated with accumulating genomic data. RESULTS Here, we cytogenetically define the zebrafish genome by first estimating the size of each linkage group (LG) chromosome using flow cytometry, followed by the cytogenetic mapping of 575 bacterial artificial chromosome (BAC) clones onto metaphase chromosomes. Of the 575 BAC clones, 544 clones localized to apparently unique chromosomal locations. 93.8% of these clones were assigned to a specific LG chromosome location using fluorescence in situ hybridization (FISH) and compared to the LG chromosome assignment reported in the zebrafish genome databases. Thirty-one BAC clones localized to multiple chromosomal locations in several different hybridization patterns. From these data, a refined second generation probe panel for each LG chromosome was also constructed. CONCLUSION The chromosomal mapping of the 575 large-insert DNA clones allows for these clones to be integrated into existing zebrafish mapping data. An accurately annotated zebrafish reference genome serves as a valuable resource for investigating the molecular basis of human diseases using zebrafish mutant models.
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38
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Schories S, Lampert KP, Lamatsch DK, de León FJG, Schartl M. Analysis of a possible independent origin of triploid P. formosa outside of the Río Purificación river system. Front Zool 2007; 4:13. [PMID: 17504521 PMCID: PMC1876798 DOI: 10.1186/1742-9994-4-13] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Accepted: 05/15/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Unisexuality, or all female reproduction, is rare among vertebrates. Studying these exceptional organisms may give useful information with respect to the evolution and maintenance of sexual reproduction. Poecilia formosa was the first unisexual vertebrate species to be detected and since then has served as a paradigmatic organism for unisexuality and studies on the evolution of sex. It reproduces through gynogenesis, using sperm of males from related species to trigger parthenogenetic development of the unreduced diploid eggs. Like in other unisexual vertebrates, triploids occur in a certain range of P. formosa. It has been suggested that the addition of the host species derived third chromosome set is evolutionary important. Clonal organisms lack sufficient genotypic diversity for adaptive changes to variable environments. Also non-recombining genomes cannot purge deleterious mutations and therefore unisexual organisms should suffer from a genomic decay. Thus, polyploidization leading to triploidy should bring "fresh" genetic material into the asexual lineage. To evaluate the importance of triploidy for maintaining the asexual species, it is important to know whether such an introgression event happens at a reasonable frequency. RESULTS In an earlier study it was found that all triploid P. formosa in the Rio Purificación river system are of monophyletic origin. Here we have analyzed fish from a different river system. Using microsatellite analysis we can show that the triploids from this new location are genetically divergent and most probably of an independent origin. CONCLUSION Our data support the hypothesis that triploidy was not a single chance event in the evolutionary history of P. formosa and hence might be a relevant mechanism to increase genotypic divergence and at least partially counteract the genetic degeneration connected to asexuality. It is, however, much rarer than in other asexual vertebrates analyzed so far and thus probably only of moderate evolutionary importance for the maintenance of the asexual breeding complex.
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Affiliation(s)
- Susanne Schories
- Physiological Chemistry I, Biocenter, University of Würzburg, Biozentrum, Am Hubland, D-97074 Würzburg, Germany
| | - Kathrin P Lampert
- Physiological Chemistry I, Biocenter, University of Würzburg, Biozentrum, Am Hubland, D-97074 Würzburg, Germany
| | - Dunja K Lamatsch
- Physiological Chemistry I, Biocenter, University of Würzburg, Biozentrum, Am Hubland, D-97074 Würzburg, Germany
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield S10 2TN, UK
| | - Francisco J García de León
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR, S.C.), Mar Bermejo No. 195, Col. Playa Palo de Santa Rita, La Paz, BCS, 23090, México
| | - Manfred Schartl
- Physiological Chemistry I, Biocenter, University of Würzburg, Biozentrum, Am Hubland, D-97074 Würzburg, Germany
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39
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Sousa-Santos C, Collares-Pereira MJ, Almada V. Fertile triploid males: an uncommon case among hybrid vertebrates. ACTA ACUST UNITED AC 2007; 307:220-5. [PMID: 17351916 DOI: 10.1002/jez.363] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The endemic Iberian minnow Squalius alburnoides is a complex of fishes of hybrid origin including both males and females with distinct ploidy levels and varying proportions of the parental genomes. In this paper we demonstrated that in contrast to many vertebrate hybrid lineages the sperm of triploid hybrid males of S. alburnoides is viable and fully functional. Flow cytometry and analysis of sequences of a fragment of the beta-actin nuclear gene applied to progenitors and offspring evidenced that these males produced their sperm clonally, as already described for diploid hybrids. The presence of different types of fertile males (nonhybrid diploids with normal meiosis and both diploid and triploid hybrids) coupled with hybridogenetic meiosis in females endows this vertebrate complex with a high level of independence from other species and contributes to maintain its genetic variability.
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Affiliation(s)
- Carla Sousa-Santos
- Instituto Superior de Psicologia Aplicada, Unidade de Investigação em Eco-Etologia, Lisboa, Portugal.
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40
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Biswas A, Roy S, De J, Kundu S, Pramanik M, Ray AK. Variations in hepatic estradiol-17beta receptor concentrations during the annual reproductive cycle of diploid and triploid female catfish, Heteropneustes fossilis (Bloch). Life Sci 2007; 80:1777-83. [PMID: 17379258 DOI: 10.1016/j.lfs.2007.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Revised: 01/24/2007] [Accepted: 02/07/2007] [Indexed: 10/23/2022]
Abstract
Concentrations of hepatic estradiol-17beta (E2) receptors (ER) in cytosolic and nuclear fractions were evaluated in diploid and triploid female catfish Heteropneustes fossilis (Bloch) during four different reproductive periods of a complete reproductive cycle. Basal level of ER concentration was noted in the resting period of both diploids and triploids. Receptor level gradually elevated through the preparatory period and reached a peak in the pre-spawning period in both diploids and triploids. However, ER concentrations were overall reduced in triploid to that of diploid females. In a single point assay, in diploids, ER concentration showed about a 3-fold rise (p<0.001) in the cytosolic and a 4-fold rise (p<0.001) in the nuclear extracts from resting to the pre-spawning period. In triploids, only a 2-fold rise was observed both in cytosolic (p<0.01) and nuclear (p<0.05) ER concentration during the same span. Finally, a sudden fall of receptor level was observed in the spawning period in both the ploidy groups with a lower concentration in the triploids. The K(d) value did not differ between the females of diploids (cytosolic 1.12+/-0.21 nM and nuclear 6.9+/-0.9 nM) and triploids (cytosolic--1.13+/-0.17 nM, nuclear--6.8+/-2 nM). However, B(max) of the diploid showed about double the value than triploid females both in the cytosolic (diploid--367.4+/-33.24 pmol/mg protein, triploid--187.3+/-13.20 pmol/mg protein, p<0.001) and nuclear extracts (diploid--946+/-66 pmol/mg DNA, triploid-558+/-98 pmol/mg DNA, p<0.01) of liver. Lower E2 binding capacity and lower amount of E2 receptors of triploid catfish liver with a stunted vitellogenic status could be one of the major causes for reduced gonadal development and sterility in female triploids.
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Affiliation(s)
- Angshuman Biswas
- Department of Animal Physiology, Bose Institute, Kolkata 700054, India
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41
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Tsyusko O, Yi Y, Coughlin D, Main D, Podolsky R, Hinton TG, Glenn TC. Radiation-induced untargeted germline mutations in Japanese medaka. Comp Biochem Physiol C Toxicol Pharmacol 2007; 145:103-10. [PMID: 17045552 DOI: 10.1016/j.cbpc.2006.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 08/22/2006] [Accepted: 08/26/2006] [Indexed: 11/24/2022]
Abstract
Radiation has been shown to increase mutation frequencies at tandem repeat loci by indirect interactions of radiation with DNA. We studied germline mutations in chronically exposed Japanese medaka (Oryzias latipes) using microsatellite loci. After screening 26 randomly selected loci among unirradiated parents and their 200 offspring, we selected seven highly mutable loci (0.5-1.0 x 10(-2) mutants per locus per gamete) and two bonus loci for further study. To determine if radiation exposure increases mutation frequencies in these loci, medaka were chronically irradiated from subadults through maturation at relatively low dose rates of 68 mGy/d. Total doses for males and females were 10.4 and 3 Gy, respectively. The mean number of mutations for the offspring of exposed families (0.149+/-0.044) was significantly higher (P=0.018) than for control families (0.080+/-0.028), indicating induction of germline mutations from chronic irradiation. This increase in the microsatellite mutation rate is greater than expected from direct interaction of radiation with DNA, suggesting indirect, untargeted mechanism(s) for mutations. This study identified microsatellite loci with a high mutational background in medaka, variation among loci and families as important variables, and demonstrated the usefulness of this fish model for studying radiation-induced germline mutations.
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Affiliation(s)
- O Tsyusko
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA.
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42
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Parton A, Forest D, Kobayashi H, Dowell L, Bayne C, Barnes D. Cell and molecular biology of SAE, a cell line from the spiny dogfish shark, Squalus acanthias. Comp Biochem Physiol C Toxicol Pharmacol 2007; 145:111-9. [PMID: 16949345 DOI: 10.1016/j.cbpc.2006.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2006] [Revised: 07/03/2006] [Accepted: 07/10/2006] [Indexed: 11/19/2022]
Abstract
Cartilaginous fish, primarily sharks, rays and skates (elasmobranchs), appeared 450 million years ago. They are the most primitive vertebrates, exhibiting jaws and teeth, adaptive immunity, a pressurized circulatory system, thymus, spleen, and a liver comparable to that of humans. The most used elasmobranch in biomedical research is the spiny dogfish shark, Squalus acanthias. Comparative genomic analysis of the dogfish shark, the little skate (Leucoraja erincea), and other elasmobranchs have yielded insights into conserved functional domains of genes associated with human liver function, multidrug resistance, cystic fibrosis, and other biomedically relevant processes. While genomic information from these animals is informative in an evolutionary framework, experimental verification of functions of genomic sequences depends heavily on cell culture approaches. We have derived the first multipassage, continuously proliferating cell line of a cartilaginous fish. The line was initiated from embryos of the spiny dogfish shark. The cells were maintained in a medium modified for fish species and supplemented with cell type-specific hormones, other proteins and sera, and plated on a collagen substrate. SAE cells have been cultured continuously for three years. These cells can be transfected by plasmids and have been cryopreserved. Expressed Sequence Tags generated from a normalized SAE cDNA library included a number of markers for cartilage and muscle, as well as proteins influencing tissue differentiation and development, suggesting that SAE cells may be of mesenchymal stem cell origin. Examination of SAE EST sequences also revealed a cartilaginous fish-specific repetitive sequence that may be evidence of an ancient mobile genetic element that most likely was introduced into the cartilaginous fish lineage after divergence from the lineage leading to teleosts.
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Affiliation(s)
- Angela Parton
- Mount Desert Island Biological Laboratories, Salisbury Cove, ME 04672, USA
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Sasaki T, Shimizu A, Ishikawa SK, Imai S, Asakawa S, Murayama Y, Khorasani MZ, Mitani H, Furutani-Seiki M, Kondoh H, Nanda I, Schmid M, Schartl M, Nonaka M, Takeda H, Hori H, Himmelbauer H, Shima A, Shimizu N. The DNA sequence of medaka chromosome LG22. Genomics 2007; 89:124-33. [PMID: 17067776 DOI: 10.1016/j.ygeno.2006.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 08/31/2006] [Accepted: 09/09/2006] [Indexed: 10/24/2022]
Abstract
We report the genomic DNA sequence of a single chromosome (linkage group 22; LG22) of the small teleost fish medaka (Oryzias latipes) as a first whole chromosome sequence from a non-mammalian vertebrate. The order and orientation of 633 protein-coding genes were deduced from 18,803,338 bp of DNA sequence, providing the opportunity to analyze chromosome evolution of vertebrate genomes by direct comparison with the human genome. The average number of genes in the "conserved gene cluster" (CGC), a strict definition of "synteny" at the sequence basis, between medaka and human was 1.6. These and other data suggest that approximately 38.8% of pair-wise gene relationships would have been broken from their common ancestor in the human and medaka lineages and further imply that approx 20,000 (15,520-23,280) breaks would have occurred from the entire genome of the common ancestor. These breaks were generated mainly by intra-chromosomal shufflings at a specific era in the vertebrate lineage. These precise comparative genomics allowed us to identify the pieces of ancient chromosomes of the common vertebrate ancestor and estimate chromosomal evolution in the vertebrate lineage.
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Affiliation(s)
- Takashi Sasaki
- Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Tokyo 160-8582, Japan
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Sirviö A, Gadau J, Rueppell O, Lamatsch D, Boomsma JJ, Pamilo P, Page RE. High recombination frequency creates genotypic diversity in colonies of the leaf-cutting ant Acromyrmex echinatior. J Evol Biol 2006; 19:1475-85. [PMID: 16910978 DOI: 10.1111/j.1420-9101.2006.01131.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Honeybees are known to have genetically diverse colonies because queens mate with many males and the recombination rate is extremely high. Genetic diversity among social insect workers has been hypothesized to improve general performance of large and complex colonies, but this idea has not been tested in other social insects. Here, we present a linkage map and an estimate of the recombination rate for Acromyrmex echinatior, a leaf-cutting ant that resembles the honeybee in having multiple mating of queens and colonies of approximately the same size. A map of 145 AFLP markers in 22 linkage groups yielded a total recombinational size of 2076 cM and an inferred recombination rate of 161 kb cM(-1) (or 6.2 cM Mb(-1)). This estimate is lower than in the honeybee but, as far as the mapping criteria can be compared, higher than in any other insect mapped so far. Earlier studies on A. echinatior have demonstrated that variation in division of labour and pathogen resistance has a genetic component and that genotypic diversity among workers may thus give colonies of this leaf-cutting ant a functional advantage. The present result is therefore consistent with the hypothesis that complex social life can select for an increased recombination rate through effects on genotypic diversity and colony performance.
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Affiliation(s)
- A Sirviö
- Department of Biology, University of Oulu, 90014 Oulu, Finland.
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Sousa‐Santos C, Collares‐Pereira M, Almada VC. May a hybridogenetic complex regenerate the nuclear genome of both sexes of a missing ancestor? First evidence on the occurrence of a nuclear non‐hybridSqualius alburnoides(Cyprinidae) female based on DNA sequencing. J NAT HIST 2006. [DOI: 10.1080/00222930600934111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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46
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Abstract
The bumblebee Bombus terrestris is an economically important pollinator and an emerging model species in quantitative and population genetics. We generated genetic linkage maps for 3 independent mapping populations of B. terrestris. The linkage map with the highest resolution had 21 linkage groups, which adequately represents the haploid chromosome number of B. terrestris (n = 18). This map can be considered saturated, with an average marker distance of 10.3 cM and an estimated genome coverage of 81%. Using flow cytometry, we have estimated the genome size of this species to be 625 Mb. With an estimated total recombination genome length of 2760 cM, this results in a ratio of 226 kb/cM between the physical and genetic genome sizes. A recurring set of microsatellites and amplified fragment length polymorphism (AFLP) markers allowed the alignment of 14 linkage groups between the 3 maps. We propose to adopt this core map as a reference tool for future genetic and molecular work in B. terrestris.
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Affiliation(s)
- Lena Wilfert
- ETH Zürich, Institute for Integrative Biology (IBZ), Experimental Ecology Group, ETH-Zentrum CHN, CH-8092 Zürich, Switzerland.
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Barnes D, Dowell L, Forest D, Parton A, Pavicevic P, Kazianis S. Characterization of XM, a NovelXiphophorusMelanoma-Derived Cell Line. Zebrafish 2006; 3:371-81. [DOI: 10.1089/zeb.2006.3.371] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- David Barnes
- Mount Desert Island Biological Laboratory, Salsbury Cove, Maine
| | - Lori Dowell
- Mount Desert Island Biological Laboratory, Salsbury Cove, Maine
| | - David Forest
- Mount Desert Island Biological Laboratory, Salsbury Cove, Maine
| | - Angela Parton
- Mount Desert Island Biological Laboratory, Salsbury Cove, Maine
| | - Peter Pavicevic
- Mount Desert Island Biological Laboratory, Salsbury Cove, Maine
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Biswas A, Kundu S, Roy S, De J, Pramanik M, Ray AK. Thyroid hormone profile during annual reproductive cycle of diploid and triploid catfish, Heteropneustes fossilis (Bloch). Gen Comp Endocrinol 2006; 147:126-32. [PMID: 16466725 DOI: 10.1016/j.ygcen.2005.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 12/08/2005] [Accepted: 12/13/2005] [Indexed: 11/19/2022]
Abstract
Triploid fishes generally show sterility along with retarded gonadal development and aneuploid gametes. In teleosts, thyroid hormones influence seasonal adaptations and annual events such as reproduction. In addition, thyroid hormone deposition in matured ova is important for reproductive success as the role of thyroid hormones in early development and metamorphosis is well established. The present study deals with measurements of free and total thyroxine (T4) and triiodothyronine (T3) in the plasma of triploid and diploid catfish Heteropneustes fossilis (Bloch) in a complete reproductive cycle. Accumulations of total T4 and T3 within the oocytes have also been measured during the spawning period from fishes of both ploidy groups. No difference of plasma free hormones was noticed between the diploids and triploids of both the sexes in any period of reproductive cycle, although, seasonal variations were noted in both the groups. A significant decrease in the total thyroid hormone levels was noticed in plasma of the diploids in the spawning period compared to triploid fish. During the same period, accumulation of THs was significantly higher in the oocytes of diploids than that of the triploids. Thyroid gland structure also revealed a higher state of activity in the female diploids than the triploids during spawning period. Lower activity of thyroid tissue, higher levels of THs in plasma, and lower accumulation of maternally derived hormones in the oocytes of triploid females during spawning period may be associated with sterility of triploids.
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Affiliation(s)
- Angshuman Biswas
- Department of Animal Physiology, Bose Institute, P 1/12 CIT Scheme VII-M, Calcutta 700054, India
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Biswas A, Pramanik M, Kundu S, Roy S, De J, Ray AK. Alterations in enzyme activities in vital organs of triploid female catfish Heteropneustes fossilis (Bloch). FISH PHYSIOLOGY AND BIOCHEMISTRY 2006; 32:73-81. [PMID: 20035482 DOI: 10.1007/s10695-006-7657-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Accepted: 02/25/2006] [Indexed: 05/28/2023]
Abstract
Triploid Heteropneustes fossilis (Bloch) showed sterility and higher growth potential than the normal diploid fish. Activities of some metabolic enzymes such as cytosolic NADP-malate dehydrogenase (NADP-MDH), mitochondrial NAD-malate dehydrogenase (NAD-MDH) and glutamate pyruvate transaminase (GPT) were evaluated in liver, brain and kidney along with glucose-6-phosphate dehydrogenase (G-6-P D) in ovary of female triploid catfish. Activities of these enzymes showed distinct seasonal periodicity, mostly with highest activities in prespawning and spawning periods, in both diploid and triploid catfish but differed in magnitude. In triploid liver, GPT showed higher activity than the diploid counterpart in prespawning and spawning periods. On the contrary, mitochondrial NAD-MDH and cytosolic NADP-MDH in this organ showed a consistent lower activity than the diploid in all stages or in some stages of reproductive cycle respectively. Interestingly, none of the enzymes in brain and kidney of triploid female catfish showed significant changes in comparison to the diploid counterpart. The triploid ovary maintained a significantly lower level of G-6-P D activity throughout the resting, preparatory and pre-spawning periods compared to the diploid ovary. Lower level of malic enzymes (NAD-MDH and NADP-MDH) in liver and G-6-P D in ovary are in close synchrony with lower level of estradiol-17beta in plasma of female triploids as found in earlier study.
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Affiliation(s)
- Angshuman Biswas
- Department of Animal Physiology, Bose Institute, P-1/12 CIT, Scheme VII M, Calcutta, 700054, India
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Sousa-Santos C, Robalo JI, Collares-Pereira MJ, Almada VC. Heterozygous indels as useful tools in the reconstruction of DNA sequences and in the assessment of ploidy level and genomic constitution of hybrid organisms. ACTA ACUST UNITED AC 2006; 16:462-7. [PMID: 16287626 DOI: 10.1080/10425170500356065] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In this paper we describe a simple approach using double peaks in chromatograms generated as artefacts in the vicinity of heterozygous indels, to identify the specific sequences present in individual strands of a given DNA fragment. This method is useful to assign bases in individuals that are heterozygous at multiple sites. In addition, the relative sizes of the double peaks help to determine the ploidy level and the relative contribution of the parental genomes in hybrids. Our interpretation was confirmed with the analysis of artificial mixtures of DNA of two different species. Results were robust with varying PCR and sequencing conditions. The applicability of this method was demonstrated in hybrids of the Squalius alburnoides complex and in heterozygotes of Chondrostoma oligolepis. Far from being limited to these fish models and the gene where it was tested (beta-actin), this sequence reconstruction methodology is expected to have a broader application.
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Affiliation(s)
- Carla Sousa-Santos
- Instituto Superior de Psicologia Aplicada ISPA, Unidade de Investigação em Eco-Etologia, Rua Jardim do Tabaco 34, 1149-041, Lisboa, Portugal.
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