1
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Dekker ML, van Son LM, Leon-Kloosterziel KM, Hagmayer A, Furness AI, van Leeuwen JL, Pollux BJA. Multiple paternity in superfetatious live-bearing fishes. J Evol Biol 2022; 35:948-961. [PMID: 35612319 DOI: 10.1111/jeb.14019] [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: 02/21/2022] [Revised: 04/13/2022] [Accepted: 04/30/2022] [Indexed: 11/30/2022]
Abstract
Superfetation, the ability to carry several overlapping broods at different developmental stages, has evolved independently multiple times within the live-bearing fish family Poeciliidae. Even though superfetation is widespread among poeciliids, its evolutionary advantages remain unclear. Theory predicts that superfetation should increase polyandry by increasing the probability that temporally overlapping broods are fertilized by different fathers. Here, we test this key prediction in two poeciliid species that each carry two temporally overlapping broods: Poeciliopsis retropinna and P. turrubarensis. We collected 25 females per species from freshwater streams in South-Eastern Costa Rica and assessed multiple paternity by genotyping all their embryos (420 embryos for P. retropinna; 788 embryos for P. turrubarensis) using existing and newly developed microsatellite markers. We observed a high frequency of unique sires in the simultaneous, temporally overlapping broods in P. retropinna (in 56% of the pregnant females) and P. turrubarensis (79%). We found that the mean number of sires within females was higher than the number of sires within the separate broods (2.92 sires within mothers vs. 2.36 within separate broods in P. retropinna; and 3.40 vs 2.56 in P. turrubarensis). We further observed that there were significant differences in the proportion of offspring sired by each male in 42% of pregnant female P. retropinna and 65% of female P. turrubarensis; however, this significance applied to only 9% and 46% of the individual broods in P. retropinna and P. turrubarensis, respectively, suggesting that the unequal reproductive success of sires (i.e. reproductive skew) mostly originated from differences in paternal contribution between, rather than within broods. Together, these findings tentatively suggest that superfetation may promote polyandry and reproductive skew in live-bearing fishes.
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Affiliation(s)
- Myrthe L Dekker
- Experimental Zoology Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Lisa M van Son
- Experimental Zoology Group, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Andres Hagmayer
- Experimental Zoology Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Andrew I Furness
- Department of Biological and Marine Sciences, University of Hull, Hull, UK
| | - Johan L van Leeuwen
- Experimental Zoology Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Bart J A Pollux
- Experimental Zoology Group, Wageningen University & Research, Wageningen, The Netherlands
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2
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Janzen T, Miró Pina V. Estimating the time since admixture from phased and unphased molecular data. Mol Ecol Resour 2021; 22:908-926. [PMID: 34599646 PMCID: PMC9291888 DOI: 10.1111/1755-0998.13519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 11/26/2022]
Abstract
After admixture, recombination breaks down genomic blocks of contiguous ancestry. The breakdown of these blocks forms a new “molecular clock” that ticks at a much faster rate than the mutation clock, enabling accurate dating of admixture events in the recent past. However, existing theory on the breakdown of these blocks, or the accumulation of delineations between blocks, so‐called “junctions”, has mostly been limited to using regularly spaced markers on phased data. Here, we present an extension to the theory of junctions using the ancestral recombination graph that describes the expected number of junctions for any distribution of markers along the genome. Furthermore, we provide a new framework to infer the time since admixture using unphased data. We demonstrate both the phased and unphased methods on simulated data and show that our new extensions have improved accuracy with respect to previous methods, especially for smaller population sizes and more ancient admixture times. Lastly, we demonstrate the applicability of our method on three empirical data sets, including labcrosses of yeast (Saccharomyces cerevisae) and two case studies of hybridization in swordtail fish and Populus trees.
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Affiliation(s)
- Thijs Janzen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands.,Carl von Ossietzky University, Oldenburg, Germany
| | - Verónica Miró Pina
- Instituto de Investigaciones en Matemáticas Aplicadas y Sistemas (IIMAS), Universidad Nacional Autónoma de México (UNAM), México City, México.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
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3
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Charlesworth D, Zhang Y, Bergero R, Graham C, Gardner J, Yong L. Using GC Content to Compare Recombination Patterns on the Sex Chromosomes and Autosomes of the Guppy, Poecilia reticulata, and Its Close Outgroup Species. Mol Biol Evol 2021; 37:3550-3562. [PMID: 32697821 DOI: 10.1093/molbev/msaa187] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genetic and physical mapping of the guppy (Poecilia reticulata) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, as in pseudoautosomal regions of mammalian sex chromosomes. We used GC content to indirectly infer recombination patterns on guppy chromosomes, based on evidence that recombination is associated with GC-biased gene conversion, so that genome regions with high recombination rates should be detectable by high GC content. We used intron sequences and third positions of codons to make comparisons between sequences that are matched, as far as possible, and are all probably under weak selection. Almost all guppy chromosomes, including the sex chromosome (LG12), have very high GC values near their assembly ends, suggesting high recombination rates due to strong crossover localization in male meiosis. Our test does not suggest that the guppy XY pair has stronger crossover localization than the autosomes, or than the homologous chromosome in the close relative, the platyfish (Xiphophorus maculatus). We therefore conclude that the guppy XY pair has not recently undergone an evolutionary change to a different recombination pattern, or reduced its crossover rate, but that the guppy evolved Y-linkage due to acquiring a male-determining factor that also conferred the male crossover pattern. We also identify the centromere ends of guppy chromosomes, which were not determined in the genome assembly.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Yexin Zhang
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Roberta Bergero
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Chay Graham
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jim Gardner
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Lengxob Yong
- Centre for Ecology and Conservation, University of Exeter, Falmouth, Cornwall, United Kingdom
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4
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Kottler VA, Feron R, Nanda I, Klopp C, Du K, Kneitz S, Helmprobst F, Lamatsch DK, Lopez-Roques C, Lluch J, Journot L, Parrinello H, Guiguen Y, Schartl M. Independent Origin of XY and ZW Sex Determination Mechanisms in Mosquitofish Sister Species. Genetics 2020; 214:193-209. [PMID: 31704715 PMCID: PMC6944411 DOI: 10.1534/genetics.119.302698] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/05/2019] [Indexed: 12/12/2022] Open
Abstract
Fish are known for the outstanding variety of their sex determination mechanisms and sex chromosome systems. The western (Gambusia affinis) and eastern mosquitofish (G. holbrooki) are sister species for which different sex determination mechanisms have been described: ZZ/ZW for G. affinis and XX/XY for G. holbrooki Here, we carried out restriction-site associated DNA (RAD-) and pool sequencing (Pool-seq) to characterize the sex chromosomes of both species. We found that the ZW chromosomes of G. affinis females and the XY chromosomes of G. holbrooki males correspond to different linkage groups, and thus evolved independently from separate autosomes. In interspecific hybrids, the Y chromosome is dominant over the W chromosome, and X is dominant over Z. In G. holbrooki, we identified a candidate region for the Y-linked melanic pigmentation locus, a rare male phenotype that constitutes a potentially sexually antagonistic trait and is associated with other such characteristics, e.g., large body size and aggressive behavior. We developed a SNP-based marker in the Y-linked allele of GIPC PDZ domain containing family member 1 (gipc1), which was linked to melanism in all tested G. holbrooki populations. This locus represents an example for a color locus that is located in close proximity to a putative sex determiner, and most likely substantially contributed to the evolution of the Y.
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Affiliation(s)
- Verena A Kottler
- Physiological Chemistry, Biocenter, University of Wuerzburg, 97074, Germany
| | - Romain Feron
- INRA, UR1037 Fish Physiology and Genomics, 35000 Rennes, France
- University of Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Indrajit Nanda
- Institute for Human Genetics, Biocenter, University of Wuerzburg, 97074, Germany
| | - Christophe Klopp
- Sigenae, Mathématiques et Informatique Appliquées de Toulouse, INRA, 31326 Castanet Tolosan, France
| | - Kang Du
- Physiological Chemistry, Biocenter, University of Wuerzburg, 97074, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biocenter, University of Wuerzburg, 97074, Germany
| | | | - Dunja K Lamatsch
- University of Innsbruck, Research Department for Limnology, Mondsee, 5310 Mondsee, Austria
| | | | - Jerôme Lluch
- INRA, US 1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France
| | - Laurent Journot
- Montpellier GenomiX (MGX), University Montpellier, CNRS, INSERM, 34094 France
| | - Hugues Parrinello
- Montpellier GenomiX (MGX), University Montpellier, CNRS, INSERM, 34094 France
| | - Yann Guiguen
- INRA, UR1037 Fish Physiology and Genomics, 35000 Rennes, France
| | - Manfred Schartl
- Physiological Chemistry, Biocenter, University of Wuerzburg, 97074, Germany
- Developmental Biochemistry, Biocenter, University of Wuerzburg, 97074, Germany
- Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, Texas 77843
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5
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Miller JT, Reid NM, Nacci DE, Whitehead A. Developing a High-Quality Linkage Map for the Atlantic Killifish Fundulus heteroclitus. G3 (BETHESDA, MD.) 2019; 9:2851-2862. [PMID: 31289021 PMCID: PMC6723127 DOI: 10.1534/g3.119.400262] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/28/2019] [Indexed: 12/27/2022]
Abstract
Killifish (Fundulus heteroclitus) are widely distributed among different aquatic environments where they demonstrate an impressive range of highly-plastic and locally adaptive phenotypes. High-throughput sequencing has begun to unravel the mechanisms and evolutionary history of these interesting features by establishing relationships in the genotype-phenotype map. However, some genotype-phenotype analyses require a higher order of contiguity than what initial scaffolded (fragmented genome assembly where contigs have been assemble into scaffolds) genome assemblies can provide. Here, we used 5,685 high-quality RAD-Seq markers from a single mapping family to order 84% of the scaffolded genome assembly to 24 chromosomes. This serves to: 1) expand the killifish genomic toolkit, 2) estimate genome-wide recombination rates, and 3) compare genome synteny to humans and other fishes. After initially building our map, we found that the selection of thresholds for sequence data filtration highly impacted scaffold placement in the map. We outline each step of the approach that dramatically improved our map to help guide others toward more effective linkage mapping for genome assembly. Our final map supports strong conservation of genomic synteny among closely related fish species and reveals previously described chromosomal rearrangements between more distantly related clades. However, we also commonly found minor scaffold misorientations in F. heteroclitus and in other assemblies, suggesting that further mapping (such as optical mapping) is necessary for finer scale resolution of genome structure. Lastly, we discuss the problems that would be expected from misoriented/unplaced scaffolds and stress the importance of a quality mapped genome as a key feature for further investigating population and comparative genomic questions with F. heteroclitus and other taxa.
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Affiliation(s)
- Jeffrey T Miller
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences Institute, University of California, Davis, CA
| | - Noah M Reid
- Department of Molecular & Cell Biology, University of Connecticut, Storrs, CT, and
| | - Diane E Nacci
- US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, Narragansett, RI
| | - Andrew Whitehead
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences Institute, University of California, Davis, CA
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6
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Exaggerated heterochiasmy in a fish with sex-linked male coloration polymorphisms. Proc Natl Acad Sci U S A 2019; 116:6924-6931. [PMID: 30894479 DOI: 10.1073/pnas.1818486116] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
It is often stated that polymorphisms for mutations affecting fitness of males and females in opposite directions [sexually antagonistic (SA) polymorphisms] are the main selective force for the evolution of recombination suppression between sex chromosomes. However, empirical evidence to discriminate between different hypotheses is difficult to obtain. We report genetic mapping results in laboratory-raised families of the guppy (Poecilia reticulata), a sexually dimorphic fish with SA polymorphisms for male coloration genes, mostly on the sex chromosomes. Comparison of the genetic and physical maps shows that crossovers are distributed very differently in the two sexes (heterochiasmy); in male meiosis, they are restricted to the termini of all four chromosomes studied, including chromosome 12, which carries the sex-determining locus. Genome resequencing of male and female guppies from a population also indicates sex linkage of variants across almost the entire chromosome 12. More than 90% of the chromosome carrying the male-determining locus is therefore transmitted largely through the male lineage. A lack of heterochiasmy in a related fish species suggests that it originated recently in the lineage leading to the guppy. Our findings do not support the hypothesis that suppressed recombination evolved in response to the presence of SA polymorphisms. Instead, a low frequency of recombination on a chromosome that carries a male-determining locus and has not undergone genetic degeneration has probably facilitated the establishment of male-beneficial coloration polymorphisms.
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7
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Poh KB, Roslan ZM, Misnan R, Sinang SC. Characterization and expression of Xiphophorus maculatus microsatellite Msb069 full sequence in subgenus Poecilia. J Genet 2018; 97:817-824. [PMID: 30262693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Msb069 primer pairs encompassed region is believed to be associated with a quantitative trait loci (QTL) of dorsal fin length in subgenus Poecilia. However, detailed investigation on Msb069 which originated from Xiphophorus on subgenus Poecilia remains unexplored. In this study, full sequence of Msb069 was characterized by sequencing bioinformatics analysis and gene expression. The sequence analysis of Msb069 primer pairs encompassed region on three species of Poecilia revealed higher number of microsatellite tandem repeats in Poecilia latipinna (ATG16) compared to P. sphenops (ATG13-14). There is no notable pattern of ATGtandem repeats discovered in the hybrids. The full sequence of Msb069 is 734 bp in length and showed a 233 bp conserved region between Xiphophorus and Poecilia. BLAST search performed on this sequence revealed no significant similarities. Nonquantitative RT-PCR exhibited the presence of Msb069 transcripts in three different tissues in subgenus Poecilia. Meanwhile, quantitative RTPCR expression on two different tissues showed relatively higher expression of Msb069 transcript in P. latipinna dorsal fin tissues in both male and female fishes, suggesting a repressive function of this transcript with respect to dorsal fin length. However the exact gene expression event of Msb069 is still unknown and requires further investigation.
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Affiliation(s)
- Keong Bun Poh
- Faculty of Science and Mathematics, Department of Biology, Universiti Pendidikan Sultan Idris, 35900, Tanjong Malim, Perak, Malaysia.
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8
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Characterization and expression of Xiphophorus maculatus microsatellite Msb069 full sequence in subgenus Poecilia. J Genet 2018. [DOI: 10.1007/s12041-018-0968-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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9
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Culumber ZW, Tobler M. Correlated evolution of thermal niches and functional physiology in tropical freshwater fishes. J Evol Biol 2018; 31:722-734. [DOI: 10.1111/jeb.13260] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/13/2018] [Accepted: 02/23/2018] [Indexed: 11/30/2022]
Affiliation(s)
| | - Michael Tobler
- Division of Biology Kansas State University Manhattan KS USA
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10
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Lu Y, Boswell M, Boswell W, Kneitz S, Hausmann M, Klotz B, Regneri J, Savage M, Amores A, Postlethwait J, Warren W, Schartl M, Walter R. Molecular genetic analysis of the melanoma regulatory locus in Xiphophorus interspecies hybrids. Mol Carcinog 2017; 56:1935-1944. [PMID: 28345808 DOI: 10.1002/mc.22651] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 03/07/2017] [Accepted: 03/23/2017] [Indexed: 01/10/2023]
Abstract
Development of spontaneous melanoma in Xiphophorus interspecies backcross hybrid progeny, (X. hellerii × [X. maculatus Jp 163 A × X. hellerii]) is due to Mendelian segregation of a oncogene (xmrk) and a molecularly uncharacterized locus, called R(Diff), on LG5. R(Diff) is thought to suppresses the activity of xmrk in healthy X. maculatus Jp 163 A parental species that rarely develop melanoma. To better understand the molecular genetics of R(Diff), we utilized RNA-Seq to study allele-specific gene expression of spontaneous melanoma tumors and corresponding normal skin samples derived from 15 first generation backcross (BC1 ) hybrids and 13 fifth generation (BC5 ) hybrids. Allele-specific expression was determined for all genes and assigned to parental allele inheritance for each backcross hybrid individual. Results showed that genes residing in a 5.81 Mbp region on LG5 were exclusively expressed from the X. hellerii alleles in tumor-bearing BC1 hybrids. This observation indicates this region is consistently homozygous for X. hellerii alleles in tumor bearing animals, and therefore defines this region to be the R(Diff) locus. The R(Diff) locus harbors 164 gene models and includes the previously characterized R(Diff) candidate, cdkn2x. Twenty-one genes in the R(Diff) region show differential expression in the tumor samples compared to normal skin tissue. These results further characterize the R(Diff) locus and suggest tumor suppression may require a multigenic region rather than a single gene variant. Differences in gene expression between tumor and normal skin tissue in this region may indicate interactions among several genes are required for backcross hybrid melanoma development.
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Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
| | - Michael Hausmann
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
| | - Barbara Klotz
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
| | - Janine Regneri
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
| | - Markita Savage
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | - Wesley Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany.,Texas A&M Institute for Advanced Studies and Department of Biology, Texas A&M University, College Station, Texas
| | - Ronald Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
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11
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Xu K, Duan W, Xiao J, Tao M, Zhang C, Liu Y, Liu S. Development and application of biological technologies in fish genetic breeding. SCIENCE CHINA-LIFE SCIENCES 2015; 58:187-201. [PMID: 25595050 DOI: 10.1007/s11427-015-4798-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/06/2014] [Indexed: 11/24/2022]
Abstract
Fish genetic breeding is a process that remolds heritable traits to obtain neotype and improved varieties. For the purpose of genetic improvement, researchers can select for desirable genetic traits, integrate a suite of traits from different donors, or alter the innate genetic traits of a species. These improved varieties have, in many cases, facilitated the development of the aquaculture industry by lowering costs and increasing both quality and yield. In this review, we present the pertinent literatures and summarize the biological bases and application of selection breeding technologies (containing traditional selective breeding, molecular marker-assisted breeding, genome-wide selective breeding and breeding by controlling single-sex groups), integration breeding technologies (containing cross breeding, nuclear transplantation, germline stem cells and germ cells transplantation, artificial gynogenesis, artificial androgenesis and polyploid breeding) and modification breeding technologies (represented by transgenic breeding) in fish genetic breeding. Additionally, we discuss the progress our laboratory has made in the field of chromosomal ploidy breeding of fish, including distant hybridization, gynogenesis, and androgenesis. Finally, we systematically summarize the research status and known problems associated with each technology.
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Affiliation(s)
- Kang Xu
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Ministry of Education of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
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12
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Paczolt KA, Passow CN, Delclos PJ, Kindsvater HK, Jones AG, Rosenthal GG. Multiple mating and reproductive skew in parental and introgressed females of the live-bearing fish Xiphophorus birchmanni. J Hered 2014; 106:57-66. [PMID: 25433083 DOI: 10.1093/jhered/esu066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Just as mating patterns can promote speciation or hybridization, the presence of hybridization can shape mating patterns within a population. In this study, we characterized patterns of multiple mating and reproductive skew in a naturally hybridizing swordtail fish species, Xiphophorus birchmanni. We quantified multiple mating using microsatellite markers to genotype embryos from 43 females collected from 2 wild populations. We also used a suite of single-nucleotide polymorphism markers to categorize females and their inferred mates as either parental X. birchmanni or as introgressed individuals, which carried alleles from a sister species, X. malinche. We found that parental and introgressed X. birchmanni females mated multiply with both parental and introgressed males. We found no difference in mating patterns or reproductive skew between parental and introgressed X. birchmanni females. However, nonintrogressed X. birchmanni males mated more often with large, fecund females. These females also had the greatest levels of skew in fertilization success of males. Thus, our results show that X. birchmanni has a polygynandrous mating system and that introgression of X. malinche alleles has only subtle effects on mating patterns in this species.
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Affiliation(s)
- Kimberly A Paczolt
- From the Department of Biology, 3258 TAMU, Texas A&M University, College Station, TX 77843 (Paczolt, Passow, Delclos, Jones, and Rosenthal); and the Centro de Investigaciones Científicas de las Huastecas "Aguazarca," Calnali, Hidalgo, Mexico (Passow, Delclos, Kindsvater, and Rosenthal).
| | - Courtney N Passow
- From the Department of Biology, 3258 TAMU, Texas A&M University, College Station, TX 77843 (Paczolt, Passow, Delclos, Jones, and Rosenthal); and the Centro de Investigaciones Científicas de las Huastecas "Aguazarca," Calnali, Hidalgo, Mexico (Passow, Delclos, Kindsvater, and Rosenthal)
| | - Pablo J Delclos
- From the Department of Biology, 3258 TAMU, Texas A&M University, College Station, TX 77843 (Paczolt, Passow, Delclos, Jones, and Rosenthal); and the Centro de Investigaciones Científicas de las Huastecas "Aguazarca," Calnali, Hidalgo, Mexico (Passow, Delclos, Kindsvater, and Rosenthal)
| | - Holly K Kindsvater
- From the Department of Biology, 3258 TAMU, Texas A&M University, College Station, TX 77843 (Paczolt, Passow, Delclos, Jones, and Rosenthal); and the Centro de Investigaciones Científicas de las Huastecas "Aguazarca," Calnali, Hidalgo, Mexico (Passow, Delclos, Kindsvater, and Rosenthal)
| | - Adam G Jones
- From the Department of Biology, 3258 TAMU, Texas A&M University, College Station, TX 77843 (Paczolt, Passow, Delclos, Jones, and Rosenthal); and the Centro de Investigaciones Científicas de las Huastecas "Aguazarca," Calnali, Hidalgo, Mexico (Passow, Delclos, Kindsvater, and Rosenthal)
| | - Gil G Rosenthal
- From the Department of Biology, 3258 TAMU, Texas A&M University, College Station, TX 77843 (Paczolt, Passow, Delclos, Jones, and Rosenthal); and the Centro de Investigaciones Científicas de las Huastecas "Aguazarca," Calnali, Hidalgo, Mexico (Passow, Delclos, Kindsvater, and Rosenthal)
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13
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Schumer M, Cui R, Powell DL, Dresner R, Rosenthal GG, Andolfatto P. High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species. eLife 2014; 3. [PMID: 24898754 PMCID: PMC4080447 DOI: 10.7554/elife.02535] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 06/02/2014] [Indexed: 12/18/2022] Open
Abstract
Hybridization is increasingly being recognized as a common process in both animal and plant species. Negative epistatic interactions between genes from different parental genomes decrease the fitness of hybrids and can limit gene flow between species. However, little is known about the number and genome-wide distribution of genetic incompatibilities separating species. To detect interacting genes, we perform a high-resolution genome scan for linkage disequilibrium between unlinked genomic regions in naturally occurring hybrid populations of swordtail fish. We estimate that hundreds of pairs of genomic regions contribute to reproductive isolation between these species, despite them being recently diverged. Many of these incompatibilities are likely the result of natural or sexual selection on hybrids, since intrinsic isolation is known to be weak. Patterns of genomic divergence at these regions imply that genetic incompatibilities play a significant role in limiting gene flow even in young species.
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Affiliation(s)
- Molly Schumer
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States
| | - Rongfeng Cui
- Department of Biology, Texas A&M University, College Station, United States
| | - Daniel L Powell
- Department of Biology, Texas A&M University, College Station, United States
| | - Rebecca Dresner
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States
| | - Gil G Rosenthal
- Department of Biology, Texas A&M University, College Station, United States
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States
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Amores A, Catchen J, Nanda I, Warren W, Walter R, Schartl M, Postlethwait JH. A RAD-tag genetic map for the platyfish (Xiphophorus maculatus) reveals mechanisms of karyotype evolution among teleost fish. Genetics 2014; 197:625-41. [PMID: 24700104 PMCID: PMC4063920 DOI: 10.1534/genetics.114.164293] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 03/20/2014] [Indexed: 11/18/2022] Open
Abstract
Mammalian genomes can vary substantially in haploid chromosome number even within a small taxon (e.g., 3-40 among deer alone); in contrast, teleost fish genomes are stable (24-25 in 58% of teleosts), but we do not yet understand the mechanisms that account for differences in karyotype stability. Among perciform teleosts, platyfish (Xiphophorus maculatus) and medaka (Oryzias latipes) both have 24 chromosome pairs, but threespine stickleback (Gasterosteus aculeatus) and green pufferfish (Tetraodon nigroviridis) have just 21 pairs. To understand the evolution of teleost genomes, we made a platyfish meiotic map containing 16,114 mapped markers scored on 267 backcross fish. We tiled genomic contigs along the map to create chromosome-length genome assemblies. Genome-wide comparisons of conserved synteny showed that platyfish and medaka karyotypes remained remarkably similar with few interchromosomal translocations but with numerous intrachromosomal rearrangements (transpositions and inversions) since their lineages diverged ∼120 million years ago. Comparative genomics with platyfish shows how reduced chromosome numbers in stickleback and green pufferfish arose by fusion of pairs of ancestral chromosomes after their lineages diverged from platyfish ∼195 million years ago. Zebrafish and human genomes provide outgroups to root observed changes. These studies identify likely genome assembly errors, characterize chromosome fusion events, distinguish lineage-independent chromosome fusions, show that the teleost genome duplication does not appear to have accelerated the rate of translocations, and reveal the stability of syntenies and gene orders in teleost chromosomes over hundreds of millions of years.
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Affiliation(s)
- Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Julian Catchen
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
| | - Indrajit Nanda
- Institute of Human Genetics, University of Würzburg, D-97074 Würzburg, Germany
| | - Wesley Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Ron Walter
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666
| | - Manfred Schartl
- Physiological Chemistry, University of Würzburg, Biozentrum, Am Hubland, and Comprehensive Cancer Center, University Clinic Würzburg, 97074 Würzburg, Germany
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15
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Culumber ZW. Pigmentation in Xiphophorus: an emerging system in ecological and evolutionary genetics. Zebrafish 2013; 11:57-70. [PMID: 24320948 DOI: 10.1089/zeb.2013.0939] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The genus Xiphophorus has great potential to contribute to the study of vertebrate pigmentation and elucidating the relative influence of ecology, physiology, and behavior on evolution at the molecular level. More importantly, the association between pigmentation and a functional oncogene offers the potential to understand the evolution and maintenance of cancer-causing genetic elements. Using criteria laid out recently in the literature, I demonstrate the power of the Xiphophorus system for studying pigment evolution through integrative organismal biology. Using the most recent phylogeny, the phylogenetic distribution of several important pigmentation loci are reevaluated. I then review support for existing hypotheses of the functional importance of pigmentation. Finally, new observations and hypotheses regarding some of the characteristics of pigment patterns in natural populations and open questions and future directions in the study of the evolution of these traits are discussed.
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Affiliation(s)
- Zachary W Culumber
- 1 Centro de Investigaciones Cientificas de las Huastecas "Aguazarca" , Calnali, Mexico
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16
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Cui R, Schumer M, Kruesi K, Walter R, Andolfatto P, Rosenthal GG. Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes. Evolution 2013; 67:2166-79. [PMID: 23888843 DOI: 10.1111/evo.12099] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 02/26/2013] [Indexed: 01/25/2023]
Abstract
Hybridization is increasingly being recognized as a widespread process, even between ecologically and behaviorally divergent animal species. Determining phylogenetic relationships in the presence of hybridization remains a major challenge for evolutionary biologists, but advances in sequencing technology and phylogenetic techniques are beginning to address these challenges. Here we reconstruct evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by remarkable morphological diversity and behavioral barriers to interspecific mating. Past attempts to reconstruct phylogenetic relationships within Xiphophorus have produced conflicting results. Because many of the 26 species in the genus are interfertile, these conflicts are likely due to hybridization. Using genomic data, we resolve a high-confidence species tree of Xiphophorus that accounts for both incomplete lineage sorting and hybridization. Our results allow us to reexamine a long-standing controversy about the evolution of the sexually selected sword in Xiphophorus, and demonstrate that hybridization has been strikingly widespread in the evolutionary history of this genus.
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Affiliation(s)
- Rongfeng Cui
- Department of Biology, Texas A&M University, TAMU, College Station, Texas, 77843, USA.
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17
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Schumer M, Cui R, Boussau B, Walter R, Rosenthal G, Andolfatto P. An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences. Evolution 2013; 67:1155-68. [PMID: 23550763 PMCID: PMC3621027 DOI: 10.1111/evo.12009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Once thought rare in animal taxa, hybridization has been increasingly recognized as an important and common force in animal evolution. In the past decade, a number of studies have suggested that hybridization has driven speciation in some animal groups. We investigate the signature of hybridization in the genome of a putative hybrid species, Xiphophorus clemenciae, through whole genome sequencing of this species and its hypothesized progenitors. Based on analysis of this data, we find that X. clemenciae is unlikely to have been derived from admixture between its proposed parental species. However, we find significant evidence for recent gene flow between Xiphophorus species. Although we detect genetic exchange in two pairs of species analyzed, the proportion of genomic regions that can be attributed to hybrid origin is small, suggesting that strong behavioral premating isolation prevents frequent hybridization in Xiphophorus. The direction of gene flow between species is potentially consistent with a role for sexual selection in mediating hybridization.
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Affiliation(s)
- Molly Schumer
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA.
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18
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The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nat Genet 2013; 45:567-72. [PMID: 23542700 PMCID: PMC3677569 DOI: 10.1038/ng.2604] [Citation(s) in RCA: 190] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 03/01/2013] [Indexed: 01/23/2023]
Abstract
Several attributes intuitively considered to be typical mammalian features, such as complex behavior, live birth, and malignant diseases like cancer, also appeared several times independently in so-called “lower” vertebrates. The genetic mechanisms underlying the evolution of these elaborate traits are poorly understood. The platyfish, Xiphophorus maculatus, offers a unique model to better understand the molecular biology of such traits. Herein we detail sequencing of the platyfish genome. Integrating genome assembly with extensive genetic maps uncovered that fish, in contrast to mammals, exhibit an unexpected evolutionary stability of chromosomes. Genes associated with viviparity show signatures of positive selection identifying new putative functional domains and rare cases of parallel evolution. We also discovered that genes implicated in cognition possess an unexpected high rate of duplicate gene retention after the teleost genome duplication suggesting a hypothesis for the evolution of the great behavioral complexity in fish, which exceeds that in amphibians and reptiles.
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Apodaca JJ, Trexler JC, Jue NK, Schrader M, Travis J. Large-Scale Natural Disturbance Alters Genetic Population Structure of the Sailfin Molly, Poecilia latipinna. Am Nat 2013; 181:254-63. [DOI: 10.1086/668831] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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20
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Kelley JL, Passow CN, Plath M, Arias Rodriguez L, Yee MC, Tobler M. Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome. BMC Genomics 2012; 13:652. [PMID: 23170846 PMCID: PMC3585874 DOI: 10.1186/1471-2164-13-652] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 10/22/2012] [Indexed: 01/12/2023] Open
Abstract
Background Elucidating the genomic basis of adaptation and speciation is a major challenge in natural systems with large quantities of environmental and phenotypic data, mostly because of the scarcity of genomic resources for non-model organisms. The Atlantic molly (Poecilia mexicana, Poeciliidae) is a small livebearing fish that has been extensively studied for evolutionary ecology research, particularly because this species has repeatedly colonized extreme environments in the form of caves and toxic hydrogen sulfide containing springs. In such extreme environments, populations show strong patterns of adaptive trait divergence and the emergence of reproductive isolation. Here, we used RNA-sequencing to assemble and annotate the first transcriptome of P. mexicana to facilitate ecological genomics studies in the future and aid the identification of genes underlying adaptation and speciation in the system. Description We provide the first annotated reference transcriptome of P. mexicana. Our transcriptome shows high congruence with other published fish transcriptomes, including that of the guppy, medaka, zebrafish, and stickleback. Transcriptome annotation uncovered the presence of candidate genes relevant in the study of adaptation to extreme environments. We describe general and oxidative stress response genes as well as genes involved in pathways induced by hypoxia or involved in sulfide metabolism. To facilitate future comparative analyses, we also conducted quantitative comparisons between P. mexicana from different river drainages. 106,524 single nucleotide polymorphisms were detected in our dataset, including potential markers that are putatively fixed across drainages. Furthermore, specimens from different drainages exhibited some consistent differences in gene regulation. Conclusions Our study provides a valuable genomic resource to study the molecular underpinnings of adaptation to extreme environments in replicated sulfide spring and cave environments. In addition, this study adds to the increasing number of genomic resources in the family Poeciliidae, which are widely used in comparative analyses of behavior, ecology, evolution, and medical genetics.
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Affiliation(s)
- Joanna L Kelley
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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21
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Popa A, Samollow P, Gautier C, Mouchiroud D. The sex-specific impact of meiotic recombination on nucleotide composition. Genome Biol Evol 2012; 4:412-22. [PMID: 22417915 PMCID: PMC3318449 DOI: 10.1093/gbe/evs023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Meiotic recombination is an important evolutionary force shaping the nucleotide landscape of genomes. For most vertebrates, the frequency of recombination varies slightly or considerably between the sexes (heterochiasmy). In humans, male, rather than female, recombination rate has been found to be more highly correlated with the guanine and cytosine (GC) content across the genome. In the present study, we review the results in human and extend the examination of the evolutionary impact of heterochiasmy beyond primates to include four additional eutherian mammals (mouse, dog, pig, and sheep), a metatherian mammal (opossum), and a bird (chicken). Specifically, we compared sex-specific recombination rates (RRs) with nucleotide substitution patterns evaluated in transposable elements. Our results, based on a comparative approach, reveal a great diversity in the relationship between heterochiasmy and nucleotide composition. We find that the stronger male impact on this relationship is a conserved feature of human, mouse, dog, and sheep. In contrast, variation in genomic GC content in pig and opossum is more strongly correlated with female, rather than male, RR. Moreover, we show that the sex-differential impact of recombination is mainly driven by the chromosomal localization of recombination events. Independent of sex, the higher the RR in a genomic region and the longer this recombination activity is conserved in time, the stronger the bias in nucleotide substitution pattern, through such mechanisms as biased gene conversion. Over time, this bias will increase the local GC content of the region.
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22
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Yang H, Savage MG, Hazlewood L, Walter RB, Tiersch TR. Offspring production with cryopreserved sperm from a live-bearing fish Xiphophorus maculatus and implications for female fecundity. Comp Biochem Physiol C Toxicol Pharmacol 2012; 155:55-63. [PMID: 21616165 PMCID: PMC3189285 DOI: 10.1016/j.cbpc.2011.04.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 04/28/2011] [Accepted: 04/28/2011] [Indexed: 11/16/2022]
Abstract
Xiphophorus fishes are well-established models for biomedical research of spontaneous or induced tumors, and their use in research dates back to the 1930s. Currently, 58 well-pedigreed lines exist among 24 Xiphophorus species housed as live animals at the Xiphophorus Genetic Stock Center. The technique of sperm cryopreservation has been applied to preserve these valuable genetic resources, and production of offspring has been reported with cryopreserved sperm in two species (X. helleri and X. couchianus). The goal of this research was to establish protocols for sperm cryopreservation and artificial insemination that yield live young in X. maculatus, a widely used research species. The objectives were to: 1) collect basic biological characteristics of males, and quantify the sperm production yield after crushing of dissected testis; 2) cryopreserve sperm from X. maculatus by adapting as necessary the protocols for sperm cryopreservation of X. helleri and X. couchianus; 3) use cryopreserved sperm to inseminate virgin females of X maculatus and other species (X. helleri and X. couchianus), and 4) compare experimental trials over a 3-year period to identify opportunities for improving female fecundity. In total, 117 males were used in this study with a standard length of 2.5 ± 0.3 cm (mean ± SD), body weight of 0.474 ± 0.149 g, and dissected testis weight of 7.1 ± 3.7 mg. Calculation of sperm availability showed 5.9 ± 2.8 × 10(6) sperm cells per mg of testis weight. Offspring were produced from cryopreserved sperm. Male-to-male variation (1-70%) was observed in post-thaw motility despite little variation in motility before freezing (60-90%) or genetic variation (~100 generations of sib-mating). Comparisons of biological factors of males did not have significant correlations with the production of live young, and the influence of females on production of young was identified from the comparison of artificial insemination over 3 years. Overall, this study describes offspring production from cryopreserved sperm in a third species of Xiphophorus fishes, and identifies the opportunities for improving female fecundity which is essential for establishment of germplasm repositories for Xiphophorus fishes.
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Affiliation(s)
- Huiping Yang
- Aquaculture Research Station, Louisiana State University Agricultural Center, 2410 Ben Hur Road, Baton Rouge, Louisiana 70820, USA.
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23
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GUTIÉRREZ MARÍALAURA, GARCÍA GRACIELA. A preliminary linkage map using spotted melanic laboratory strains of the livebearing fish Phalloceros caudimaculatus var. reticulata (Cyprinodontiformes: Poeciliidae). J Genet 2011. [DOI: 10.1007/s12041-011-0085-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Culumber ZW, Fisher HS, Tobler M, Mateos M, Barber PH, Sorenson MD, Rosenthal GG. Replicated hybrid zones of Xiphophorus swordtails along an elevational gradient. Mol Ecol 2010; 20:342-56. [PMID: 21210879 DOI: 10.1111/j.1365-294x.2010.04949.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Natural hybrid zones provide opportunities to study a range of evolutionary phenomena from speciation to the genetic basis of fitness-related traits. We show that widespread hybridization has occurred between two neo-tropical stream fishes with partial reproductive isolation. Phylogenetic analyses of mitochondrial sequence data showed that the swordtail fish Xiphophorus birchmanni is monophyletic and that X. malinche is part of an independent monophyletic clade with other species. Using informative single nucleotide polymorphisms in one mitochondrial and three nuclear intron loci, we genotyped 776 specimens collected from twenty-three sites along seven separate stream reaches. Hybrid zones occurred in replicated fashion in all stream reaches along a gradient from high to low elevation. Genotyping revealed substantial variation in parental and hybrid frequencies among localities. Tests of F(IS) and linkage disequilibrium (LD) revealed generally low F(IS) and LD except in five populations where both parental species and hybrids were found suggesting incomplete reproductive isolation. In these locations, heterozygote deficiency and LD were high, which suggests either selection against early generation hybrids or assortative mating. These data lay the foundation to study the adaptive basis of the replicated hybrid zone structure and for future integration of behaviour and genetics to determine the processes that lead to the population genetic patterns observed in these hybrid zones.
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Affiliation(s)
- Z W Culumber
- Texas A&M Department of Biology, 3258 TAMU, College Station, TX 77843-3258, USA.
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25
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Portnoy DS, Renshaw MA, Hollenbeck CM, Gold JR. A genetic linkage map of red drum, Sciaenops ocellatus. Anim Genet 2010; 41:630-41. [DOI: 10.1111/j.1365-2052.2010.02059.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Experimental animal models are extremely valuable for the study of human diseases, especially those with underlying genetic components. The exploitation of various animal models, from fruitflies to mice, has led to major advances in our understanding of the etiologies of many diseases, including cancer. Cutaneous malignant melanoma is a form of cancer for which both environmental insult (i.e., UV) and hereditary predisposition are major causative factors. Fish melanoma models have been used in studies of both spontaneous and induced melanoma formation. Genetic hybrids between platyfish and swordtails, different species of the genus Xiphophorus, have been studied since the 1920s to identify genetic determinants of pigmentation and melanoma formation. Recently, transgenesis has been used to develop zebrafish and medaka models for melanoma research. This review will provide a historical perspective on the use of fish models in melanoma research, and an updated summary of current and prospective studies using these unique experimental systems.
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Affiliation(s)
- E Elizabeth Patton
- Institute for Genetics and Molecular Medicine, MRC Human Genetics Unit and Division of Cancer Research, The University of Edinburgh, Edinburgh, UK.
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27
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TATARENKOV A, HEALEY CIM, AVISE JC. Microgeographic population structure of green swordail fish: genetic differentiation despite abundant migration. Mol Ecol 2009; 19:257-68. [DOI: 10.1111/j.1365-294x.2009.04464.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Mapping loci associated with tail color and sex determination in the short-lived fish Nothobranchius furzeri. Genetics 2009; 183:1385-95. [PMID: 19786620 DOI: 10.1534/genetics.109.108670] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The African fish Nothobranchius furzeri is the shortest-lived vertebrate species that can reproduce in captivity, with a median life span of 9-11 weeks for the shortest-lived strain. Natural populations of N. furzeri display differences in life span, aging biomarkers, behavior, and color, which make N. furzeri a unique vertebrate system for studying the genetic basis of these traits. We mapped regions of the genome involved in sex determination and tail color by genotyping microsatellite markers in the F(2) progeny of a cross between a short-lived, yellow-tailed strain and a long-lived, red-tailed strain of N. furzeri. We identified one region linked with the yellow/red tail color that maps close to melanocortin 1 receptor (mc1r), a gene involved in pigmentation in several vertebrate species. Analysis of the segregation of sex-linked markers revealed that N. furzeri has a genetic sex determination system with males as the heterogametic sex and markedly reduced recombination in the male sex-determining region. Our results demonstrate that both naturally-evolved pigmentation differences and sex determination in N. furzeri are controlled by simple genetic mechanisms and set the stage for the molecular genetic dissection of factors underlying such traits. The microsatellite-based linkage map we developed for N. furzeri will also facilitate analysis of the genetic architecture of traits that characterize this group of vertebrates, including short life span and adaptation to extreme environmental conditions.
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Bai JJ, Liu YF, Quan YC, He XP, Ye X. The complete mitochondrial genome of the RR-B strain of swordtail (Xiphophorus helleri). MITOCHONDRIAL DNA 2009; 20:72-7. [PMID: 19575330 DOI: 10.1080/19401730903033105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
BACKGROUND AND AIMS The swordtail (Xiphophorus helleri) has been used in studies of behavior, phylogenetics, genetics, physiology, cell biology, cancer research, and biomedicine. Mitochondrial DNA (mtDNA) studies are of pressing need in order to assess the population history of the species. MATERIALS AND METHOD In this study, we present the complete mtDNA genome sequence of two specimens: one from a RR-B strain, a 27-generation inbred line; and one non-selective swordtail with red eyes and red body color from the Guangzhou market, measuring 16,638 and 16,635 bp, respectively. RESULTS The genome comprises 13 protein-coding genes, 22 tRNAs, two rRNAs and a major non-coding region. The comparison of the two specimens' mitogenomes revealed a relatively low number (57) of single nucleotide polymorphisms-29 located in protein-coding genes, 11 in rRNA genes, six in tRNA genes, and six in the non-coding region. CONCLUSION We present an important genetic resource for the RR-B strain of swordtails and swordtail species in general.
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Affiliation(s)
- Jun-Jie Bai
- Key Laboratory of Tropical and Subtropical Fish Breeding & Cultivation, CAFS, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, People's Republic of China.
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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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31
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Tatarenkov A, Healey CIM, Grether GF, Avise JC. Pronounced reproductive skew in a natural population of green swordtails, Xiphophorus helleri. Mol Ecol 2008; 17:4522-34. [PMID: 18986497 DOI: 10.1111/j.1365-294x.2008.03936.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
For many species in nature, a sire's progeny may be distributed among a few or many dams. This poses logistical challenges--typically much greater across males than across females--for assessing means and variances in mating success (number of mates) and reproductive success (number of progeny). Here we overcome these difficulties by exhaustively analyzing a population of green swordtail fish (Xiphophorus helleri) for genetic paternity (and maternity) using a suite of highly polymorphic microsatellite loci. Genetic analyses of 1476 progeny from 69 pregnant females and 158 candidate sires revealed pronounced skews in male reproductive success both within and among broods. These skews were statistically significant, greater than in females, and correlated in males but not in females with mating success. We also compare the standardized variances in swordtail reproductive success to the few such available estimates for other taxa, notably several mammal species with varied mating systems and degrees of sexual dimorphism. The comparison showed that the opportunity for selection on male X. helleri is among the highest yet reported in fishes, and it is intermediate compared to estimates available for mammals. This study is one of a few exhaustive genetic assessments of joint-sex parentage in a natural fish population, and results are relevant to the operation of sexual selection in this sexually dimorphic, high-fecundity species.
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Affiliation(s)
- Andrey Tatarenkov
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA.
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Aliza D, Ismail IS, Kuah MK, Shu-Chien AC, Tengku Muhammad TS. Identification of Wap65, a human homologue of hemopexin as a copper-inducible gene in swordtail fish, Xiphophorus helleri. FISH PHYSIOLOGY AND BIOCHEMISTRY 2008; 34:129-138. [PMID: 18649030 DOI: 10.1007/s10695-007-9153-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Accepted: 06/26/2007] [Indexed: 05/26/2023]
Abstract
Copper is one of the major heavy metal pollutants found in the aquatic environment. Therefore, it is important for determining the genes that play a key role in copper metabolism in aquatic organisms. This study, thus, aimed to identify a new copper-inducible gene in swordtail fish, Xiphophorus helleri. Using ACP-based RT-PCR coupled with RLM-RACE, we cloned Wap65, a mammalian homologue of hemopexin gene. The gene exhibits high identity at amino acid levels with the Wap65 gene of other fish species (42-68%) and mammalian hemopexin gene (35-37%). In addition, ten cysteine and two histidine residues are conserved in the swordtail fish Wap65 gene. These cysteine residues are vital for structural integrity, and histidine residues provide high binding affinity towards heme. As revealed by RT-PCR, the gene was upregulated in swordtail fish that were exposed to copper in a dose- and time-dependent manner. Therefore, the identification of Wap65, a mammalian homologue of hemopexin, as a new copper-inducible gene will provide greater insight into the role of this gene in copper metabolism.
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Affiliation(s)
- Dwinna Aliza
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
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Ruymgaart AP, Heater SJ, Oehlers LP, Rains JD, Walter RB. Characterization and purification of flap endonuclease-1 (xiFEN-1) from Xiphophorus maculatus. Zebrafish 2008; 1:273-85. [PMID: 18248237 DOI: 10.1089/zeb.2004.1.273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The cloning, gene structure, and expression of flap endonuclease-1 (xiFEN1) from Xiphophorus maculates are presented. The xiFEN1 gene structure was found to include 8 exons and 7 introns. The Xiphophorus FEN1 cDNA sequence contained an open reading frame that encoded a 380 amino acid protein with a predicted mass of 43 kDa. The intact FEN1 cDNA was subcloned into a bacterial expression vector (pET101-xiFEN1ct) and recombinant xiFEN1 enzyme purified from E. colicell extracts. The pET101-xiFEN1ct translation product was a 3' fusion protein with a ~3 kDa vector-encoded carboxy terminal extension designed to facilitate protein recognition and purification. The xiFEN1 fusion protein was purified and its amino acid sequence verified by Western blot analysis and tryptic peptide mass fingerprinting. The purified recombinant protein was assessed for enzyme specificity using several different oligonucleotide substrates having select flap overhangs. Also reported are Michaelis steady state kinetic values of enzymatic activity for the xiFEN1 directly compared with human FEN1 activity. xiFEN1 displayed a five-fold greater Km and six-fold lower catalytic efficiency (kcat/Km) than observed for the hFEN1.
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Affiliation(s)
- Arnold P Ruymgaart
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, USA
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Kazianis S, Nairn RS, Walter RB, Johnston DA, Kumar J, Trono D, Della-Coletta L, Gimenez-Conti I, Rains JD, Williams EL, Pino BM, Mamerow MM, Kochan KJ, Schartl M, Vielkind JR, Volff JN, Woolcock B, Morizot DC. The genetic map of Xiphophorus fishes represented by 24 multipoint linkage groups. Zebrafish 2008; 1:287-304. [PMID: 18248238 DOI: 10.1089/zeb.2004.1.287] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hybrids between distinct Xiphophorus species have been utilized for over 70 years to study melanoma and other neoplasms that can develop spontaneously in hybrid offspring. Genetic linkage mapping has proven to be important in delineating genomic areas that harbor oncogenes and tumor suppressors. Within this report, two parallel backcrosses have been utilized to generate a genetic linkage map for Xiphophorus fishes. Isozyme/allozyme, RFLP and PCR-based mapping techniques, including AP-PCR/RAPDs and microsatellite loci were utilized. The derived linkage map provides a total of 403 mapped polymorphisms distributed among 24 linkage groups, representative of 24 acro- and telocentric chromosome pairs. Genomic coverage is approximately one marker per 5.8 cM. Detailed genotypic analysis of the utilized hybrids revealed two areas of the genome that show significant segregation distortion. Loci within the linkage group harboring the sex determining locus (LG 24) and an autosomal linkage group (LG 21) show highly significant deviations from Mendelian expectations. This phenomenon is not present in a hybrid cross that utilizes a different backcross hybrid progenitor species. The derived map with sequence-tagged markers provides a framework for physical map generation, large-scale genomic sequencing and will further enable cross-genome comparisons of vertebrate genomes.
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Affiliation(s)
- Steven Kazianis
- Wistar Institute, Program of Molecular and Cellular Oncogenesis, Philadelphia, Pennsylvania 19104, USA.
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Walter RB, Ju Z, Martinez A, Amemiya C, Samollow PB. Genomic resources for Xiphophorus research. Zebrafish 2008; 3:11-22. [PMID: 18248243 DOI: 10.1089/zeb.2006.3.11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Xiphophorus fishes and interspecies hybrids are used in many areas of contemporary research. Due to their high degree of heterozygosity Xiphophorus interspecies hybrids are extremely valuable models for molecular genetic study of gene regulation in physiology and behavior. Historically, Xiphophorus fish have made a contribution to understanding the genetics underlying tumorigenesis but the role this experimental model system may play in contemporary comparative biology has only just begun to be realized. In spite of many advantages a genome-level Xiphophorus sequencing project has not yet been initiated. In order to set a stage for a genome-level initiative, many Xiphophorus resources have recently been, or are currently being developed. Recent completion of the Xiphophorus gene linkage map, construction of microsatellite marker and EST databases, and the accessibility of BAC library resources hallmark the progress in development of genomic capabilities for Xiphophorus investigations. Herein we review current Xiphophorus genomic resources and to provide the reader with information that will enable them to access these resources available to enhance their investigations.
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Affiliation(s)
- Ronald B Walter
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666-4616, USA.
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Affiliation(s)
- Ferenc Müller
- Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, Karlsruhe D-76021, Germany.
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Abstract
The poeciliid fish genus Xiphophorus provides important models for investigating the etiology and genetics of sunlight-induced melanoma. Interspecific hybrids generated among platyfish and swordtails have been used as genetic tumor models, particularly for cutaneous malignant melanoma (CMM), for more than 6 decades. Oncogene and tumor suppressor gene involvement in a variety of spontaneous and carcinogen-induced tumors has been and continues to be extensively studied. Select hybrids develop melanoma spontaneously or after acute or chronic exposure to ultraviolet radiation. Many scientists believe that the etiology of CMM and particularly its initiation is different from other types of sunlight-induced skin cancers, and may involve free radical chemistry rather than the direct absorption of UVB by DNA. Xiphophorus offers a unique platform to scrutinize this question and determine the types of DNA damage that are involved, the solar wavelength ranges that are important, and the role of DNA repair genes in early tumorigenesis. The diverse photochemical and photobiological responses observed in the different Xiphophorus species and interspecies hybrids suggest that heritable traits governing DNA damage induction and repair may be involved in the susceptibility of Xiphophorus hybrids to melanomagenesis.
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Affiliation(s)
- David L Mitchell
- Department of Carcinogenesis, University of Texas M.D. Anderson Cancer Center, Park Road 1C, P.O. Box 389, Smithville, TX 78957, USA.
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Brummell M, Kazianis S, Davidson WS, Breden F. Conservation of synteny between guppy and Xiphophorus genomes. Zebrafish 2008; 3:347-57. [PMID: 18377215 DOI: 10.1089/zeb.2006.3.347] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The guppy and fish in the genus Xiphophorus have both been important model systems for the study of natural and sexual selection for over 50 years. Whereas the guppy is unique in the degree to which the environmental variables shaping phenotypic variation are known, Xiphophorus has the advantage that genomic resources have been developed due to the utility of this taxon for the study of melanoma. If linkage maps for the guppy and Xiphophorus are similar, genomic resources developed in Xiphophorus will be useful in the guppy. The authors used an F2 mapping cross of divergent populations of the guppy to construct partial female and male genetic linkage maps incorporating microsatellite markers derived from Xiphophorus mapping efforts. Flanking regions for a sample of microsatellites occurring in maps for both taxa were sequenced in the guppy and compared to published sequences from Xiphophorus. This confirmed that these loci were homologous and estimated the divergence in neutral nuclear DNA to be 0.21 substitutions per site. The female map comprises 16 linked markers on six linkage groups, and the male map comprises 24 markers on nine linkage groups. Linkage relationships among loci homologous in the guppy and Xiphophorus primarily show conservation of genetic architecture between species, but several major changes were detected.
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Affiliation(s)
- Martin Brummell
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
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HANKISON SJ, PTACEK MB. Geographical variation of genetic and phenotypic traits in the Mexican sailfin mollies,Poecilia veliferaandP. petenensis. Mol Ecol 2008; 17:2219-33. [DOI: 10.1111/j.1365-294x.2008.03736.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Literature watch. Xiphophorus. Zebrafish 2008; 3:105-10. [PMID: 18248251 DOI: 10.1089/zeb.2006.3.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Recent papers on zebrafish and other aquarium fish models. Zebrafish 2008; 1:305-11. [PMID: 18248239 DOI: 10.1089/zeb.2004.1.305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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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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Butler AP, Trono D, Coletta LD, Beard R, Fraijo R, Kazianis S, Nairn RS. Regulation of CDKN2A/B and Retinoblastoma genes in Xiphophorus melanoma. Comp Biochem Physiol C Toxicol Pharmacol 2007; 145:145-55. [PMID: 17011832 DOI: 10.1016/j.cbpc.2006.07.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2006] [Revised: 07/12/2006] [Accepted: 07/31/2006] [Indexed: 02/02/2023]
Abstract
Xiphophorus interspecies hybrids provide several well-characterized genetic models of melanoma susceptibility. The Xiphophorus CDKN2A/B gene, homologous to mammalian CDKN2A/B cyclin-dependent kinase inhibitors (p16 and p15), is a candidate tumor susceptibility gene in these models. Using real-time PCR and Western blot analysis, we analyzed expression of CDKN2A/B in spontaneous and UV-induced primary melanomas from individual backcross hybrid fish. We found that CDKN2A/B mRNA is highly expressed in melanomas (18-fold), relative to other fish tissues. Expression is also elevated, to a lesser extent (9.5-fold), in melanized skin from tumor-bearing fish. However, quantitative levels of CDKN2A/B mRNA in tumors varied considerably and positively correlated with expression of the Xmrk oncogene, suggesting possible functional interaction between Xmrk and CDKN2A/B expression. As a homolog corresponding to members of the mammalian CDKN2 family which regulate cell cycle progression at the G1 checkpoint, the CDKN2A/B p13 protein is a putative regulator of the G1 checkpoint apparatus in Xiphophorus. Since CDKN2A is often observed to be inversely regulated compared to RB in some human tumors, and is capable of transcriptionally regulating RB in human ovarian tumors, we cloned the Xiphophorus maculatus RB cDNA and analyzed RB expression by real-time PCR and Western blot analysis in the fish melanomas. These experiments were designed to ascertain whether CDKN2A/B and RB expression were inversely correlated. Our results indicate that RB mRNA was consistently expressed at only a 2-fold higher level in both tumors and melanized skin than in muscle. Qualitatively similar results were obtained for protein expression. These results collectively suggest that (i) Xmrk and CDKN2A/B may be co-regulated at the transcriptional level, and (ii) there is little, if any, alteration of RB expression in Xiphophorus melanomas.
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Affiliation(s)
- Andrew P Butler
- Virginia Harris Cockrell Cancer Research Center, Department of Carcinogenesis, Science Park-Research Division, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
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Franch R, Louro B, Tsalavouta M, Chatziplis D, Tsigenopoulos CS, Sarropoulou E, Antonello J, Magoulas A, Mylonas CC, Babbucci M, Patarnello T, Power DM, Kotoulas G, Bargelloni L. A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L. Genetics 2006; 174:851-61. [PMID: 16951080 PMCID: PMC1602104 DOI: 10.1534/genetics.106.059014] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The gilthead sea bream (Sparus aurata L.) is a marine fish of great importance for fisheries and aquaculture. It has also a peculiar sex-determination system, being a protandrous hermaphrodite. Here we report the construction of a first-generation genetic linkage map for S. aurata, based on 204 microsatellite markers. Twenty-six linkage groups (LG) were found. The total map length was 1241.9 cM. The ratio between sex-specific map lengths was 1:1.2 (male:female). Comparison with a preliminary radiation hybrid (RH) map reveals a good concordance, as all markers located in a single LG are located in a single RH group, except for Ad-25 and CId-31. Comparison with the Tetraodon nigroviridis genome revealed a considerable number of evolutionary conserved regions (ECRs) between the two species. The mean size of ECRs was 182 bp (sequence identity 60-90%). Forty-one ECRs have a known chromosomal location in the pufferfish genome. Despite the limited number of anchoring points, significant syntenic relationships were found. The linkage map presented here provides a robust comparative framework for QTL analysis in S. aurata and is a step toward the identification of genetic loci involved both in the determination of economically important traits and in the individual timing of sex reversal.
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Affiliation(s)
- Rafaella Franch
- Department of Public Health, University of Padova, 35121 Padova, Italy
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45
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Lampert KP, Lamatsch DK, Schories S, Hopf A, García de León FJ, Schartl M. Microsatellites for the gynogenetic Amazon molly, Poecilia formosa: useful tools for detection of mutation rate, ploidy determination and overall genetic diversity. J Genet 2006; 85:67-71. [PMID: 16809843 DOI: 10.1007/bf02728973] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kathrin P Lampert
- Department of Physiological Chemistry I, University of Wuerzburg, Biozentrum, Am Hubland, 97074 Wuerzburg, Germany.
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46
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Yang H, Hazlewood L, Walter RB, Tiersch TR. Effect of osmotic immobilization on refrigerated storage and cryopreservation of sperm from a viviparous fish, the green swordtail Xiphophorus helleri. Cryobiology 2006; 52:209-18. [PMID: 16375884 PMCID: PMC5593140 DOI: 10.1016/j.cryobiol.2005.11.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2005] [Revised: 11/01/2005] [Accepted: 11/07/2005] [Indexed: 11/20/2022]
Abstract
In this study, refrigerated storage and cryopreservation of sperm from the green swordtail Xiphophorus helleri were investigated. Previous cryopreservation research in this species utilized motile sperm because unlike in most fish species, Xiphophorus sperm can remain continuously motile after collection for a week with refrigerated storage. However, this species reproduces by internal fertilization, and given the significant requirements for motility within the female reproductive tract and potential limitations on sperm energetic capacities, immobilization of sperm prior to insemination could be used to improve fertilization success. Thus, the goal in this study was to use osmotic pressure to inhibit the motility of sperm after collection from X. helleri, and to test the effect of immobilization on refrigerated storage and cryopreservation. The objectives were to: (1) estimate the motility of sperm at different osmotic pressures, and determine an osmotic pressure suitable for immobilization; (2) cryopreserve the immobilized sperm, and estimate the motility after thawing with or without dilution, and (3) compare motility of non-immobilized and immobilized sperm after thawing, centrifugation, and washing to remove cryoprotectant. Motility was determined when sperm were suspended in 11 different osmotic pressures (24-500 mOsmol/kg) of Hanks' balanced salt solution (HBSS). Motility was observed between 116 and 425 mOsmol/kg. Sperm were not motile when the osmolality was lower than 116 or higher than 425 mOsmol/kg. Motility of the immobilized (non-motile) sperm could be activated by changing the osmotic pressure to 291-316 mOsmol/kg, and motility of immobilized sperm from hypertonic HBSS (425 mOsmol/kg) was significantly higher than that from hypotonic HBSS (145 mOsmol/kg) after 48 h of storage. At an osmolality of 500 mOsmol/kg, HBSS was used as extender to maintain immobilized sperm during cryopreservation with glycerol as the cryoprotectant. High motility (approximately 55%) was obtained in sperm after thawing when cryopreserved with 10-15% glycerol, and dilution of thawed sperm in fresh HBSS (1:4; V:V) was found to decrease the motility significantly. No difference was found in the motility of thawed sperm cryopreserved with 14% glycerol and extended in 310 and 500 mOsmol/kg HBSS. Washing by centrifugation prolonged the motility of thawed sperm from 24 to 72 h in HBSS at 310 and 500 mOsmol/kg. This study showed that sperm from X. helleri could be immobilized by use of specific osmotic pressures, and that the immobilization did not affect sperm motility after thawing. The immobilization of sperm by osmotic pressure could minimize reduction of the energetic capacities necessary for insemination, traversal, and residence within the female reproductive tract, and fertilization.
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Affiliation(s)
- Huiping Yang
- Aquaculture Research Station, Louisiana Agricultural Experiment Station, Louisiana State University Agricultural Center, 2410 Ben Hur Road, Baton Rouge, LA 70820, USA
- Graduate School of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, People’s Republic of China
| | - Leona Hazlewood
- Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX 78666, USA
| | - Ronald B. Walter
- Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX 78666, USA
| | - Terrence R. Tiersch
- Aquaculture Research Station, Louisiana Agricultural Experiment Station, Louisiana State University Agricultural Center, 2410 Ben Hur Road, Baton Rouge, LA 70820, USA
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Woolcock B, Kazianis S, Lucito R, Walter R, Kallman K, Morizot D, Vielkind J. Allele-Specific Marker Generation and Linkage Mapping on theXiphophorusSex Chromosomes. Zebrafish 2006; 3:23-37. [DOI: 10.1089/zeb.2006.3.23] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- B. Woolcock
- British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - S. Kazianis
- The Wistar Institute, Program of Molecular and Cellular Oncogenesis, Philadelphia, Pennsylvania
| | - R. Lucito
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - R.B. Walter
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marco, Texas
| | - K.D. Kallman
- Division of Vertebrate Zoology (Ichthyology), American Museum of Natural History, New York, New York
| | - D.C. Morizot
- Science Park Research Division, MD Anderson Cancer Center, Smithville, Texas
| | - J.R. Vielkind
- British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
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48
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Rosenthal GG, De León FJG. Sexual Behavior, Genes, and Evolution inXiphophorus. Zebrafish 2006; 3:85-90. [DOI: 10.1089/zeb.2006.3.85] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Gil G. Rosenthal
- Department of Biology, Texas A & M University, College Station, Texas
| | - Francisco J. García De León
- Programa Planeación Ambiental y Conservación, Centro de Investigaciones Biológicas del Noroeste, La Paz, Mexico
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49
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Barnes DW, Mattingly CJ, Parton A, Dowell LM, Bayne CJ, Forrest JN. Marine organism cell biology and regulatory sequence discoveryin comparative functional genomics. Cytotechnology 2005; 46:123-37. [PMID: 19003267 PMCID: PMC3449718 DOI: 10.1007/s10616-005-1719-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2005] [Accepted: 08/04/2005] [Indexed: 01/28/2023] Open
Abstract
The use of bioinformatics to integrate phenotypic and genomic data from mammalian models is well established as a means of understanding human biology and disease. Beyond direct biomedical applications of these approaches in predicting structure–function relationships between coding sequences and protein activities, comparative studies also promote understanding of molecular evolution and the relationship between genomic sequence and morphological and physiological specialization. Recently recognized is the potential of comparative studies to identify functionally significant regulatory regions and to generate experimentally testable hypotheses that contribute to understanding mechanisms that regulate gene expression, including transcriptional activity, alternative splicing and transcript stability. Functional tests of hypotheses generated by computational approaches require experimentally tractable in vitro systems, including cell cultures. Comparative sequence analysis strategies that use genomic sequences from a variety of evolutionarily diverse organisms are critical for identifying conserved regulatory motifs in the 5′-upstream, 3′-downstream and introns of genes. Genomic sequences and gene orthologues in the first aquatic vertebrate and protovertebrate organisms to be fully sequenced (Fugu rubripes, Ciona intestinalis, Tetraodon nigroviridis, Danio rerio) as well as in the elasmobranchs, spiny dogfish shark (Squalus acanthias) and little skate (Raja erinacea), and marine invertebrate models such as the sea urchin (Strongylocentrotus purpuratus) are valuable in the prediction of putative genomic regulatory regions. Cell cultures have been derived for these and other model species. Data and tools resulting from these kinds of studies will contribute to understanding transcriptional regulation of biomedically important genes and provide new avenues for medical therapeutics and disease prevention.
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Affiliation(s)
- David W Barnes
- Mount Desert Island Biological Laboratory, Center for Marine Functional Genomics Studies, P.O. Box 35, Old Bar Harbour Road, Salisbury Cove, MA, 04672, USA,
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50
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Oehlers LP, Heater SJ, Rains JD, Wells MC, David WM, Walter RB. Gene structure, purification and characterization of DNA polymerase beta from Xiphophorus maculatus. Comp Biochem Physiol C Toxicol Pharmacol 2004; 138:311-24. [PMID: 15533789 DOI: 10.1016/j.cca.2004.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2004] [Revised: 06/23/2004] [Accepted: 06/30/2004] [Indexed: 11/28/2022]
Abstract
Cloning of the Xiphophorus maculatus Polbeta gene and overexpression of the recombinant Polbeta protein has been performed. The organization of the XiphPolbeta introns and exons, including intron-exon boundaries, have been assigned and were found to be similar to that for human Polbeta with identical exon sizes except for exon XII coding for an additional two amino acid residues in Xiphophorus. The cDNA sequence encoding the 337-amino acid X. maculatus DNA polymerase beta (Polbeta) protein was subcloned into the Escherichia coli expression plasmid pET. Induction of transformed E. coli cells resulted in the high-level expression of soluble recombinant Polbeta, which catalyzed DNA synthesis on template-primer substrates. The steady-state Michaelis constants (Km) and catalytic efficiencies (kcat/Km) of the recombinant XiphPolbeta for nucleotide insertion opposite single-nucleotide gap DNA substrates were measured and compared with previously published values for recombinant human Polbeta. Steady-state in vitro Km and kcat/Km values for correct nucleotide insertion by XiphPolbeta and human Polbeta were similar, although the recombinant Xiphophorus protein exhibited 2.5-7-fold higher catalytic efficiencies for dGTP and dCTP insertion versus human Polbeta. In contrast, the recombinant XiphPolbeta displayed significantly lower fidelities than human Polbeta for dNTP insertion opposite a single-nucleotide gap at 37 degrees C.
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Affiliation(s)
- Leon P Oehlers
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
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