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Hallingbäck HR, Pucholt P, Ingvarsson PK, Rönnberg-Wästljung AC, Berlin S. Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis. BMC Genomics 2021; 22:710. [PMID: 34600471 PMCID: PMC8487499 DOI: 10.1186/s12864-021-08021-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/14/2021] [Indexed: 01/24/2023] Open
Abstract
Background Sex chromosomes are in some species largely undifferentiated (homomorphic) with restricted sex determination regions. Homomorphic but different sex chromosomes are found in the closely related genera Populus and Salix indicating flexible sex determination systems, ideal for studies of processes involved in sex chromosome evolution. We have performed genome-wide association studies of sex and analysed sex chromosomes in a population of 265 wild collected Salix viminalis accessions and studied the sex determining locus. Results A total of 19,592 markers were used in association analyses using both Fisher’s exact tests and a single-marker mixed linear model, which resulted in 48 and 41 sex-associated (SA) markers respectively. Across all 48 SA markers, females were much more often heterozygous than males, which is expected if females were the heterogametic sex. The majority of the SA markers were, based on positions in the S. purpurea genome, located on chromosome 15, previously demonstrated to be the sex chromosome. Interestingly, when mapping the genotyping-by-sequencing sequence tag harbouring the two SA markers with the highest significance to the S. viminalis genomic scaffolds, five regions of very high similarity were found: three on a scaffold that represents a part of chromosome 15, one on a scaffold that represents a part of chromosome 9 and one on a scaffold not anchored to the genome. Based on segregation differences of the alleles at the two marker positions and on differences in PCR amplification between females and males we conclude that females had multiple copies of this DNA fragment (chromosome 9 and 15), whereas males only had one (chromosome 9). We therefore postulate that the female specific sequences have been copied from chromosome 9 and inserted on chromosome 15, subsequently developing into a hemizygous W chromosome linked region. Conclusions Our results support that sex determination in S. viminalis is controlled by one locus on chromosome 15. The segregation patterns observed at the SA markers furthermore confirm that S. viminalis females are the heterogametic sex. We also identified a translocation from chromosome 9 to the W chromosome. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08021-2.
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Affiliation(s)
- Henrik R Hallingbäck
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Box 7080, SE-750 07, Uppsala, Sweden.,Present Address: Skogforsk (The Forestry Research Institute of Sweden), Uppsala Science Park, SE-751 83, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Box 7080, SE-750 07, Uppsala, Sweden
| | - Pär K Ingvarsson
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Box 7080, SE-750 07, Uppsala, Sweden
| | - Ann Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Box 7080, SE-750 07, Uppsala, Sweden.
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Box 7080, SE-750 07, Uppsala, Sweden
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2
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McKinney GJ, Nichols KM, Ford MJ. A mobile sex-determining region, male-specific haplotypes and rearing environment influence age at maturity in Chinook salmon. Mol Ecol 2020; 30:131-147. [PMID: 33111366 DOI: 10.1111/mec.15712] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/28/2020] [Accepted: 10/15/2020] [Indexed: 12/14/2022]
Abstract
Variation in age at maturity is an important contributor to life history and demographic variation within and among species. The optimal age at maturity can vary by sex, and the ability of each sex to evolve towards its fitness optimum depends on the genetic architecture of maturation. Using GWAS of RAD sequencing data, we show that age at maturity in Chinook salmon exhibits sex-specific genetic architecture, with age at maturity in males influenced by large (up to 20 Mb) male-specific haplotypes. These regions showed no such effect in females. We also provide evidence for translocation of the sex-determining gene between two different chromosomes. This has important implications for sexually antagonistic selection, particularly that sex linkage of adaptive genes may differ within and among populations based on chromosomal location of the sex-determining gene. Our findings will facilitate research into the genetic causes of shifting demography in Chinook salmon as well as a better understanding of sex determination in this species and Pacific salmon in general.
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Affiliation(s)
- Garrett J McKinney
- NRC Research Associateship Program, Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Krista M Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Michael J Ford
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
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3
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The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome. PLoS One 2020; 15:e0240935. [PMID: 33119641 PMCID: PMC7595290 DOI: 10.1371/journal.pone.0240935] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022] Open
Abstract
Sockeye salmon (Oncorhynchus nerka) is a commercially and culturally important species to the people that live along the northern Pacific Ocean coast. There are two main sockeye salmon ecotypes—the ocean-going (anadromous) ecotype and the fresh-water ecotype known as kokanee. The goal of this study was to better understand the population structure of sockeye salmon and identify possible genomic differences among populations and between the two ecotypes. In pursuit of this goal, we generated the first reference sockeye salmon genome assembly and an RNA-seq transcriptome data set to better annotate features of the assembly. Resequenced whole-genomes of 140 sockeye salmon and kokanee were analyzed to understand population structure and identify genomic differences between ecotypes. Three distinct geographic and genetic groups were identified from analyses of the resequencing data. Nucleotide variants in an immunoglobulin heavy chain variable gene cluster on chromosome 26 were found to differentiate the northwestern group from the southern and upper Columbia River groups. Several candidate genes were found to be associated with the kokanee ecotype. Many of these genes were related to ammonia tolerance or vision. Finally, the sex chromosomes of this species were better characterized, and an alternative sex-determination mechanism was identified in a subset of upper Columbia River kokanee.
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Al-Rikabi ABH, Cioffi MDB, Liehr T. Chromosome Microdissection on Semi-Archived Material. Cytometry A 2019; 95:1285-1288. [PMID: 31532073 DOI: 10.1002/cyto.a.23896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/01/2019] [Accepted: 08/29/2019] [Indexed: 12/14/2022]
Abstract
Glass needle-based chromosome microdissection (midi) is a standard approach developed in the 1980s and remains more frequently applied in testing than the comparable technique using laser-based platforms. As the amount of DNA extracted by this technique is minimal and often in the range of picograms, the isolated DNA must be further amplified prior to use; the isolated amplified product can be readily utilized in multiple molecular research and diagnostic investigation. DNA libraries created by midi are either chromosome- or chromosome-region-specific. However, a critical component to this process is the need for timely chromosome preparation via the air-drying method not to exceed a ~2-3 h before midi is performed. Failure of this time-sensitive step often results in the chromosomes drying out after dropping, and upon initiation of the midi technique, the dissected material can jump away while touching by the needle, and collection of a suitable sample is inhibited. Herein, we demonstrate with a simple adaptation of the standard procedure, midi can be performed on semi-archived material stored for longer periods at -20°C. Thus, the critical step to obtain well-spread chromosome preparations can be completed under established conditions, for example, in the primary laboratory, stored at -20°C, and sent directly to specialized reference laboratories offering midi. In our study, we were able to obtain high-quality DNA libraries, as verified by gel electrophoreses and reverse fluorescence in situ hybridization, via midi extracted chromosome spreads derived from human, fish, snake, lampbrush, and insect stored for up to 6 months. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Ahmed B Hamid Al-Rikabi
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Jena, Germany
| | - Marcelo de Bello Cioffi
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Jena, Germany.,Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Thomas Liehr
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Jena, Germany
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5
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de Moraes RLR, Sember A, Bertollo LAC, de Oliveira EA, Ráb P, Hatanaka T, Marinho MMF, Liehr T, Al-Rikabi ABH, Feldberg E, Viana PF, Cioffi MDB. Comparative Cytogenetics and Neo-Y Formation in Small-Sized Fish Species of the Genus Pyrrhulina (Characiformes, Lebiasinidae). Front Genet 2019; 10:678. [PMID: 31428127 PMCID: PMC6689988 DOI: 10.3389/fgene.2019.00678] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/27/2019] [Indexed: 12/20/2022] Open
Abstract
Although fishes have traditionally been the subject of comparative evolutionary studies, few reports have concentrated on the application of multipronged modern molecular cytogenetic techniques (such as comparative genomic hybridization = CGH and whole chromosome painting = WCP) to analyze deeper the karyotype evolution of specific groups, especially the historically neglected small-sized ones. Representatives of the family Lebiasinidae (Characiformes) are a notable example, where only a few cytogenetic investigations have been conducted thus far. Here, we aim to elucidate the evolutionary processes behind the karyotype differentiation of Pyrrhulina species on a finer-scale cytogenetic level. To achieve this, we applied C-banding, repetitive DNA mapping, CGH and WCP in Pyrrhulina semifasciata and P. brevis. Our results showed 2n = 42 in both sexes of P. brevis, while the difference in 2n between male and female in P. semifasciata (♂41/♀42) stands out due to the presence of a multiple X1X2Y sex chromosome system, until now undetected in this family. As a remarkable common feature, multiple 18S and 5S rDNA sites are present, with an occasional synteny or tandem-repeat amplification. Male-vs.-female CGH experiments in P. semifasciata highlighted the accumulation of male-enriched repetitive sequences in the pericentromeric region of the Y chromosome. Inter-specific CGH experiments evidenced a divergence between both species’ genomes based on the presence of several species-specific signals, highlighting their inner genomic diversity. WCP with the P. semifasciata-derived Y (PSEMI-Y) probe painted not only the entire metacentric Y chromosome in males but also the X1 and X2 chromosomes in both male and female chromosomes of P. semifasciata. In the cross-species experiments, the PSEMI-Y probe painted four acrocentric chromosomes in both males and females of the other tested Pyrrhulina species. In summary, our results show that both intra- and interchromosomal rearrangements together with the dynamics of repetitive DNA significantly contributed to the karyotype divergence among Pyrrhulina species, possibly promoted by specific populational and ecological traits and accompanied in one species by the origin of neo-sex chromosomes. The present results suggest how particular evolutionary scenarios found in fish species can help to clarify several issues related to genome organization and the karyotype evolution of vertebrates in general.
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Affiliation(s)
- Renata Luiza Rosa de Moraes
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czechia
| | - Luiz Antônio Carlos Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Ezequiel Aguiar de Oliveira
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil.,Secretaria de Estado de Educação de Mato Grosso - SEDUC-MT, Cuiabá, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czechia
| | - Terumi Hatanaka
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | | | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | | | - Eliana Feldberg
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, Brazil
| | - Patrik F Viana
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil.,Institute of Human Genetics, University Hospital Jena, Jena, Germany
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Franchini P, Jones JC, Xiong P, Kneitz S, Gompert Z, Warren WC, Walter RB, Meyer A, Schartl M. Long-term experimental hybridisation results in the evolution of a new sex chromosome in swordtail fish. Nat Commun 2018; 9:5136. [PMID: 30510159 PMCID: PMC6277394 DOI: 10.1038/s41467-018-07648-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/13/2018] [Indexed: 01/13/2023] Open
Abstract
The remarkable diversity of sex determination mechanisms known in fish may be fuelled by exceptionally high rates of sex chromosome turnovers or transitions. However, the evolutionary causes and genomic mechanisms underlying this variation and instability are yet to be understood. Here we report on an over 30-year evolutionary experiment in which we tested the genomic consequences of hybridisation and selection between two Xiphophorus fish species with different sex chromosome systems. We find that introgression and imposing selection for pigmentation phenotypes results in the retention of an unexpectedly large maternally derived genomic region. During the hybridisation process, the sex-determining region of the X chromosome from one parental species was translocated to an autosome in the hybrids leading to the evolution of a new sex chromosome. Our results highlight the complexity of factors contributing to patterns observed in hybrid genomes, and we experimentally demonstrate that hybridisation can catalyze rapid evolution of a new sex chromosome. Fish have a high diversity of sex-determining systems, but the mechanisms responsible for this are not well understood. Here, Franchini et al. show how hybridization and backcrossing have led to the evolution of a new sex chromosome in swordtail fish during 30 years of experimental evolution.
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Affiliation(s)
- Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Julia C Jones
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany.,Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 75123, Sweden
| | - Peiwen Xiong
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | | | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, 78666-4616, TX, USA
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany. .,Radcliffe Institute for Advanced Study, Harvard University, 9 Garden Street, Cambridge, MA, 02139, USA.
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany. .,Comprehensive Cancer Centre, University Clinic Würzburg, Josef Schneider Straße 6, 97074, Würzburg, Germany. .,Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
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7
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Lourenço de Freitas N, Al-Rikabi ABH, Bertollo LAC, Ezaz T, Yano CF, Aguiar de Oliveira E, Hatanaka T, Cioffi MDB. Early Stages of XY Sex Chromosomes Differentiation in the Fish Hoplias malabaricus (Characiformes, Erythrinidae) Revealed by DNA Repeats Accumulation. Curr Genomics 2018; 19:216-226. [PMID: 29606909 PMCID: PMC5850510 DOI: 10.2174/1389202918666170711160528] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/27/2017] [Accepted: 01/30/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Species with 'young' or nascent sex chromosomes provide unique opportunities to understand early evolutionary mechanisms (e.g. accumulation of repetitive sequences, cessation of recombination and gene loss) that drive the evolution of sex chromosomes. Among vertebrates, fishes exhibit highly diverse and a wide spectrum of sex-determining mechanisms and sex chromosomes, ranging from cryptic to highly differentiated ones, as well as, from simple to multiple sex chromosome systems. Such variability in sex chromosome morphology and composition not only exists within closely related taxa, but often within races/populations of the same species. Inside this context, the wolf fish Hoplias malabaricus offers opportunity to investigate the evolution of morphologically variable sex chromosomes within a species complex, as homomorphic to highly differentiated sex chromosome systems occur among its different karyomorphs. MATERIALS & METHODS To discover various evolutionary stages of sex chromosomes and to compare their sequence composition among the wolf fish´s karyomorphs, we applied multipronged molecular cytogenetic approaches, including C-banding, repetitive DNAs mapping, Comparative Genomic Hybridization (CGH) and Whole Chromosomal Painting (WCP). Our study was able to characterize a cryptically differentiated XX/XY sex chromosome system in the karyomorph F of this species. CONCLUSION The Y chromosome was clearly identified by an interstitial heterochromatic block on the short arms, primarily composed of microsatellite motifs and retrotransposons. Additionally, CGH also identified a male specific chromosome region in the same chromosomal location, implying that the accumulation of these repeats may have initiated the Y chromosome differentiation, as well as played a critical role towards the evolution and differentiation of sex chromosomes in various karyomorphs of this species.
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Affiliation(s)
| | - Ahmed Basheer Hamid Al-Rikabi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743Jena, Germany
| | | | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Cassia Fernanda Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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8
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Pucholt P, Wright AE, Conze LL, Mank JE, Berlin S. Recent Sex Chromosome Divergence despite Ancient Dioecy in the Willow Salix viminalis. Mol Biol Evol 2018; 34:1991-2001. [PMID: 28453634 PMCID: PMC5850815 DOI: 10.1093/molbev/msx144] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Sex chromosomes can evolve when recombination is halted between a pair of chromosomes, and this can lead to degeneration of the sex-limited chromosome. In the early stages of differentiation sex chromosomes are homomorphic, and even though homomorphic sex chromosomes are very common throughout animals and plants, we know little about the evolutionary forces shaping these types of sex chromosomes. We used DNA- and RNA-Seq data from females and males to explore the sex chromosomes in the female heterogametic willow, Salix viminalis, a species with ancient dioecy but with homomorphic sex chromosomes. We detected no major sex differences in read coverage in the sex determination (SD) region, indicating that the W region has not significantly degenerated. However, single nucleotide polymorphism densities in the SD region are higher in females compared with males, indicating very recent recombination suppression, followed by the accumulation of sex-specific single nucleotide polymorphisms. Interestingly, we identified two female-specific scaffolds that likely represent W-chromosome-specific sequence. We show that genes located in the SD region display a mild excess of male-biased expression in sex-specific tissue, and we use allele-specific gene expression analysis to show that this is the result of masculinization of expression on the Z chromosome rather than degeneration of female-expression on the W chromosome. Together, our results demonstrate that insertion of small DNA fragments and accumulation of sex-biased gene expression can occur before the detectable decay of the sex-limited chromosome.
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Affiliation(s)
- Pascal Pucholt
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Alison E Wright
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Lei Liu Conze
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Judith E Mank
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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9
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Yano CF, Bertollo LAC, Cioffi MDB. Fish-FISH: Molecular Cytogenetics in Fish Species. SPRINGER PROTOCOLS HANDBOOKS 2017. [DOI: 10.1007/978-3-662-52959-1_44] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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10
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Yano CF, Bertollo LAC, Ezaz T, Trifonov V, Sember A, Liehr T, Cioffi MB. Highly conserved Z and molecularly diverged W chromosomes in the fish genus Triportheus (Characiformes, Triportheidae). Heredity (Edinb) 2016; 118:276-283. [PMID: 28000659 DOI: 10.1038/hdy.2016.83] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/24/2016] [Accepted: 07/08/2016] [Indexed: 11/09/2022] Open
Abstract
The main objectives of this study were to test: (1) whether the W-chromosome differentiation matches to species' evolutionary divergence (phylogenetic concordance) and (2) whether sex chromosomes share a common ancestor within a congeneric group. The monophyletic genus Triportheus (Characiformes, Triportheidae) was the model group for this study. All species in this genus so far analyzed have ZW sex chromosome system, where the Z is always the largest chromosome of the karyotype, whereas the W chromosome is highly variable ranging from almost homomorphic to highly heteromorphic. We applied conventional and molecular cytogenetic approaches including C-banding, ribosomal DNA mapping, comparative genomic hybridization (CGH) and cross-species whole chromosome painting (WCP) to test our questions. We developed Z- and W-chromosome paints from T. auritus for cross-species WCP and performed CGH in a representative species (T. signatus) to decipher level of homologies and rates of differentiation of W chromosomes. Our study revealed that the ZW sex chromosome system had a common origin, showing highly conserved Z chromosomes and remarkably divergent W chromosomes. Notably, the W chromosomes have evolved to different shapes and sequence contents within ~15-25 Myr of divergence time. Such differentiation highlights a dynamic process of W-chromosome evolution within congeneric species of Triportheus.
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Affiliation(s)
- C F Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - L A C Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - T Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - V Trifonov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - A Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - T Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - M B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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Genomic Instability of the Sex-Determining Locus in Atlantic Salmon (Salmo salar). G3-GENES GENOMES GENETICS 2015; 5:2513-22. [PMID: 26401030 PMCID: PMC4632069 DOI: 10.1534/g3.115.020115] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Atlantic salmon and rainbow trout, like other members of the subfamily Salmoninae, are gonochoristic with male heterogamety. The finding that sex-linked genetic markers varied between species suggested that the sex-determining gene differs among salmonid species, or that there is one sex-determining gene that has the capacity to move around the genome. The discovery of sdY, the sex-determining gene in rainbow trout, and its presence in many male salmonids gave support to the latter. Additional evidence for a salmonid-specific, sex-determining jumping gene came from the mapping of the sex-determining locus to three different chromosomes in Tasmanian male Atlantic salmon lineages. To characterize the sex-determining region, we isolated three sdY containing BACs from an Atlantic salmon male library. Sequencing of these BACs yielded two contigs, one of which contained the sdY gene. Sequence analysis of the borders of male-specific and female/male common regions revealed highly repetitive sequences associated with mobile elements, which may allow an sdY cassette to jump around the genome. FISH analysis using a BAC or a plasmid containing the sdY gene showed that the sdY gene did indeed localize to the chromosomes where SEX had been mapped in different Tasmanian Atlantic salmon families. Moreover, the plasmid sdY gene probe hybridized primarily to one of the sex chromosomes as would be expected of a male-specific gene. Our results suggest that a common salmonid sex-determining gene (sdY) can move between three specific loci on chromosomes 2, 3, and 6, giving the impression that there are multiple SEX loci both within and between salmonid species.
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12
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Śliwińska-Jewsiewicka A, Kuciński M, Kirtiklis L, Dobosz S, Ocalewicz K, Jankun M. Chromosomal characteristics and distribution of rDNA sequences in the brook trout Salvelinus fontinalis (Mitchill, 1814). Genetica 2015; 143:425-32. [PMID: 25958180 PMCID: PMC4486110 DOI: 10.1007/s10709-015-9841-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/04/2015] [Indexed: 11/09/2022]
Abstract
Brook trout Salvelinus fontinalis (Mitchill, 1814) chromosomes have been analyzed using conventional and molecular cytogenetic techniques enabling characteristics and chromosomal location of heterochromatin, nucleolus organizer regions (NORs), ribosomal RNA-encoding genes and telomeric DNA sequences. The C-banding and chromosome digestion with the restriction endonucleases demonstrated distribution and heterogeneity of the heterochromatin in the brook trout genome. DNA sequences of the ribosomal RNA genes, namely the nucleolus-forming 28S (major) and non-nucleolus-forming 5S (minor) rDNAs, were physically mapped using fluorescence in situ hybridization (FISH) and primed in situ labelling. The minor rDNA locus was located on the subtelo-acrocentric chromosome pair No. 9, whereas the major rDNA loci were dispersed on 14 chromosome pairs, showing a considerable inter-individual variation in the number and location. The major and minor rDNA loci were located at different chromosomes. Multichromosomal location (3-6 sites) of the NORs was demonstrated by silver nitrate (AgNO3) impregnation. All Ag-positive i.e. active NORs corresponded to the GC-rich blocks of heterochromatin. FISH with telomeric probe showed the presence of the interstitial telomeric site (ITS) adjacent to the NOR/28S rDNA site on the chromosome 11. This ITS was presumably remnant of the chromosome rearrangement(s) leading to the genomic redistribution of the rDNA sequences. Comparative analysis of the cytogenetic data among several related salmonid species confirmed huge variation in the number and the chromosomal location of rRNA gene clusters in the Salvelinus genome.
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Affiliation(s)
- A. Śliwińska-Jewsiewicka
- />Department of Human Histology and Embryology, Faculty of Medical Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - M. Kuciński
- />Department of Ichthyology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - L. Kirtiklis
- />Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - S. Dobosz
- />Department of Salmonid Research, Inland Fisheries Institute in Olsztyn, Olsztyn, Poland
| | - K. Ocalewicz
- />Department of Marine Biology and Ecology, Faculty of Oceanography and Geography, University of Gdansk, Gdańsk, Poland
| | - Malgorzata Jankun
- />Department of Ichthyology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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Faber-Hammond JJ, Phillips RB, Brown KH. Comparative Analysis of the Shared Sex-Determination Region (SDR) among Salmonid Fishes. Genome Biol Evol 2015; 7:1972-87. [PMID: 26112966 PMCID: PMC4524489 DOI: 10.1093/gbe/evv123] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Salmonids present an excellent model for studying evolution of young sex-chromosomes. Within the genus, Oncorhynchus, at least six independent sex-chromosome pairs have evolved, many unique to individual species. This variation results from the movement of the sex-determining gene, sdY, throughout the salmonid genome. While sdY is known to define sexual differentiation in salmonids, the mechanism of its movement throughout the genome has remained elusive due to high frequencies of repetitive elements, rDNA sequences, and transposons surrounding the sex-determining regions (SDR). Despite these difficulties, bacterial artificial chromosome (BAC) library clones from both rainbow trout and Atlantic salmon containing the sdY region have been reported. Here, we report the sequences for these BACs as well as the extended sequence for the known SDR in Chinook gained through genome walking methods. Comparative analysis allowed us to study the overlapping SDRs from three unique salmonid Y chromosomes to define the specific content, size, and variation present between the species. We found approximately 4.1 kb of orthologous sequence common to all three species, which contains the genetic content necessary for masculinization. The regions contain transposable elements that may be responsible for the translocations of the SDR throughout salmonid genomes and we examine potential mechanistic roles of each one.
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Affiliation(s)
- Joshua J Faber-Hammond
- Department of Biology, Portland State University School of Biological Sciences, Washington State University Vancouver
| | - Ruth B Phillips
- School of Biological Sciences, Washington State University Vancouver Center for Reproductive Biology, Washington State University, Pullman
| | - Kim H Brown
- Department of Biology, Portland State University
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14
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Martínez P, Viñas AM, Sánchez L, Díaz N, Ribas L, Piferrer F. Genetic architecture of sex determination in fish: applications to sex ratio control in aquaculture. Front Genet 2014; 5:340. [PMID: 25324858 PMCID: PMC4179683 DOI: 10.3389/fgene.2014.00340] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 09/10/2014] [Indexed: 01/05/2023] Open
Abstract
Controlling the sex ratio is essential in finfish farming. A balanced sex ratio is usually good for broodstock management, since it enables to develop appropriate breeding schemes. However, in some species the production of monosex populations is desirable because the existence of sexual dimorphism, primarily in growth or first time of sexual maturation, but also in color or shape, can render one sex more valuable. The knowledge of the genetic architecture of sex determination (SD) is convenient for controlling sex ratio and for the implementation of breeding programs. Unlike mammals and birds, which show highly conserved master genes that control a conserved genetic network responsible for gonad differentiation (GD), a huge diversity of SD mechanisms has been reported in fish. Despite theory predictions, more than one gene is in many cases involved in fish SD and genetic differences have been observed in the GD network. Environmental factors also play a relevant role and epigenetic mechanisms are becoming increasingly recognized for the establishment and maintenance of the GD pathways. Although major genetic factors are frequently involved in fish SD, these observations strongly suggest that SD in this group resembles a complex trait. Accordingly, the application of quantitative genetics combined with genomic tools is desirable to address its study and in fact, when applied, it has frequently demonstrated a multigene trait interacting with environmental factors in model and cultured fish species. This scenario has notable implications for aquaculture and, depending upon the species, from chromosome manipulation or environmental control techniques up to classical selection or marker assisted selection programs, are being applied. In this review, we selected four relevant species or fish groups to illustrate this diversity and hence the technologies that can be used by the industry for the control of sex ratio: turbot and European sea bass, two reference species of the European aquaculture, and salmonids and tilapia, representing the fish for which there are well established breeding programs.
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Affiliation(s)
- Paulino Martínez
- Departamento de Genética, Facultad de Veterinaria, Universidad de Santiago de CompostelaLugo, Spain
| | - Ana M. Viñas
- Departamento de Genética, Facultad de Biología, Universidad de Santiago de CompostelaSantiago de Compostela, Spain
| | - Laura Sánchez
- Departamento de Genética, Facultad de Veterinaria, Universidad de Santiago de CompostelaLugo, Spain
| | - Noelia Díaz
- Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | | | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
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15
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Matsubara K, Gamble T, Matsuda Y, Zarkower D, Sarre SD, Georges A, Graves JAM, Ezaz T. Non-homologous sex chromosomes in two geckos (Gekkonidae: Gekkota) with female heterogamety. Cytogenet Genome Res 2014; 143:251-8. [PMID: 25227445 DOI: 10.1159/000366172] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2014] [Indexed: 11/19/2022] Open
Abstract
Evaluating homology between the sex chromosomes of different species is an important first step in deducing the origins and evolution of sex-determining mechanisms in a clade. Here, we describe the preparation of Z and W chromosome paints via chromosome microdissection from the Australian marbled gecko (Christinus marmoratus) and their subsequent use in evaluating sex chromosome homology with the ZW chromosomes of the Kwangsi gecko (Gekko hokouensis) from eastern Asia. We show that the ZW sex chromosomes of C. marmoratus and G. hokouensis are not homologous and represent independent origins of female heterogamety within the Gekkonidae. We also show that the C. marmoratus Z and W chromosomes are genetically similar to each other as revealed by C-banding, comparative genomic hybridization, and the reciprocal painting of Z and W chromosome probes. This implies that sex chromosomes in C. marmoratus are at an early stage of differentiation, suggesting a recent origin.
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Affiliation(s)
- Kazumi Matsubara
- Institute for Applied Ecology, University of Canberra, Canberra, A.C.T., Australia
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16
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Fine mapping and evolution of the major sex determining region in turbot (Scophthalmus maximus). G3-GENES GENOMES GENETICS 2014; 4:1871-80. [PMID: 25106948 PMCID: PMC4199694 DOI: 10.1534/g3.114.012328] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Fish sex determination (SD) systems are varied, suggesting evolutionary changes including either multiple evolution origins of genetic SD from nongenetic systems (such as environmental SD) and/or turnover events replacing one genetic system by another. When genetic SD is found, cytological differentiation between the two members of the sex chromosome pair is often minor or undetectable. The turbot (Scophthalmus maximus), a valuable commercial flatfish, has a ZZ/ZW system and a major SD region on linkage group 5 (LG5), but there are also other minor genetic and environmental influences. We here report refined mapping of the turbot SD region, supported by comparative mapping with model fish species, to identify the turbot master SD gene. Six genes were located to the SD region, two of them associated with gonad development (sox2 and dnajc19). All showed a high association with sex within families (P = 0), but not at the population level, so they are probably partially sex-linked genes, but not SD gene itself. Analysis of crossovers in LG5 using two families confirmed a ZZ/ZW system in turbot and suggested a revised map position for the master gene. Genetic diversity and differentiation for 25 LG5 genetic markers showed no differences between males and females sampled from a wild population, suggesting a recent origin of the SD region in turbot. We also analyzed associations with markers of the most relevant sex-related linkage groups in brill (S. rhombus), a closely related species to turbot; the data suggest that an ancient XX/XY system in brill changed to a ZZ/ZW mechanism in turbot.
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Comparative mapping between Coho Salmon (Oncorhynchus kisutch) and three other salmonids suggests a role for chromosomal rearrangements in the retention of duplicated regions following a whole genome duplication event. G3-GENES GENOMES GENETICS 2014; 4:1717-30. [PMID: 25053705 PMCID: PMC4169165 DOI: 10.1534/g3.114.012294] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Whole genome duplication has been implicated in evolutionary innovation and rapid diversification. In salmonid fishes, however, whole genome duplication significantly pre-dates major transitions across the family, and re-diploidization has been a gradual process between genomes that have remained essentially collinear. Nevertheless, pairs of duplicated chromosome arms have diverged at different rates from each other, suggesting that the retention of duplicated regions through occasional pairing between homeologous chromosomes may have played an evolutionary role across species pairs. Extensive chromosomal arm rearrangements have been a key mechanism involved in re-dipliodization of the salmonid genome; therefore, we investigated their influence on degree of differentiation between homeologs across salmon species. We derived a linkage map for coho salmon and performed comparative mapping across syntenic arms within the genus Oncorhynchus, and with the genus Salmo, to determine the phylogenetic relationship between chromosome arrangements and the retention of undifferentiated duplicated regions. A 6596.7 cM female coho salmon map, comprising 30 linkage groups with 7415 and 1266 nonduplicated and duplicated loci, respectively, revealed uneven distribution of duplicated loci along and between chromosome arms. These duplicated regions were conserved across syntenic arms across Oncorhynchus species and were identified in metacentric chromosomes likely formed ancestrally to the divergence of Oncorhynchus from Salmo. These findings support previous studies in which observed pairings involved at least one metacentric chromosome. Re-diploidization in salmon may have been prevented or retarded by the formation of metacentric chromosomes after the whole genome duplication event and may explain lineage-specific innovations in salmon species if functional genes are found in these regions.
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18
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Schmid M, Steinlein C, Feichtinger W, Bogart JP. Chromosome banding in Amphibia. XXXI. The neotropical anuran families Centrolenidae and Allophrynidae. Cytogenet Genome Res 2014; 142:268-85. [PMID: 24776617 DOI: 10.1159/000362216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2014] [Indexed: 11/19/2022] Open
Abstract
The mitotic chromosomes of 11 species from the anuran families Centrolenidae and Allophrynidae were analyzed by means of conventional staining, banding techniques, and in situ hybridization. The amount, location, and fluorochrome affinities of constitutive heterochromatin, the number and positions of nucleolus organizer regions, and the patterns of telomeric DNA sequences were determined for most of the species. The karyotypes were found to be highly conserved with a low diploid chromosome number of 2n = 20 and morphologically similar chromosomes. The sister group relationship between the Centrolenidae and Allophrynidae (unranked taxon Allocentroleniae) is clearly corroborated by the cytogenetic data. The existence of heteromorphic XY♂/XX♀ sex chromosomes in an initial stage of morphological differentiation was confirmed in Vitreorana antisthenesi. The genome sizes of 4 centrolenid species were determined using flow cytometry. For completeness and for comparative purposes, all previously published cytogenetic data on centrolenids are included.
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Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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19
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Sex chromosome polymorphism in guppies. Chromosoma 2014; 123:373-83. [PMID: 24676866 DOI: 10.1007/s00412-014-0455-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/24/2014] [Accepted: 03/03/2014] [Indexed: 12/18/2022]
Abstract
Sex chromosomes differ from autosomes by dissimilar gene content and, at a more advanced stage of their evolution, also in structure and size. This is driven by the divergence of the Y or W from their counterparts, X and Z, due to reduced recombination and the resulting degeneration as well as the accumulation of sex-specific and sexually antagonistic genes. A paradigmatic example for Y-chromosome evolution is found in guppies. In these fishes, conflicting data exist for a morphological and molecular differentiation of sex chromosomes. Using molecular probes and the previously established linkage map, we performed a cytogenetic analysis of sex chromosomes. We show that the Y chromosome has a very large pseudoautosomal region, which is followed by a heterochromatin block (HCY) separating the subtelomeric male-specific region from the rest of the chromosome. Interestingly, the size of the HCY is highly variable between individuals from different population. The largest HCY was found in one population of Poecilia wingei, making the Y almost double the size of the X and the largest chromosome of the complement. Comparative analysis revealed that the Y chromosomes of different guppy species are homologous and share the same structure and organization. The observed size differences are explained by an expansion of the HCY, which is due to increased amounts of repetitive DNA. In one population, we observed also a polymorphism of the X chromosome. We suggest that sex chromosome-linked color patterns and other sexually selected genes are important for maintaining the observed structural polymorphism of sex chromosomes.
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20
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21
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Blaser O, Neuenschwander S, Perrin N. Sex-chromosome turnovers: the hot-potato model. Am Nat 2013; 183:140-6. [PMID: 24334743 DOI: 10.1086/674026] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Sex-determining systems often undergo high rates of turnover but for reasons that remain largely obscure. Two recent evolutionary models assign key roles, respectively, to sex-antagonistic (SA) mutations occurring on autosomes and to deleterious mutations accumulating on sex chromosomes. These two models capture essential but distinct key features of sex-chromosome evolution; accordingly, they make different predictions and present distinct limitations. Here we show that a combination of features from the two models has the potential to generate endless cycles of sex-chromosome transitions: SA alleles accruing on a chromosome after it has been co-opted for sex induce an arrest of recombination; the ensuing accumulation of deleterious mutations will soon make a new transition ineluctable. The dynamics generated by these interactions share several important features with empirical data, namely, (i) that patterns of heterogamety tend to be conserved during transitions and (ii) that autosomes are not recruited randomly, with some chromosome pairs more likely than others to be co-opted for sex.
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Affiliation(s)
- Olivier Blaser
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
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22
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Cioffi MB, Liehr T, Trifonov V, Molina WF, Bertollo LAC. Independent sex chromosome evolution in lower vertebrates: a molecular cytogenetic overview in the Erythrinidae fish family. Cytogenet Genome Res 2013; 141:186-94. [PMID: 23919986 DOI: 10.1159/000354039] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The Erythrinidae fish family is an excellent model for analyzing the evolution of sex chromosomes. Different stages of sex chromosome differentiation from homomorphic to highly differentiated ones can be found among the species of this family. Here, whole chromosome painting, together with the cytogenetic mapping of repetitive DNAs, highlighted the evolutionary relationships of the sex chromosomes among different erythrinid species and genera. It was demonstrated that the sex chromosomes can follow distinct evolutionary pathways inside this family. Reciprocal hybridizations with whole sex chromosome probes revealed that different autosomal pairs have evolved as the sex pair, even among closely related species. In addition, distinct origins and different patterns of differentiation were found for the same type of sex chromosome system. These features expose the high plasticity of the sex chromosome evolution in lower vertebrates, in contrast to that occurring in higher ones. A possible role of this sex chromosome turnover in the speciation processes is also discussed.
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Affiliation(s)
- M B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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23
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Parise-Maltempi PP, da Silva EL, Rens W, Dearden F, O'Brien PCM, Trifonov V, Ferguson-Smith MA. Comparative analysis of sex chromosomes in Leporinus species (Teleostei, Characiformes) using chromosome painting. BMC Genet 2013; 14:60. [PMID: 23822802 PMCID: PMC3708793 DOI: 10.1186/1471-2156-14-60] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 07/01/2013] [Indexed: 11/10/2022] Open
Abstract
Background The Leporinus genus, belonging to the Anostomidae family, is an interesting model for studies of sex chromosome evolution in fish, particularly because of the presence of heteromorphic sex chromosomes only in some species of the genus. In this study we used W chromosome-derived probes in a series of cross species chromosome painting experiments to try to understand events of sex chromosome evolution in this family. Results W chromosome painting probes from Leporinus elongatus, L. macrocephalus and L. obtusidens were hybridized to each others chromosomes. The results showed signals along their W chromosomes and the use of L. elongatus W probe against L. macrocephalus and L. obtusidens also showed signals over the Z chromosome. No signals were observed when the later aforementioned probe was used in hybridization procedures against other four Anostomidae species without sex chromosomes. Conclusions Our results demonstrate a common origin of sex chromosomes in L. elongatus, L. macrocephalus and L. obtusidens but suggest that the L. elongatus chromosome system is at a different evolutionary stage. The absence of signals in the species without differentiated sex chromosomes does not exclude the possibility of cryptic sex chromosomes, but they must contain other Leporinus W sequences than those described here.
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Affiliation(s)
- Patrícia Pasquali Parise-Maltempi
- Departamento de Biologia, Laboratório de Citogenética, Instituto de Biociências, Universidade Estadual Paulista Julio de Mesquita Filho - UNESP, Rio Claro, Av. 24A, 1515, CEP 13506-900 Rio Claro, SP, Brazil.
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Evidence for multiple sex-determining loci in Tasmanian Atlantic salmon (Salmo salar). Heredity (Edinb) 2013; 113:86-92. [PMID: 23759729 PMCID: PMC4815647 DOI: 10.1038/hdy.2013.55] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 04/30/2013] [Accepted: 05/02/2013] [Indexed: 11/11/2022] Open
Abstract
Phenotypic sex in salmonids is determined primarily by a genetic male heterogametic system; yet, sex reversal can be accomplished via hormonal treatment. In Tasmanian Atlantic salmon aquaculture, to overcome problems associated with early sexual maturation in males, sex-reversed females are crossed with normal females to produce all female stock. However, phenotypic distinction of sex-reversed females (neo-males) from true males is problematic. We set out to identify genetic markers that could make this distinction. Microsatellite markers from chromosome 2 (Ssa02), to which the sex-determining locus (SEX) has been mapped in two Scottish Atlantic salmon families, did not predict sex in a pilot study of seven families. A TaqMan 64 SNP genome-wide scan suggested SEX was on Ssa06 in these families, and this was confirmed by microsatellite markers. A survey of 58 families in total representing 38 male lineages in the SALTAS breeding program found that 34 of the families had SEX on Ssa02, in 22 of the families SEX was on Ssa06, and two of the families had a third SEX locus, on Ssa03. A PCR test using primers designed from the recently published sdY gene is consistent with Tasmanian Atlantic salmon having a single sex-determining gene that may be located on at least three linkage groups.
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25
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Pazian MF, Shimabukuro-Dias CK, Pansonato-Alves JC, Oliveira C, Foresti F. Chromosome painting of Z and W sex chromosomes in Characidium (Characiformes, Crenuchidae). Genetica 2013; 141:1-9. [PMID: 23344657 DOI: 10.1007/s10709-013-9701-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 01/17/2013] [Indexed: 01/23/2023]
Abstract
Some species of the genus Characidium have heteromorphic ZZ/ZW sex chromosomes with a totally heterochromatic W chromosome. Methods for chromosome microdissection associated with chromosome painting have become important tools for cytogenetic studies in Neotropical fish. In Characidium cf. fasciatum, the Z chromosome contains a pericentromeric heterochromatin block, whereas the W chromosome is completely heterochromatic. Therefore, a probe was produced from the W chromosome through microdissection and degenerate oligonucleotide-primed polymerase chain reaction amplification. FISH was performed using the W probe on the chromosomes of specimens of this species. This revealed expressive marks in the pericentromeric region of the Z chromosome as well as a completely painted W chromosome. When applying the same probe on chromosome preparations of C. cf. gomesi and Characidium sp., a pattern similar to C. cf. fasciatum was found, while C. cf. zebra, C. cf. lagosantense and Crenuchus spilurus species showed no hybridization signals. Structural changes in the chromosomes of an ancestral sexual system in the group that includes the species C. cf. gomesi, C. cf. fasciatum and Characidium sp., could have contributed to the process of speciation and could represent a causal mechanism of chromosomal diversification in this group. The heterochromatinization process possibly began in homomorphic and homologous chromosomes of an ancestral form, and this process could have given rise to the current patterns found in the species with sex chromosome heteromorphism.
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Affiliation(s)
- Marlon F Pazian
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior S/N, Rubião Júnior, Botucatu, SP, Brazil.
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26
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Phillips R. Evolution of the Sex Chromosomes in Salmonid Fishes. Cytogenet Genome Res 2013; 141:177-85. [DOI: 10.1159/000355149] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Blaser O, Grossen C, Neuenschwander S, Perrin N. SEX-CHROMOSOME TURNOVERS INDUCED BY DELETERIOUS MUTATION LOAD. Evolution 2012; 67:635-45. [DOI: 10.1111/j.1558-5646.2012.01810.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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28
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Brunelli JP, Mallatt JM, Leary RF, Alfaqih M, Phillips RB, Thorgaard GH. Y chromosome phylogeny for cutthroat trout (Oncorhynchus clarkii) subspecies is generally concordant with those of other markers. Mol Phylogenet Evol 2012; 66:592-602. [PMID: 23059727 DOI: 10.1016/j.ympev.2012.09.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 09/17/2012] [Accepted: 09/18/2012] [Indexed: 11/16/2022]
Abstract
Sequence divergence was evaluated in the non-recombining, male-specific OmyY1 region of the Y chromosome among the subspecies of cutthroat trout (Oncorhynchus clarkii) in the western United States. This evaluation identified subspecies-discriminating OmyY1-haplotypes within a ∼1200bp region of the OmyY1 locus and localized the region to the end of the Y chromosome by FISH analysis. OmyY1 sequences were aligned and used to reconstruct a phylogeny of the cutthroat trout subspecies and related species via maximum-parsimony and Bayesian analyses. In the Y-haplotype phylogeny, clade distributions generally corresponded to the geographic distributions of the recognized subspecies. This phylogeny generally corresponded to a mitochondrial tree obtained for these subspecies in a previous study. Both support a clade of trout vs. Pacific salmon, of rainbow trout, and of a Yellowstone cutthroat group within the cutthroat trout. In our OmyY1 tree, however, the cutthroat "clade", although present topologically, was not statistically significant. Some key differences were found between trees obtained from the paternally-inherited OmyY1 vs. maternally-inherited mitochondrial haplotypes in cutthroat trout compared to rainbow trout. Other findings are: The trout OmyY1 region evolves between 3 and 13 times slower than the trout mitochondrial regions that have been studied. The Lahontan cutthroat trout had a fixed OmyY1 sequence throughout ten separate populations, suggesting this subspecies underwent a severe population bottleneck prior to its current dispersal throughout the Great Basin during the pluvial phase of the last ice age. The Yellowstone group is the most derived among the cutthroat trout and consists of the Yellowstone, Bonneville, Colorado, Rio Grande and greenback subspecies. Identification of subspecies and sex with this Y-chromosome marker may prove useful in conservation efforts.
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Affiliation(s)
- Joseph P Brunelli
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, United States
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29
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Blaser O, Neuenschwander S, Perrin N. On the Maintenance of Sex Chromosome Polymorphism by Sex-Antagonistic Selection. Am Nat 2011; 178:515-24. [DOI: 10.1086/661895] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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30
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de Bello Cioffi M, Sánchez A, Marchal JA, Kosyakova N, Liehr T, Trifonov V, Bertollo LAC. Whole chromosome painting reveals independent origin of sex chromosomes in closely related forms of a fish species. Genetica 2011; 139:1065-72. [PMID: 21927842 DOI: 10.1007/s10709-011-9610-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 09/08/2011] [Indexed: 11/29/2022]
Abstract
The wolf fish Hoplias malabaricus includes well differentiated sex systems (XY and X(1)X(2)Y in karyomorphs B and D, respectively), a nascent XY pair (karyomorph C) and not recognized sex chromosomes (karyomorph A). We performed the evolutionary analysis of these sex chromosomes, using two X chromosome-specific probes derived by microdissection from the XY and X(1)X(2)Y sex systems. A putative-sex pair in karyomorph A was identified, from which the differentiated XY system was evolved, as well as the clearly evolutionary relationship between the nascent XY system and the origin of the multiple X(1)X(2)Y chromosomes. The lack of recognizable signals on the sex chromosomes after the reciprocal cross-FISH experiments highlighted that they evolved independently from non-homologous autosomal pairs. It is noteworthy that these distinct pathways occur inside the same nominal species, thus exposing the high plasticity of sex chromosome evolution in lower vertebrates. Possible mechanisms underlying this sex determination liability are also discussed.
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Affiliation(s)
- Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.
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Cioffi MB, Sánchez A, Marchal JA, Kosyakova N, Liehr T, Trifonov V, Bertollo LA. Cross-species chromosome painting tracks the independent origin of multiple sex chromosomes in two cofamiliar Erythrinidae fishes. BMC Evol Biol 2011; 11:186. [PMID: 21718509 PMCID: PMC3141436 DOI: 10.1186/1471-2148-11-186] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 06/30/2011] [Indexed: 11/13/2022] Open
Abstract
Background The Erythrinidae fish family is characterized by a large variation with respect to diploid chromosome numbers and sex-determining systems among its species, including two multiple X1X2Y sex systems in Hoplias malabaricus and Erythrinus erythrinus. At first, the occurrence of a same sex chromosome system within a family suggests that the sex chromosomes are correlated and originated from ancestral XY chromosomes that were either homomorphic or at an early stage of differentiation. To identify the origin and evolution of these X1X2Y sex chromosomes, we performed reciprocal cross-species FISH experiments with two sex-chromosome-specific probes designed from microdissected X1 and Y chromosomes of H. malabaricus and E. erythrinus, respectively. Results Our results yield valuable information regarding the origin and evolution of these sex chromosome systems. Our data indicate that these sex chromosomes evolved independently in these two closed related Erythrinidae species. Different autosomes were first converted into a poorly differentiated XY sex pair in each species, and additional chromosomal rearrangements produced both X1X2Y sex systems that are currently present. Conclusions Our data provide new insights into the origin and evolution of sex chromosomes, which increases our knowledge about fish sex chromosome evolution.
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Affiliation(s)
- Marcelo B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil.
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Henning F, Moysés CB, Calcagnotto D, Meyer A, de Almeida-Toledo LF. Independent fusions and recent origins of sex chromosomes in the evolution and diversification of glass knife fishes (Eigenmannia). Heredity (Edinb) 2011; 106:391-400. [PMID: 20571513 PMCID: PMC3183873 DOI: 10.1038/hdy.2010.82] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2010] [Revised: 03/30/2010] [Accepted: 04/12/2010] [Indexed: 01/24/2023] Open
Abstract
The genus Eigenmannia comprises several species groups that display a surprising variety of diploid chromosome numbers and sex-determining systems. In this study, hypotheses regarding phylogenetic relationships and karyotype evolution were investigated using a combination of molecular and cytogenetic methods. Phylogenetic relationships were analyzed for 11 cytotypes based on sequences from five mitochondrial DNA regions. Parsimony-based character mapping of sex chromosomes confirms previous suggestions of multiple origins of sex chromosomes. Molecular cytogenetic analyses involved chromosome painting using probes derived from whole sex chromosomes from two taxa that were hybridized to metaphases of their respective sister cytotypes. These analyses showed that a multiple XY system evolved recently (<7 mya) by fusion. Furthermore, one of the chromosomes that fused to form the neo-Y chromosome is fused independently to another chromosome in the sister cytotype. This may constitute an efficient post-mating barrier and might imply a direct function of sex chromosomes in the speciation processes in Eigenmannia. The other chromosomal sex-determination system investigated is shown to have differentiated by an accumulation of heterochromatin on the X chromosome. This has occurred in the past 0.6 my, and is the most recent chromosomal sex-determining system described to date. These results show that the evolution of sex-determining systems can proceed very rapidly.
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Affiliation(s)
- F Henning
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Lehrstuhl für Zoologie und Evolutionsbiologie, Fachbereich Biologie, Universität Konstanz, Konstanz, Germany
| | - C B Moysés
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - D Calcagnotto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - A Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Fachbereich Biologie, Universität Konstanz, Konstanz, Germany
| | - L F de Almeida-Toledo
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Li J, Phillips RB, Harwood AS, Koop BF, Davidson WS. Identification of the sex chromosomes of brown trout (Salmo trutta) and their comparison with the corresponding chromosomes in Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). Cytogenet Genome Res 2011; 133:25-33. [PMID: 21252487 DOI: 10.1159/000323410] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2010] [Indexed: 12/26/2022] Open
Abstract
Males are the heterogametic sex in salmonid fishes. In brown trout (Salmo trutta) the sex-determining locus, SEX, has been mapped to the end of linkage group BT-28, which corresponds to linkage group AS-8 and chromosome SSA15 in Atlantic salmon (Salmo salar). We set out to identify the sex chromosomes in brown trout. We isolated Atlantic salmon BAC clones containing microsatellite markers that are on BT-28 and also on AS-8, and used these BACs as probes for fluorescent in situ hybridization (FISH) analysis. SEX is located on the short arm of a small subtelocentric/acrocentric chromosome in brown trout, which is consistent with linkage analysis. The acrocentric chromosome SSA15 in Atlantic salmon appears to have arisen by a centric fusion of 2 small acrocentric chromosomes in the common ancestor of Salmo sp. We speculate that the fusion process that produced Atlantic salmon chromosome SSA15 disrupted the ancestral sex-determining locus in the Atlantic salmon lineage, providing the impetus either for the relocation of SEX or selection pressure for a novel sex-determining gene to arise in this species. Thus, the sex-determining genes may differ in Atlantic salmon and brown trout.
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Affiliation(s)
- J Li
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, B.C., Canada
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34
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Cioffi M, Molina W, Moreira-Filho O, Bertollo L. Chromosomal Distribution of Repetitive DNA Sequences Highlights the Independent Differentiation of Multiple Sex Chromosomes in Two Closely Related Fish Species. Cytogenet Genome Res 2011; 134:295-302. [DOI: 10.1159/000329481] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2011] [Indexed: 11/19/2022] Open
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35
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Origin and molecular organization of supernumerary chromosomes of Prochilodus lineatus (characiformes, prochilodontidae) obtained by DNA probes. Genetica 2010; 138:1133-9. [PMID: 20872170 DOI: 10.1007/s10709-010-9502-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 09/14/2010] [Indexed: 10/19/2022]
Abstract
In Prochilodus lineatus B-chromosomes are visualized as reduced size extra elements identified as microchromosomes and are variable in morphology and number. We describe the specific total probe (B-chromosome probe) in P. lineatus obtained by chromosome microdissection and a whole genomic probe (genomic probe) from an individual without B-chromosome. The specific B-chromosome was scraped and processed to obtain DNA with amplification by DOP-PCR, and so did the genomic probe DNA. Fluorescence in situ hybridization using the B-chromosome probe labeled with dUTP-Tetramethyl-rhodamine and the genomic probe labeled with digoxigenin-FITC permitted to establish that in this species supernumerary chromosomes with varying number and morphology had different structure of chromatin when compared to that of the regular chromosomes or A complement, since only these extra elements were labeled in the metaphases. The present findings suggest that modifications in the chromatin structure of B-chromosomes to differentiate them from the A chromosomes could occur along their dispersion in the individuals of the population.
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36
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Nagamachi CY, Pieczarka JC, Milhomem SSR, O'Brien PCM, de Souza ACP, Ferguson-Smith MA. Multiple rearrangements in cryptic species of electric knifefish, Gymnotus carapo (Gymnotidae, Gymnotiformes) revealed by chromosome painting. BMC Genet 2010; 11:28. [PMID: 20420709 PMCID: PMC2873553 DOI: 10.1186/1471-2156-11-28] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 04/27/2010] [Indexed: 11/10/2022] Open
Abstract
Background Gymnotus (Gymnotidae, Gymnotiformes) is the Neotropical electric fish genus with the largest geographic distribution and the largest number of species, 33 of which have been validated. The diploid number varies from 2n = 39-40 to 2n = 54. Recently we studied the karyotype of morphologically indistinguishable samples from five populations of G. carapo sensu stricto from the Eastern Amazon of Brazil. We found two cytotypes, 2n = 42 (30 M/SM + 12 ST/A) and 2n = 40 (34 M/SM + 6 ST/A) and we concluded that the differences between the two cryptic species are due to pericentric inversions and one tandem fusion. Results In this study we use for the first time, whole chromosome probes prepared by FACS of the Gymnotus carapo sensu strictu species, cytotype with 2n = 42. Using two color hybridizations we were able to distinguish pairs 1, 2, 3, 7, 9, 14, 16, 18, 19, 20 and 21. It was not possible to separate by FACS and distinguish each of the following chromosome pairs even with dual color FISH: {4,8}; {10,11}; {5,6,17}; {12,13,15}. The FISH probes were then used in chromosome painting experiments on metaphases of the 2n = 40 cytotype. While some chromosomes show conserved synteny, others are rearranged in different chromosomes. Eight syntenic associations were found. Conclusions These results show that the karyotype differences between these cryptic species are greater than assumed by classical cytogenetics. These data reinforce the previous supposition that these two cytotypes are different species, despite the absence of morphological differences. Additionally, the homology of repetitive DNA between the two provides evidence of recent speciation.
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Affiliation(s)
- Cleusa Y Nagamachi
- Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil.
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37
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Brunelli JP, Wertzler KJ, Sundin K, Thorgaard GH. Y-specific sequences and polymorphisms in rainbow trout and Chinook salmon. Genome 2008; 51:739-48. [PMID: 18772952 DOI: 10.1139/g08-060] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Improved methods for genetically sexing salmonids and for characterization of Y-chromosome homologies between species can contribute to understanding the evolution of sex chromosomes and sex-determining mechanisms. In this study we have explored 12.5 kb of Y-chromosome-specific sequence flanking the previously described OtY2 locus in Chinook salmon (Oncorhynchus tshawytscha) and 21 kb of homologous rainbow trout (Oncorhynchus mykiss) Y-chromosome-specific sequence. This is the first confirmed Y-specific sequence for rainbow trout. New Y-specific markers are described for Chinook salmon (OtY3) and rainbow trout (OmyY1), which are readily detected by PCR assays and are advantageous because they also produce autosomal control amplification products. Additionally, AFLP analysis of Chinook salmon yielded another potential Y-chromosome marker. These descriptions will facilitate genotypic sexing and should be useful for population studies of Y-chromosome polymorphisms and for future studies to characterize what appears to be a common sex-determining mechanism between these species.
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Affiliation(s)
- Joseph P Brunelli
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-4236, USA
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38
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Penman DJ, Piferrer F. Fish Gonadogenesis. Part I: Genetic and Environmental Mechanisms of Sex Determination. ACTA ACUST UNITED AC 2008. [DOI: 10.1080/10641260802324610] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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39
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Ráb P, Rábová M, Pereira CS, Collares-Pereira MJ, Pelikánová Š. Chromosome studies of European cyprinid fishes: interspecific homology of leuciscine cytotaxonomic marker—the largest subtelocentric chromosome pair as revealed by cross-species painting. Chromosome Res 2008; 16:863-73. [DOI: 10.1007/s10577-008-1245-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Revised: 05/30/2008] [Accepted: 05/30/2008] [Indexed: 10/21/2022]
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40
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Ross JA, Peichel CL. Molecular cytogenetic evidence of rearrangements on the Y chromosome of the threespine stickleback fish. Genetics 2008; 179:2173-82. [PMID: 18689886 PMCID: PMC2516089 DOI: 10.1534/genetics.108.088559] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Accepted: 06/10/2008] [Indexed: 11/18/2022] Open
Abstract
To identify the processes shaping vertebrate sex chromosomes during the early stages of their evolution, it is necessary to study systems in which genetic sex determination was recently acquired. Previous cytogenetic studies suggested that threespine stickleback fish (Gasterosteus aculeatus) do not have a heteromorphic sex chromosome pair, although recent genetic studies found evidence of an XY genetic sex-determination system. Using fluorescence in situ hybridization (FISH), we report that the threespine stickleback Y chromosome is heteromorphic and has suffered both inversions and deletion. Using the FISH data, we reconstruct the rearrangements that have led to the current physical state of the threespine stickleback Y chromosome. These data demonstrate that the threespine Y is more degenerate than previously thought, suggesting that the process of sex chromosome evolution can occur rapidly following acquisition of a sex-determining region.
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Affiliation(s)
- Joseph A Ross
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98101, USA
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41
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Pervasive sex-linked effects on transcription regulation as revealed by expression quantitative trait loci mapping in lake whitefish species pairs (Coregonus sp., Salmonidae). Genetics 2008; 179:1903-17. [PMID: 18660540 DOI: 10.1534/genetics.107.086306] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mapping of expression quantitative trait loci (eQTL) is a powerful means for elucidating the genetic architecture of gene regulation. Yet, eQTL mapping has not been applied toward investigating the regulation architecture of genes involved in the process of population divergence, ultimately leading to speciation events. Here, we conducted an eQTL mapping experiment to compare the genetic architecture of transcript regulation in adaptive traits, differentiating the recently evolved limnetic (dwarf) and benthic (normal) species pairs of lake whitefish. The eQTL were mapped in three data sets derived from an F(1) hybrid-dwarf backcrossed family: the entire set of 66 genotyped individuals and the two sexes treated separately. We identified strikingly more eQTL in the female data set (174), compared to both male (54) and combined (33) data sets. The majority of these genes were not differentially expressed between male and female progeny of the backcross family, thus providing evidence for a strong pleiotropic sex-linked effect in transcriptomic regulation. The subtelomeric region of a linkage group segregating in females encompassed >50% of all eQTL, which exhibited the most pronounced additive effects. We also conducted a direct comparison of transcriptomic profiles between pure dwarf and normal progeny reared in controlled conditions. We detected 34 differentially expressed transcripts associated with eQTL segregating only in sex-specific data sets and mostly belonging to functional groups that differentiate dwarf and normal whitefish in natural populations. Therefore, these eQTL are not related to interindividual variation, but instead to the adaptive and historical genetic divergence between dwarf and normal whitefish. This study exemplifies how the integration of genetic and transcriptomic data offers a strong means for dissecting the functional genomic response to selection by separating mapping family-specific effects from genetic factors under selection, potentially involved in the phenotypic divergence of natural populations.
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42
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Henning F, Trifonov V, Almeida-Toledo LFD. Use of chromosome microdissection in fish molecular cytogenetics. Genet Mol Biol 2008. [DOI: 10.1590/s1415-47572008000200022] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
| | - Vladimir Trifonov
- Siberian Branch of the Russian Academy of Sciences, Russia; University of Cambridge
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43
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Streelman J, Peichel C, Parichy D. Developmental Genetics of Adaptation in Fishes: The Case for Novelty. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2007. [DOI: 10.1146/annurev.ecolsys.38.091206.095537] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- J.T. Streelman
- School of Biology, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0230;
| | - C.L. Peichel
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024;
| | - D.M. Parichy
- Department of Biology, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington 98195-1800;
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44
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Cassidy CL, Lemon JA, Boreham DR. Impacts of low-dose gamma-radiation on genotoxic risk in aquatic ecosystems. Dose Response 2007; 5:323-32. [PMID: 18648569 DOI: 10.2203/dose-response.07-026.cassidy] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Chinook salmon cells were exposed to gamma radiation and chromosome damage was assessed using the micronucleus assay. The salmon cells were resistant to radiation at all doses compared to human and mammalian cells. We used an indirect approach to determine if prior low dose exposures at environmental dose levels might alter the consequences of radiation exposures to high doses of radiation (adaptive response). The cells adapted but only at doses which were above levels that might be expected environmentally. The "adaptive response" endpoint was useful to show biological responses to exposure, however, under these conditions it might not help in risk assessment of aquatic organisms since the cells seem to be very resistant and environmental radiation levels are typically extremely low. Preliminary experiments were conducted on two other fish cell model systems (Rainbow Trout and Medaka) to optimize conditions for the micronucleus assay for future environmental radiation studies. Since fish cells appear to be more radiation resistant than mammalian cells, we postulate that radiation risk in the whole organism may also be lower. Therefore whole body studies designed to test effects with the specific aim of assessing relative risk between species are in process.
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Affiliation(s)
- Cheryl L Cassidy
- Medical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada
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45
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Molecular divergence of the W chromosomes in pyralid moths (Lepidoptera). Chromosome Res 2007; 15:917-30. [PMID: 17985203 DOI: 10.1007/s10577-007-1173-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Revised: 09/08/2007] [Accepted: 09/08/2007] [Indexed: 10/22/2022]
Abstract
Most Lepidoptera have a WZ/ZZ sex chromosome system. We compared structure of W chromosomes in four representatives of the family Pyralidae--Ephestia kuehniella, Cadra cautella, Plodia interpunctella, and Galleria mellonella--tracing pachytene bivalents which provide much higher resolution than metaphase chromosomes. In each species, we prepared a W-chromosome painting probe from laser-microdissected W-chromatin of female polyploid nuclei. The Ephestia W-probe was cross-hybridized to chromosomes of the other pyralids to detect common parts of their W chromosomes, while the species-specific W-probes identified the respective W chromosome. This so-called Zoo-FISH revealed a partial homology of W-chromosome regions between E. kuehniella and two other pyralids, C. cautella and P. interpunctella, but almost no homology with G. mellonella. The results were consistent with phylogenetic relationships between the species. We also performed comparative genomic hybridization, which indicated that the W chromosome of C. cautella is composed mainly of repetitive DNA common to both sexes but accumulated in the W chromosome, whereas E. kuehniella, P. interpunctella, and G. mellonella W chromosomes also possess a large amount of female specific DNA sequences, but differently organized. Our results support the hypothesis of the accelerated molecular divergence of the lepidopteran W chromosomes in the absence of meiotic recombination.
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46
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Takehana Y, Demiyah D, Naruse K, Hamaguchi S, Sakaizumi M. Evolution of different Y chromosomes in two medaka species, Oryzias dancena and O. latipes. Genetics 2006; 175:1335-40. [PMID: 17194774 PMCID: PMC1840079 DOI: 10.1534/genetics.106.068247] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the sex-determining gene DMY has been identified on the Y chromosome in the medaka (Oryzias latipes), this gene is absent in most Oryzias species, suggesting that closely related species have different sex-determining genes. Here, we investigated the sex-determination mechanism in O. dancena, which does not possess the DMY gene. Since heteromorphic sex chromosomes have not been reported in this species, a progeny test of sex-reversed individuals produced by hormone treatment was performed. Sex-reversed males yielded all-female progeny, indicating that O. dancena has an XX/XY sex-determination system. To uncover the cryptic sex chromosomes, sex-linked DNA markers were screened using expressed sequence tags (ESTs) established in O. latipes. Linkage analysis of isolated sex-linked ESTs showed a conserved synteny between the sex chromosomes in O. dancena and an autosome in O. latipes. Fluorescence in situ hybridization (FISH) analysis of these markers confirmed that sex chromosomes of these species are not homologous. These findings strongly suggest an independent origin of sex chromosomes in O. dancena and O. latipes. Further analysis of the sex-determining region in O. dancena should provide crucial insights into the evolution of sex-determination mechanisms in vertebrates.
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Affiliation(s)
- Yusuke Takehana
- Graduate School of Science and Technology, Niigata University, Ikarashi, Niigata 950-2181, Japan.
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47
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Artieri CG, Mitchell LA, Ng SHS, Parisotto SE, Danzmann RG, Hoyheim B, Phillips RB, Morasch M, Koop BF, Davidson WS. Identification of the sex-determining locus of Atlantic salmon (Salmo salar) on chromosome 2. Cytogenet Genome Res 2006; 112:152-9. [PMID: 16276105 DOI: 10.1159/000087528] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2005] [Accepted: 04/27/2005] [Indexed: 11/19/2022] Open
Abstract
We have integrated data from linkage mapping, physical mapping and karyotyping to gain a better understanding of the sex-determining locus, SEX, in Atlantic salmon (Salmo salar). SEX has been mapped to Atlantic salmon linkage group 1 (ASL1) and is associated with several microsatellite markers. We have used probes designed from the flanking regions of these sex-linked microsatellite markers to screen a bacterial artificial chromosome (BAC) library, representing an 11.7x coverage of the Atlantic salmon genome, which has been HindIII fingerprinted and assembled into contigs. BACs containing sex-linked microsatellites and their related contigs have been identified and representative BACs have been placed on the Atlantic salmon chromosomes by fluorescent in situ hybridization (FISH). This identified chromosome 2, a large metacentric, as the sex chromosome. By positioning several BACs on this chromosome by FISH, it was possible to orient ASL1 with respect to chromosome 2. The region containing SEX appears to lie on the long arm between marker Ssa202DU and a region of heterochromatin identified by DAPI staining. BAC end-sequencing of clones within sex-linked contigs revealed five hitherto unmapped genes along the sex chromosome. We are using an in silico approach coupled with physical probing of the BAC library to extend the BAC contigs to provide a physical map of ASL1, with a view to sequencing chromosome 2 and, in the process, identifying the sex-determining gene.
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Affiliation(s)
- C G Artieri
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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48
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Felip A, Fujiwara A, Young WP, Wheeler PA, Noakes M, Phillips RB, Thorgaard GH. Polymorphism and differentiation of rainbow trout Y chromosomes. Genome 2004; 47:1105-13. [PMID: 15644968 DOI: 10.1139/g04-059] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Most fish species show little morphological differentiation in the sex chromosomes. We have coupled molecular and cytogenetic analyses to characterize the male-determining region of the rainbow trout (Oncorhynchus mykiss) Y chromosome. Four genetically diverse male clonal lines of this species were used for genetic and physical mapping of regions in the vicinity of the sex locus. Five markers were genetically mapped to the Y chromosome in these male lines, indicating that the sex locus was located on the same linkage group in each of the lines. We also confirmed the presence of a Y chromosome morphological polymorphism among these lines, with the Y chromosomes from two of the lines having the more common heteromorphic Y chromosome and two of the lines having Y chromosomes morphologically similar to the X chromosome. The fluorescence in situ hybridization (FISH) pattern of two probes linked to sex suggested that the sex locus is physically located on the long arm of the Y chromosome. Fishes appear to be an excellent group of organisms for studying sex chromosome evolution and differentiation in vertebrates because they show considerable variability in the mechanisms and (or) patterns involved in sex determination.Key words: sex chromosomes, sex markers, cytogenetics, rainbow trout, fish.
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Affiliation(s)
- Alicia Felip
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
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Liu JD, Yi MS, Zhao G, Zhou F, Wang DQ, Yu QX. Sex chromosomes in the spiny eel (Mastacembelus aculeatus) revealed by mitotic and meiotic analysis. Cytogenet Genome Res 2003; 98:291-7. [PMID: 12826756 DOI: 10.1159/000071051] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2003] [Accepted: 03/11/2003] [Indexed: 11/19/2022] Open
Abstract
Lower vertebrates like fish exhibit tremendous diversity in sex determination. There are wide interplays between environment-dependent sex differentiation ranging from natural hermaphroditism to sex reversal and genetic sex determination. Diverse systems of male and female heterogamety coexist in fish and sex chromosomes are rarely distinguishable in morphology. Here we show that the spiny eel ((Mastacembelus aculeatus) of the Perciformes, has evolved highly heteromorphic X and Y chromosomes. The metacentric X and Y chromosomes are the largest among 24 homologous pairs, differ from each other in size and morphology, and become distinct after C-banding because of conspicuous heterochromatin blocks which exhibit alternate distribution around the centromeric region. Chromosome painting using probes from the microdissected X chromosome revealed sequence homology between X and Y. During the pachytene stage of meiosis the X and Y form a bivalent. However, their synapsis is delayed which is particularly evident in one terminus. Therefore, the X and Y have resulted from a pericentric inversion in the Y. We conclude that M. aculeatus represents an example of a highly advanced stage of sex chromosome evolution in fish.
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Affiliation(s)
- J D Liu
- School of Life Sciences, Wuhan University, Wuhan 430072 Hubei, P.R. China
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Nichols KM, Young WP, Danzmann RG, Robison BD, Rexroad C, Noakes M, Phillips RB, Bentzen P, Spies I, Knudsen K, Allendorf FW, Cunningham BM, Brunelli J, Zhang H, Ristow S, Drew R, Brown KH, Wheeler PA, Thorgaard GH. A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Anim Genet 2003; 34:102-15. [PMID: 12648093 DOI: 10.1046/j.1365-2052.2003.00957.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Androgenetic doubled haploid progeny produced from a cross between the Oregon State University and Arlee clonal rainbow trout (Oncorhynchus mykiss) lines, used for a previous published rainbow trout map, were used to update the map with the addition of more amplified fragment length polymorphic (AFLP) markers, microsatellites, type I and allozyme markers. We have added more than 900 markers, bringing the total number to 1359 genetic markers and the sex phenotype including 799 EcoRI AFLPs, 174 PstI AFLPs, 226 microsatellites, 72 VNTR, 38 SINE markers, 29 known genes, 12 minisatellites, five RAPDs, and four allozymes. Thirty major linkage groups were identified. Synteny of linkage groups in our map with the outcrossed microsatellite map has been established for all except one linkage group in this doubled haploid cross. Putative homeologous relationships among linkage groups, resulting from the autotetraploid nature of the salmonid genome, have been revealed based on the placement of duplicated microsatellites and type I loci.
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Affiliation(s)
- K M Nichols
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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