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Dulz TA, Azambuja M, Lorscheider CA, Noleto RB, Moreira-Filho O, Nogaroto V, Nascimento VD, Diniz D, de Mello Affonso PRA, Vicari MR. Repetitive DNAs and chromosome evolution in Megaleporinus obtusidens and M. reinhardti (Characiformes: Anostomidae). Genetica 2024; 152:63-70. [PMID: 38587599 DOI: 10.1007/s10709-024-00206-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
The high dynamism of repetitive DNAs is a major driver of chromosome evolution. In particular, the accumulation of repetitive DNA sequences has been reported as part of the differentiation of sex-specific chromosomes. In turn, the fish species of the genus Megaleporinus are a monophyletic clade in which the presence of differentiated ZZ/ZW sex chromosomes represents a synapomorphic condition, thus serving as a suitable model to evaluate the dynamic evolution of repetitive DNA classes. Therefore, transposable elements (TEs) and in tandem repeats were isolated and located on chromosomes of Megaleporinus obtusidens and M. reinhardti to infer their role in chromosome differentiation with emphasis on sex chromosome systems. Despite the conserved karyotype features of both species, the location of repetitive sequences - Rex 1, Rex 3, (TTAGGG)n, (GATA)n, (GA)n, (CA)n, and (A)n - varied both intra and interspecifically, being mainly accumulated in Z and W chromosomes. The physical mapping of repetitive sequences confirmed the remarkable dynamics of repetitive DNA classes on sex chromosomes that might have promoted chromosome diversification and reproductive isolation in Megaleporinus species.
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Affiliation(s)
- Thais Aparecida Dulz
- Graduate Program in Genetics, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Matheus Azambuja
- Graduate Program in Animal Science, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Carla Andrea Lorscheider
- Department of Biological Sciences, Universidade Estadual do Paraná, União da Vitória, PR, Brazil
| | - Rafael Bueno Noleto
- Department of Biological Sciences, Universidade Estadual do Paraná, União da Vitória, PR, Brazil
| | - Orlando Moreira-Filho
- Department of Genetics and Evolution, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Viviane Nogaroto
- Graduate Program in Animal Science, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | | | - Débora Diniz
- Graduate Program in Genetics, Biodiversity and Conservation, Universidade Estadual do Sudoeste da Bahia, Jequié, BA, Brazil
| | | | - Marcelo Ricardo Vicari
- Graduate Program in Genetics, Universidade Federal do Paraná, Curitiba, PR, Brazil
- Graduate Program in Animal Science, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
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2
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Crepaldi C, Cabral-de-Mello DC, Parise-Maltempi PP. Comparative analysis of transposable elements dynamics in fish with different sex chromosome systems. Genome 2024. [PMID: 38739948 DOI: 10.1139/gen-2023-0134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Transposable elements (TEs) are widespread genomic components with substantial roles in genome evolution and sex chromosome differentiation. In this study, we compared the TE composition of three closely related fish with different sex chromosome systems: Megaleporinus elongatus (Z1Z1Z2Z2/Z1W1Z2W2), Megaleporinus macrocephalus (ZZ/ZW) (both with highly differentiated W sex chromosomes), and Leporinus friderici (without heteromorphic sex chromosomes). We created custom TE libraries for each species using clustering methods and manual annotation and prediction, and we predicted TE temporal dynamics through divergence-based analysis. The TE abundance ranged from 16% to 21% in the three mobilomes, with L. friderici having the lowest overall. Despite the recent amplification of TEs in all three species, we observed differing expansion activities, particularly between the two genera. Both Megaleporinus recently experienced high retrotransposon activity, with a reduction in DNA TEs, which could have implications in sex chromosome composition. In contrast, L. friderici showed the opposite pattern. Therefore, despite having similar TE compositions, Megaleporinus and Leporinus exhibit distinct TE histories that likely evolved after their separation, highlighting a rapid TE expansion over short evolutionary periods.
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Affiliation(s)
- Carolina Crepaldi
- Universidade Estadual Paulista (UNESP) "Júlio de Mesquita Filho", Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Rio Claro, Brazil
| | - Diogo Cavalcanti Cabral-de-Mello
- Universidade Estadual Paulista (UNESP) "Júlio de Mesquita Filho", Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Rio Claro, Brazil
| | - Patricia Pasquali Parise-Maltempi
- Universidade Estadual Paulista (UNESP) "Júlio de Mesquita Filho", Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Rio Claro, Brazil
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Luo H, Zhang Y, Liu F, Zhao Y, Peng J, Xu Y, Chen X, Huang Y, Ji C, Liu Q, He P, Feng P, Yang C, Wei P, Ma Z, Qin J, Zhou S, Dai S, Zhang Y, Zhao Z, Liu H, Zheng H, Zhang J, Lin Y, Chen X. The male and female genomes of golden pompano (Trachinotus ovatus) provide insights into the sex chromosome evolution and rapid growth. J Adv Res 2023:S2090-1232(23)00369-7. [PMID: 38043610 DOI: 10.1016/j.jare.2023.11.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 12/05/2023] Open
Abstract
INTRODUCTION Golden pompano (Trachinotus ovatus) is economically significant important for offshore cage aquaculture in China and Southeast Asian countries. Lack of high-quality genomic data and accurate gene annotations greatly restricts its genetic breeding progress. OBJECTIVES To decode the mechanisms of sex determination and rapid growth in golden pompano and facilitate the sex- and growth-aimed genetic breeding. METHODS Genome assemblies of male and female golden pompano were generated using Illumina, PacBio, BioNano, genetic maps and Hi-C sequencing data. Genomic comparisons, whole genome re-sequencing of 202 F1 individuals, QTL mapping and gonadal transcriptomes were used to analyze the sex determining region, sex chromosome evolution, SNP loci, and growth candidate genes. Zebrafish model was used to investigate the functions of growth candidate gene. RESULTS Female (644.45 Mb) and male (652.12 Mb) genomes of golden pompano were assembled and annotated at the chromosome level. Both genomes are highly conserved and no new or highly differentiated sex chromosomes occur. A 3.5 Mb sex determining region on LG15 was identified, where Hsd17b1, Micall2 and Lmx1a were putative candidates for sex determination. Three SNP loci significantly linked to growth were pinpointed, and a growth-linked gene gpsstr1 was identified by locus BSNP1369 (G→C, 17489695, Chr23). Loss of sstr1a (homologue of gpsstr1) in zebrafish caused growth retardation. CONCLUSION This study provides insights into sex chromosome evolution, sex determination and rapid growth of golden pompano.
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Affiliation(s)
- Honglin Luo
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China; Institute of Oncology, Guangxi Academy of Medical Sciences, Nanning, Guangxi, 530021, China
| | - Yongde Zhang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Fuyan Liu
- Biomarker Technologies, Beijing, 101300, China; BGI-Beijing, Beijing, 102601, China
| | - Yongzhen Zhao
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Jinxia Peng
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Yuhui Xu
- Biomarker Technologies, Beijing, 101300, China
| | - Xiuli Chen
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Yin Huang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | | | - Qingyun Liu
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Pingping He
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Pengfei Feng
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Chunling Yang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Pinyuan Wei
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Zhenhua Ma
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Jianguang Qin
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Shengjie Zhou
- Sanya Tropical Fisheries Research Institute, Sanya, 572018, China
| | - Shiming Dai
- Sanya Tropical Fisheries Research Institute, Sanya, 572018, China
| | - Yaoyao Zhang
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
| | - Zhongquan Zhao
- College of Animal Science and Technology, Southwest University, Beibei, Chongqing, 400715, China
| | | | - Hongkun Zheng
- Biomarker Technologies, Beijing, 101300, China; Institute of Oncology, Guangxi Academy of Medical Sciences, Nanning, Guangxi, 530021, China.
| | - Jisen Zhang
- Center for Genomics and Biotechnology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China; State Key Lab for Conservation and Utilization of Subtropical Agro-Biological Resources & Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China.
| | - Yong Lin
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
| | - Xiaohan Chen
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
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Schartl M, Georges A, Marshall Graves JA. Polygenic sex determination in vertebrates - is there any such thing? Trends Genet 2023; 39:242-250. [PMID: 36669949 PMCID: PMC10148267 DOI: 10.1016/j.tig.2022.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/28/2022] [Accepted: 12/15/2022] [Indexed: 01/20/2023]
Abstract
Genetic sex determination (SD) in most vertebrates is controlled by a single master sex gene, which ensures a 1:1 sex ratio. However, more complex systems abound, and several have been ascribed to polygenic SD (PSD), in which many genes at different loci interact to produce the sexual phenotype. Here we examine claims for PSD in vertebrates, finding that most constitute transient states during sex chromosome turnover, or aberrant systems in species hybrids. To avoid confusion about terminology, we propose a consistent nomenclature for genetic SD systems.
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Affiliation(s)
- Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA; Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany.
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, ACT, 2601, Australia
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Crepaldi C, Martí E, Gonçalves ÉM, Martí DA, Parise-Maltempi PP. Genomic Differences Between the Sexes in a Fish Species Seen Through Satellite DNAs. Front Genet 2021; 12:728670. [PMID: 34659353 PMCID: PMC8514694 DOI: 10.3389/fgene.2021.728670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/13/2021] [Indexed: 11/14/2022] Open
Abstract
Neotropical fishes have highly diversified karyotypic and genomic characteristics and present many diverse sex chromosome systems, with various degrees of sex chromosome differentiation. Knowledge on their sex-specific composition and evolution, however, is still limited. Satellite DNAs (satDNAs) are tandemly repeated sequences with pervasive genomic distribution and distinctive evolutionary pathways, and investigating satDNA content might shed light into how genome architecture is organized in fishes and in their sex chromosomes. The present study investigated the satellitome of Megaleporinus elongatus, a freshwater fish with a proposed Z1Z1Z2Z2/Z1W1Z2W2 multiple sex chromosome system that encompasses a highly heterochromatic and differentiated W1 chromosome. The species satellitome comprises of 140 different satDNA families, including previously isolated sequences and new families found in this study. This diversity is remarkable considering the relatively low proportion that satDNAs generally account for the M. elongatus genome (around only 5%). Differences between the sexes in regards of satDNA content were also evidenced, as these sequences are 14% more abundant in the female genome. The occurrence of sex-biased signatures of satDNA evolution in the species is tightly linked to satellite enrichment associated with W1 in females. Although both sexes share practically all satDNAs, the overall massive amplification of only a few of them accompanied the W1 differentiation. We also investigated the expansion and diversification of the two most abundant satDNAs of M. elongatus, MelSat01-36 and MelSat02-26, both highly amplified sequences in W1 and, in MelSat02-26’s case, also harbored by Z2 and W2 chromosomes. We compared their occurrences in M. elongatus and the sister species M. macrocephalus (with a standard ZW sex chromosome system) and concluded that both satDNAs have led to the formation of highly amplified arrays in both species; however, they formed species-specific organization on female-restricted sex chromosomes. Our results show how satDNA composition is highly diversified in M. elongatus, in which their accumulation is significantly contributing to W1 differentiation and not satDNA diversity per se. Also, the evolutionary behavior of these repeats may be associated with genome plasticity and satDNA variability between the sexes and between closely related species, influencing how seemingly homeologous heteromorphic sex chromosomes undergo independent satDNA evolution.
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Affiliation(s)
- Carolina Crepaldi
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Emiliano Martí
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Évelin Mariani Gonçalves
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Dardo Andrea Martí
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (IBS), Universidad Nacional de Misiones (UNaM), CONICET, Posadas, Argentina
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6
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Sember A, Nguyen P, Perez MF, Altmanová M, Ráb P, Cioffi MDB. Multiple sex chromosomes in teleost fishes from a cytogenetic perspective: state of the art and future challenges. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200098. [PMID: 34304595 PMCID: PMC8310710 DOI: 10.1098/rstb.2020.0098] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2020] [Indexed: 12/15/2022] Open
Abstract
Despite decades of cytogenetic and genomic research of dynamic sex chromosome evolution in teleost fishes, multiple sex chromosomes have been largely neglected. In this review, we compiled available data on teleost multiple sex chromosomes, identified major trends in their evolution and suggest further trajectories in their investigation. In a compiled dataset of 440 verified records of fish sex chromosomes, we counted 75 multiple sex chromosome systems with 60 estimated independent origins. We showed that male-heterogametic systems created by Y-autosome fusion predominate and that multiple sex chromosomes are over-represented in the order Perciformes. We documented a striking difference in patterns of differentiation of sex chromosomes between male and female heterogamety and hypothesize that faster W sex chromosome differentiation may constrain sex chromosome turnover in female-heterogametic systems. We also found no significant association between the mechanism of multiple sex chromosome formation and percentage of uni-armed chromosomes in teleost karyotypes. Last but not least, we hypothesized that interaction between fish populations, which differ in their sex chromosomes, can drive the evolution of multiple sex chromosomes in fishes. This underlines the importance of broader inter-population sampling in studies of fish sex chromosomes. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Petr Nguyen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Manolo F. Perez
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, 13565-905, São Carlos, Brazil
| | - Marie Altmanová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, 13565-905, São Carlos, Brazil
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Salgado FS, Cunha MS, Melo S, Dergam JA. Cytogenetic analysis of Hypomasticus copelandii and H. steindachneri: relevance of cytotaxonomic markers in the Anostomidae family (Characiformes). COMPARATIVE CYTOGENETICS 2021; 15:65-76. [PMID: 33777329 PMCID: PMC7969579 DOI: 10.3897/compcytogen.v15.i1.61957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/24/2021] [Indexed: 06/12/2023]
Abstract
Recent phylogenetic hypotheses within Anostomidae, based on morphological and molecular data, resulted in the description of new genera (Megaleporinus Ramirez, Birindelli et Galetti, 2017) and the synonymization of others, such as the reallocation of Leporinus copelandii Steindachner, 1875 and Leporinus steindachneri Eigenmann, 1907 to Hypomasticus Borodin, 1929. Despite high levels of conservatism of the chromosomal macrostructure in this family, species groups have been corroborated using banding patterns and the presence of different sex chromosome systems. Due to the absence of cytogenetic studies in H. copelandii (Steindachner, 1875) and H. steindachneri (Eigenmann, 1907), the goal of this study was to characterize their karyotypes and investigate the presence/absence of sex chromosome systems using different repetitive DNA probes. Cytogenetic techniques included: Giemsa staining, Ag-NOR banding and FISH using 18S and 5S rDNA probes, as well as microsatellite probes (CA)15 and (GA)15. Both species had 2n = 54, absence of heteromorphic sex chromosomes, one chromosome pair bearing Ag-NOR, 18S and 5S rDNA regions. The (CA)15 and (GA)15 probes marked mainly the subtelomeric regions of all chromosomes and were useful as species-specific chromosomal markers. Our results underline that chromosomal macrostructure is congruent with higher systematic arrangements in Anostomidae, while microsatellite probes are informative about autapomorphic differences between species.
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Affiliation(s)
- Filipe Schitini Salgado
- Departamento de Biologia Animal, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Centro, Viçosa, 36570-900, Minas Gerais, Brazil
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Centro, Viçosa, 36570-900, Minas Gerais, Brazil
| | - Marina Souza Cunha
- Departamento de Biologia Animal, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Centro, Viçosa, 36570-900, Minas Gerais, Brazil
| | - Silvana Melo
- Departamento de Biologia Animal, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Centro, Viçosa, 36570-900, Minas Gerais, Brazil
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Centro, Viçosa, 36570-900, Minas Gerais, Brazil
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, R. Prof. Dr. Antônio Celso Wagner Zanin, s/n, Distrito de Rubião Junior, Botucatu, 18618-689, São Paulo, Brazil
| | - Jorge Abdala Dergam
- Departamento de Biologia Animal, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Centro, Viçosa, 36570-900, Minas Gerais, Brazil
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8
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Dulz TA, Azambuja M, Nascimento VD, Lorscheider CA, Noleto RB, Moreira-Filho O, Nogaroto V, Diniz D, Affonso PRADM, Vicari MR. Karyotypic Diversification in Two Megaleporinus Species (Characiformes, Anostomidae) Inferred from In Situ Localization of Repetitive DNA Sequences. Zebrafish 2020; 17:333-341. [PMID: 32990531 DOI: 10.1089/zeb.2020.1918] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Anostomidae species have conserved diploid numbers (2n = 54), although comparative cytogenetic studies have demonstrated chromosomal rearrangements occurrence among them, especially in repetitive DNA rich regions. The location and distribution of ribosomal DNA (rDNA) and small nuclear RNAs (snRNAs) multigene families are highly dynamic in the genomes of several organisms. In this study, we in situ located the rDNA and snRNA sites in two populations of Megaleporinus obtusidens and a sample of Megaleporinus reinhardti to infer their chromosomal changes in the evolutionary lineages. Both species of Megaleporinus shared 2n = 54 chromosomes with the presence of ZZ/ZW sex chromosome system, but they diverged in relationship to the location of 5S and 45S rDNAs as well as the distribution of snRNAs sites. The characterization of the analyzed sequences revealed the presence of complete rDNA and snRNAs sequences as well as snRNAs containing transposable elements (TEs) and microsatellite repeats. After chromosomal mapping, the sequences encompassing TEs proved to be dispersed through autosomes and accumulated on sex chromosomes. The data demonstrate that intra- and interspecific chromosomal changes occurred involving the multigene family's sites in Megaleporinus karyotypes. Furthermore, we detected TE-like sequences in the differentiation of sex chromosome systems in M. obtusidens and M. reinhardti.
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Affiliation(s)
- Thais Aparecida Dulz
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil.,Departamento de Ciências Biológicas, Universidade Estadual do Paraná, União da Vitória, Brazil
| | - Matheus Azambuja
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | | | | | - Rafael Bueno Noleto
- Departamento de Ciências Biológicas, Universidade Estadual do Paraná, União da Vitória, Brazil
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Débora Diniz
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | | | - Marcelo Ricardo Vicari
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil.,Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
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9
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Xiao Y, Xiao Z, Ma D, Zhao C, Liu L, Wu H, Nie W, Xiao S, Liu J, Li J, Herrera-Ulloa A. Chromosome-Level Genome Reveals the Origin of Neo-Y Chromosome in the Male Barred Knifejaw Oplegnathus fasciatus. iScience 2020; 23:101039. [PMID: 32305860 PMCID: PMC7171519 DOI: 10.1016/j.isci.2020.101039] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/05/2020] [Accepted: 04/01/2020] [Indexed: 12/13/2022] Open
Abstract
The barred knifejaw, Oplegnathus fasciatus, is characterized by an X1X2Y system with a neo-Y chromosome for males. Here, a chromosome-level genome was assembled to investigate the origin of neo-Y chromosome to the male O. fasciatus. Twenty-three chromosomes corresponding to the male karyotypes were scaffolded to 762-Mb genome with a contig N50 length of 2.18 Mb. A large neo-Y chromosome (Ch9) in the male O. fasciatus genome was also assembled and exhibited high identity to those of the female chromosomes Ch8 and Ch10. Chromosome rearrangements events were detected in the neo-chromosome Ch9. Our results suggested that a centric fusion of acrocentric chromosomes Ch8 and Ch10 should be responsible for the formation of the X1X2Y system. The high-quality genome will not only provide a solid foundation for further sex-determining mechanism research in the X1X2Y system but also facilitate the artificial breeding aiming to improve the yield and disease resistance for Oplegnathus. Construction of a chromosome-level reference genome for the male O. fasciatus Identification of the origin of neo-Y chromosome to the X1X2Y system Accurate comparisons of sequences and genes between female X1X1X2X2 and male X1X2Y
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Affiliation(s)
- Yongshuang Xiao
- Center for Ocean Mega-Science, The Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhizhong Xiao
- Center for Ocean Mega-Science, The Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Daoyuan Ma
- Center for Ocean Mega-Science, The Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chenxi Zhao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Lin Liu
- Wuhan Frasergen Bioinformatics Co., Ltd. East Lake High-Tech Zone, Wuhan, China
| | - Hao Wu
- Wuhan Frasergen Bioinformatics Co., Ltd. East Lake High-Tech Zone, Wuhan, China
| | - Wenchao Nie
- Wuhan Frasergen Bioinformatics Co., Ltd. East Lake High-Tech Zone, Wuhan, China
| | - Shijun Xiao
- College of Plant Protection, Jilin Agriculture University, Changchun, Jilin, China; School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China.
| | - Jing Liu
- Center for Ocean Mega-Science, The Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Jun Li
- Center for Ocean Mega-Science, The Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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Crepaldi C, Parise-Maltempi PP. Heteromorphic Sex Chromosomes and Their DNA Content in Fish: An Insight through Satellite DNA Accumulation in Megaleporinus elongatus. Cytogenet Genome Res 2020; 160:38-46. [DOI: 10.1159/000506265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2019] [Indexed: 12/12/2022] Open
Abstract
The repetitive DNA content of fish sex chromosomes provides valuable insights into specificities and patterns of their genetic sex determination systems. In this study, we revealed the genomic satellite DNA (satDNA) content of Megaleporinuselongatus, a Neotropical fish species with Z1Z1Z2Z2/Z1W1Z2W2 multiple sex chromosomes, through high-throughput analysis and graph-based clustering, isolating 68 satDNA families. By physically mapping these sequences in female metaphases, we discovered 15 of the most abundant satDNAs clustered in its chromosomes, 9 of which were found exclusively in the highly heterochromatic W1. This heteromorphic sex chromosome showed the highest amount of satDNA accumulations in this species. The second most abundant family, MelSat02-26, shared FISH signals with the NOR-bearing pair in similar patterns and is linked to the multiple sex chromosome system. Our results demonstrate the diverse satDNA content in M. elongatus, especially in its heteromorphic sex chromosome. Additionally, we highlighted the different accumulation patterns and distribution of these sequences across species by physically mapping these satDNAs in other Anostomidae, Megaleporinusmacrocephalus and Leporinusfriderici (a species without differentiated sex chromosomes).
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Xu D, Sember A, Zhu Q, Oliveira EAD, Liehr T, Al-Rikabi ABH, Xiao Z, Song H, Cioffi MDB. Deciphering the Origin and Evolution of the X 1X 2Y System in Two Closely-Related Oplegnathus Species (Oplegnathidae and Centrarchiformes). Int J Mol Sci 2019; 20:E3571. [PMID: 31336568 PMCID: PMC6678977 DOI: 10.3390/ijms20143571] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/05/2019] [Accepted: 07/13/2019] [Indexed: 01/18/2023] Open
Abstract
Oplegnathus fasciatus and O. punctatus (Teleostei: Centrarchiformes: Oplegnathidae), are commercially important rocky reef fishes, endemic to East Asia. Both species present an X1X2Y sex chromosome system. Here, we investigated the evolutionary forces behind the origin and differentiation of these sex chromosomes, with the aim to elucidate whether they had a single or convergent origin. To achieve this, conventional and molecular cytogenetic protocols, involving the mapping of repetitive DNA markers, comparative genomic hybridization (CGH), and whole chromosome painting (WCP) were applied. Both species presented similar 2n, karyotype structure and hybridization patterns of repetitive DNA classes. 5S rDNA loci, besides being placed on the autosomal pair 22, resided in the terminal region of the long arms of both X1 chromosomes in females, and on the X1 and Y chromosomes in males. Furthermore, WCP experiments with a probe derived from the Y chromosome of O. fasciatus (OFAS-Y) entirely painted the X1 and X2 chromosomes in females and the X1, X2, and Y chromosomes in males of both species. CGH failed to reveal any sign of sequence differentiation on the Y chromosome in both species, thereby suggesting the shared early stage of neo-Y chromosome differentiation. Altogether, the present findings confirmed the origin of the X1X2Y sex chromosomes via Y-autosome centric fusion and strongly suggested their common origin.
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Affiliation(s)
- Dongdong Xu
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan 316100, China
- College of Fisheries, Zhejiang Ocean University, Zhoushan 316100, China
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Qihui Zhu
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan 316100, China
| | - Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos SP 13565-905, Brazil
- Secretaria de Estado de Educação de Mato Grosso-SEDUC-MT, Cuiabá MT 78049-909, Brazil
| | - Thomas Liehr
- University Clinic Jena, Institute of Human Genetics, 07747 Jena, Germany
| | | | - Zhizhong Xiao
- Laboratory for Marine Biology and Biotechnology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Hongbin Song
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan 316100, China
- College of Fisheries, Zhejiang Ocean University, Zhoushan 316100, China
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos SP 13565-905, Brazil.
- University Clinic Jena, Institute of Human Genetics, 07747 Jena, Germany.
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Utsunomia R, Silva DMZDA, Ruiz-Ruano FJ, Goes CAG, Melo S, Ramos LP, Oliveira C, Porto-Foresti F, Foresti F, Hashimoto DT. Satellitome landscape analysis of Megaleporinus macrocephalus (Teleostei, Anostomidae) reveals intense accumulation of satellite sequences on the heteromorphic sex chromosome. Sci Rep 2019; 9:5856. [PMID: 30971780 PMCID: PMC6458115 DOI: 10.1038/s41598-019-42383-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 03/26/2019] [Indexed: 11/09/2022] Open
Abstract
The accumulation of repetitive DNA sequences on the sex-limited W or Y chromosomes is a well-known process that is likely triggered by the suppression of recombination between the sex chromosomes, which leads to major differences in their sizes and genetic content. Here, we report an analysis conducted on the satellitome of Megaleporinus macrocephalus that focuses specifically on the satDNAs that have been shown to have higher abundances in females and are putatively located on the W chromosome in this species. We characterized 164 satellite families in M. macrocephalus, which is, by far, the most satellite-rich species discovered to date. Subsequently, we mapped 30 satellites, 22 of which were located on the W chromosome, and 14 were shown to exist only on the W chromosome. Finally, we report two simple, quick and reliable methods that can be used for sex identification in M. macrocephalus individuals using fin clips or scales, which could be applicable to future studies conducted in the field of aquaculture.
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Affiliation(s)
- Ricardo Utsunomia
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Distrito de Rubião Junior, s/n, 18618-970, Botucatu, SP, Brazil. .,Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.
| | | | | | - Caio Augusto Gomes Goes
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista - UNESP, Campus de Bauru, 17033-360, Bauru, SP, Brazil
| | - Silvana Melo
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Distrito de Rubião Junior, s/n, 18618-970, Botucatu, SP, Brazil
| | - Lucas Peres Ramos
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Distrito de Rubião Junior, s/n, 18618-970, Botucatu, SP, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Distrito de Rubião Junior, s/n, 18618-970, Botucatu, SP, Brazil
| | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista - UNESP, Campus de Bauru, 17033-360, Bauru, SP, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Distrito de Rubião Junior, s/n, 18618-970, Botucatu, SP, Brazil
| | - Diogo Teruo Hashimoto
- CAUNESP, Universidade Estadual Paulista - UNESP, Campus Jaboticabal, 14884-900, Jaboticabal, SP, Brazil
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Caetano de Barros L, Piscor D, Parise-Maltempi PP, Feldberg E. Differentiation and Evolution of the W Chromosome in the Fish Species of Megaleporinus (Characiformes, Anostomidae). Sex Dev 2018; 12:204-209. [DOI: 10.1159/000489693] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2018] [Indexed: 02/01/2023] Open
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14
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Chromosomal locations of U2 snDNA clusters in Megaleporinus, Leporinus and Schizodon (Characiformes: Anostomidae). Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-0031-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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15
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Tracking the evolutionary pathway of sex chromosomes among fishes: characterizing the unique XX/XY1Y2 system in Hoplias malabaricus (Teleostei, Characiformes). Chromosoma 2017; 127:115-128. [DOI: 10.1007/s00412-017-0648-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/16/2017] [Accepted: 10/17/2017] [Indexed: 10/18/2022]
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Chromosomal Evolution in Lower Vertebrates: Sex Chromosomes in Neotropical Fishes. Genes (Basel) 2017; 8:genes8100258. [PMID: 28981468 PMCID: PMC5664108 DOI: 10.3390/genes8100258] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 09/27/2017] [Accepted: 09/29/2017] [Indexed: 11/17/2022] Open
Abstract
Fishes exhibit the greatest diversity of species among vertebrates, offering a number of relevant models for genetic and evolutionary studies. The investigation of sex chromosome differentiation is a very active and striking research area of fish cytogenetics, as fishes represent one of the most vital model groups. Neotropical fish species show an amazing variety of sex chromosome systems, where different stages of differentiation can be found, ranging from homomorphic to highly differentiated sex chromosomes. Here, we draw attention on the impact of recent developments in molecular cytogenetic analyses that helped to elucidate many unknown questions about fish sex chromosome evolution, using excellent characiform models occurring in the Neotropical region, namely the Erythrinidae family and the Triportheus genus. While in Erythrinidae distinct XY and/or multiple XY-derived sex chromosome systems have independently evolved at least four different times, representatives of Triportheus show an opposite scenario, i.e., highly conserved ZZ/ZW system with a monophyletic origin. In both cases, recent molecular approaches, such as mapping of repetitive DNA classes, comparative genomic hybridization (CGH), and whole chromosome painting (WCP), allowed us to unmask several new features linked to the molecular composition and differentiation processes of sex chromosomes in fishes.
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Takagui FH, Moura LFD, Ferreira DC, Centofante L, Vitorino CDA, Bueno V, Margarido VP, Venere PC. Karyotype Diversity in Doradidae (Siluriformes, Doradoidea) and Presence of the Heteromorphic ZZ/ZW Sex Chromosome System in the Family. Zebrafish 2017; 14:236-243. [PMID: 28192063 DOI: 10.1089/zeb.2016.1368] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Karyotypes and other chromosomal markers as revealed by conventional and molecular cytogenetic protocols in four species of the catfish family Doradidae from the Araguaia-Tocantins river basin, namely Hassar wilderi, Leptodoras cataniae, Tenellus leporhinus and Tenellus trimaculatus were examined. All species had diploid chromosome number 2n = 58 and karyotypes dominated by biarmed chromosomes, simple NOR phenotype, that is, one chromosome pair bearing this site in terminal position, but some differences in karyotypes and distribution of constitutive heterochromatin, position of rDNA sites. Such characteristics appeared species-specific. A ZZ/ZW sex chromosome system was found in Tenellus trimaculatus, resulting likely from the amplification of the heterochromatin, followed by a paracentric inversion. Our results confirmed low karyotype differentiation observed until now among representatives of this endemic catfish family.
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Affiliation(s)
- Fábio Hiroshi Takagui
- 1 Laboratório de Citogenética Animal, Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina , Londrina, Brazil
| | - Lucas Ferreira de Moura
- 2 Laboratório de Ictiologia, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Mato Grosso , Pontal do Araguaia, Brazil
| | - Daniela Cristina Ferreira
- 3 Laboratório de Citogenética e Genética Animal, Instituto de Biociências, Universidade Federal de Mato Grosso , Cuiabá, Brazil
| | - Liano Centofante
- 3 Laboratório de Citogenética e Genética Animal, Instituto de Biociências, Universidade Federal de Mato Grosso , Cuiabá, Brazil
| | - Carla de Andrade Vitorino
- 4 Programa de Pós Graduação em Ecologia e Conservação da Biodiversidade, Instituto de Biociências, Universidade Federal de Mato Grosso , Cuiabá, Brazil
| | - Vanessa Bueno
- 5 Universidade Tecnológica Federal do Paraná , Prolongamento da Rua Cerejeira s/n, Paraná, Brazil
| | - Vladimir Pavan Margarido
- 6 Laboratório de Citogenética de peixes, Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná , Paraná, Brazil
| | - Paulo Cesar Venere
- 3 Laboratório de Citogenética e Genética Animal, Instituto de Biociências, Universidade Federal de Mato Grosso , Cuiabá, Brazil .,4 Programa de Pós Graduação em Ecologia e Conservação da Biodiversidade, Instituto de Biociências, Universidade Federal de Mato Grosso , Cuiabá, Brazil
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18
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da Silva KR, Mariotto S, Centofante L, Parise-Maltempi PP. Chromosome mapping of a Tc1-like transposon in species of the catfish Ancistrus. COMPARATIVE CYTOGENETICS 2017; 11:65-79. [PMID: 28919950 PMCID: PMC5599695 DOI: 10.3897/compcytogen.v11i1.10519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/28/2016] [Indexed: 06/07/2023]
Abstract
The Tc1 mariner element is widely distributed among organisms and have been already described in different species of fish. The genus Ancistrus (Kner, 1854) has 68 nominal species and is part of an interesting taxonomic and cytogenetic group, as well as presenting a variation of chromosome number, ranging from 2n=34 to 54 chromosomes, and the existence of simple and multiple sex chromosome system and the occurrence of chromosomal polymorphisms involving chromosomes that carry the nucleolus organizer region. In this study, a repetitive element by restriction enzyme, from Ancistrus sp.1 "Flecha" was isolated, which showed similarity with a transposable element Tc1-mariner. Its chromosomal location is distributed in heterochromatic regions and along the chromosomal arms of all specimens covered in this study, confirming the pattern dispersed of this element found in other studies carried out with other species. Thus, this result reinforces the hypothesis that the sequence AnDraI is really a dispersed element isolated. As this isolated sequence showed the same pattern in all species which have different sex chromosomes systems, including in all sex chromosomes, we could know that it is not involved in sex chromosome differentiation.
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Affiliation(s)
- Keteryne Rodrigues da Silva
- Laboratório de Citogenética Animal – Universidade Estadual Paulista “Júlio de Mesquita Filho” Campus de Rio Claro – Av 24A, 1515 Jardim Bela Vista- 13600-000- Rio Claro/SP, Brasil
| | - Sandra Mariotto
- Instituto Federal de Ciências e Tecnologia do Mato Grosso, campus de Cuiabá – Bela Vista, MT, Brasil
| | - Liano Centofante
- Instituto de Biociências, UFMT Universidade Federal de Mato Grosso, Cuiabá, MT, Brasil
| | - Patricia Pasquali Parise-Maltempi
- Laboratório de Citogenética Animal – Universidade Estadual Paulista “Júlio de Mesquita Filho” Campus de Rio Claro – Av 24A, 1515 Jardim Bela Vista- 13600-000- Rio Claro/SP, Brasil
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19
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Unraveling the Sex Chromosome Heteromorphism of the Paradoxical Frog Pseudis tocantins. PLoS One 2016; 11:e0156176. [PMID: 27214234 PMCID: PMC4877019 DOI: 10.1371/journal.pone.0156176] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/10/2016] [Indexed: 11/25/2022] Open
Abstract
The paradoxical frog Pseudis tocantins is the only species in the Hylidae family with known heteromorphic Z and W sex chromosomes. The Z chromosome is metacentric and presents an interstitial nucleolar organizer region (NOR) on the long arm that is adjacent to a pericentromeric heterochromatic band. In contrast, the submetacentric W chromosome carries a pericentromeric NOR on the long arm, which is adjacent to a clearly evident heterochromatic band that is larger than the band found on the Z chromosome and justify the size difference observed between these chromosomes. Here, we provide evidence that the non-centromeric heterochromatic bands in Zq and Wq differ not only in size and location but also in composition, based on comparative genomic hybridization (CGH) and an analysis of the anuran PcP190 satellite DNA. The finding of PcP190 sequences in P. tocantins extends the presence of this satellite DNA, which was previously detected among Leptodactylidae and Hylodidae, suggesting that this family of repetitive DNA is even older than it was formerly considered. Seven groups of PcP190 sequences were recognized in the genome of P. tocantins. PcP190 probes mapped to the heterochromatic band in Wq, and a Southern blot analysis indicated the accumulation of PcP190 in the female genome of P. tocantins, which suggests the involvement of this satellite DNA in the evolution of the sex chromosomes of this species.
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Costa GWWFD, Cioffi MDB, Bertollo LAC, Molina WF. The Evolutionary Dynamics of Ribosomal Genes, Histone H3, and Transposable Rex Elements in the Genome of Atlantic Snappers. J Hered 2016; 107:173-80. [PMID: 26792596 DOI: 10.1093/jhered/esv136] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/17/2015] [Indexed: 11/12/2022] Open
Abstract
Lutjanidae is a family of primarily marine and carnivorous fishes distributed in the Atlantic, Indian, and Pacific oceans, with enormous economic and ecological importance. In order to better clarify the conservative chromosomal evolution of Lutjanidae, we analyzed the evolutionary dynamics of 5 repetitive DNA classes in 5 Lutjanus and in 1 Ocyurus species from the Western Atlantic. The ribosomal 18S sites were generally located in a single chromosome pair, except for L. jocu and L. alexandrei where they are found in 2 pairs. In turn, the 5S rDNA sites are unique, terminal and nonsyntenic with the 18S rDNA sites. In 3 species analyzed, H3 hisDNA genes were found in 1 chromosomal pair. However, while L. jocu presented 2 H3 sites, O. chrysurus showed a noteworthy dispersion of this gene in almost all chromosomes of the karyotype. Retrotransposons Rex1 and Rex3 do not exhibit any association with the explosive distribution of H3 sequences in O. chrysurus. The low compartmentalization of Rex elements, in addition to the general nondynamic distribution of ribosomal and H3 genes, corroborate the karyotype conservatism in Lutjanidae species, also at the microstructural level. However, some "disturbing evolutionary waves" can break down this conservative scenario, as evidenced by the massive random dispersion of H3 hisDNA in the genome of O. chrysurus. The implication of the genomic expansion of H3 histone genes and their functionality remain unknown, although suggesting that they have higher evolutionary dynamics than previously thought.
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Affiliation(s)
- Gideão Wagner Werneck Félix da Costa
- From the Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, 59.078-970 Natal, RN, Brasil (Costa and Molina); Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luis, Km 235 13.565-905 São Carlos, SP, Brasil (Cioffi and Bertollo)
| | - Marcelo de Bello Cioffi
- From the Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, 59.078-970 Natal, RN, Brasil (Costa and Molina); Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luis, Km 235 13.565-905 São Carlos, SP, Brasil (Cioffi and Bertollo)
| | - Luiz Antonio Carlos Bertollo
- From the Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, 59.078-970 Natal, RN, Brasil (Costa and Molina); Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luis, Km 235 13.565-905 São Carlos, SP, Brasil (Cioffi and Bertollo)
| | - Wagner Franco Molina
- From the Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, 59.078-970 Natal, RN, Brasil (Costa and Molina); Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luis, Km 235 13.565-905 São Carlos, SP, Brasil (Cioffi and Bertollo).
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Sex chromosome composition revealed in Characidium fishes (Characiformes: Crenuchidae) by molecular cytogenetic methods. Biologia (Bratisl) 2014. [DOI: 10.2478/s11756-014-0434-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Sex determination in Antarctic notothenioid fish: chromosomal clues and evolutionary hypotheses. Polar Biol 2014. [DOI: 10.1007/s00300-014-1601-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Poltronieri J, Marquioni V, Bertollo L, Kejnovsky E, Molina W, Liehr T, Cioffi M. Comparative Chromosomal Mapping of Microsatellites inLeporinusSpecies (Characiformes, Anostomidae): Unequal Accumulation on the W Chromosomes. Cytogenet Genome Res 2014; 142:40-5. [DOI: 10.1159/000355908] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2013] [Indexed: 11/19/2022] Open
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Splendore de Borba R, Lourenço da Silva E, Parise-Maltempi PP. Chromosome mapping of retrotransposable elements Rex1 and Rex3 in Leporinus Spix, 1829 species (Characiformes: Anostomidae) and its relationships among heterochromatic segments and W sex chromosome. Mob Genet Elements 2013; 3:e27460. [PMID: 24404417 DOI: 10.4161/mge.27460] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 11/28/2013] [Accepted: 12/08/2013] [Indexed: 01/21/2023] Open
Abstract
The family Anostomidae is an interesting model for studies of repetitive elements, mainly because of the presence of high numbers of heterochromatic segments related to a peculiar system of female heterogamety, which is restricted to a few species of Leporinus genus. Thus, cytogenetic mapping of the retrotransposable elements Rex1, Rex3, and Rex6 was performed in six Leporinus species, to elucidate the genomic organization of this genus. The sequencing of the Rex1 and Rex3 elements detected different base pair compositions in these elements among species, whereas the Rex6 element was not identified in the genomes of these species. FISH analysis using Rex1 detected different distribution patterns, L. elongatus, L. macrocephalus, and L. obtusidens had clusters in the terminal regions, whereas the signals were dispersed throughout all of the chromosomes with some signals in the terminal position in other species. The Rex3 signals were found mainly in the terminal positions in all the chromosomes of all species. The W chromosomes of L. elongatus, L. macrocephalus, and L. obtusidens contained the Rex1 and Rex3 signal in an interstitial position. These results suggest the emergence of different activity levels for these elements during the evolution of the species analyzed. Despite the conserved karyotype macrostructure species Leporinus often discussed, our results show some variation in hybridization patterns, particularly between the species with specific patterns in their sex chromosomes and species without this differentiated system.
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Affiliation(s)
- Rafael Splendore de Borba
- Instituto de Biociências; Universidade Estadual Paulista (UNESP) "Julio de Mesquita Filho," Rio Claro; Departamento de Biologia; Laboratório de Citogenética; Rio Claro, SP Brazil
| | | | - Patrícia Pasquali Parise-Maltempi
- Instituto de Biociências; Universidade Estadual Paulista (UNESP) "Julio de Mesquita Filho," Rio Claro; Departamento de Biologia; Laboratório de Citogenética; Rio Claro, SP Brazil
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25
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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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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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da Silva EL, de Borba RS, Parise-Maltempi PP. Chromosome mapping of repetitive sequences in Anostomidae species: implications for genomic and sex chromosome evolution. Mol Cytogenet 2012; 5:45. [PMID: 23228116 PMCID: PMC3541136 DOI: 10.1186/1755-8166-5-45] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 10/31/2012] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED BACKGROUND Members of the Anostomidae family provide an interesting model system for the study of the influence of repetitive elements on genome composition, mainly because they possess numerous heterochromatic segments and a peculiar system of female heterogamety that is restricted to a few species of the Leporinus genus. The aim of this study was to isolate and identify important new repetitive DNA elements in Anostomidae through restriction enzyme digestion, followed by cloning, characterisation and chromosome mapping of this fragment. To identify repetitive elements in other Leporinus species and expand on studies of repetitive elements in Anostomidae, hybridisation experiments were also performed using previously described probes of LeSpeI repetitive elements. RESULTS The 628-base pair (bp) LeSpeII fragment was hybridised to metaphase cells of L. elongatus individuals as well as those of L. macrocephalus, L. obtusidens, L. striatus, L. lacustris, L. friderici, Schizodon borellii and S. isognathus. In L. elongatus, both male and female cells contained small clusters of LeSpeII repetitive elements dispersed on all of the chromosomes, with enrichment near most of the terminal portions of the chromosomes. In the female sex chromosomes of L. elongatus (Z2,Z2/W1W2), however, this repeated element was absent. In the remaining species, a dispersed pattern of hybridisation was observed on all chromosomes irrespective of whether or not they were sex chromosomes. The repetitive element LeSpeI produced positive hybridisations signals only in L. elongatus, L. macrocephalus and L. obtusidens, i.e., species with differentiated sex chromosomes. In the remaining species, the LeSpeI element did not produce hybridisation signals. CONCLUSIONS Results are discussed in terms of the effects of repetitive sequences on the differentiation of the Anostomidae genome, especially with respect to sex chromosome evolution. LeSpeII showed hybridisation patterns typical of Long Interspersed Elements (LINEs). The differential distribution of this element may be linked to sex chromosome differentiation in L. elongatus species. The relationship between sex chromosome specificity and the LeSpeI element is confirmed in the species L. elongatus, L. macrocephalus and L. obtusidens.
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Affiliation(s)
- Edson Lourenço da Silva
- Departamento de Biologia, Laboratório de Citogenética, Instituto de Biociências, Universidade Estadual Paulista “Julio de Mesquita Filho” - UNESP, Av. 24A, 1515, Rio Claro, SP, CEP 13506-900, Brazil
| | - Rafael Splendore de Borba
- Departamento de Biologia, Laboratório de Citogenética, Instituto de Biociências, Universidade Estadual Paulista “Julio de Mesquita Filho” - UNESP, Av. 24A, 1515, Rio Claro, SP, CEP 13506-900, Brazil
| | - Patrícia Pasquali Parise-Maltempi
- Departamento de Biologia, Laboratório de Citogenética, Instituto de Biociências, Universidade Estadual Paulista “Julio de Mesquita Filho” - UNESP, Av. 24A, 1515, Rio Claro, SP, CEP 13506-900, Brazil
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Bellafronte E, Schemberger MO, Artoni RF, Filho OM, Vicari MR. Sex chromosome system ZZ/ZW in Apareiodon hasemani Eigenmann, 1916 (Characiformes, Parodontidae) and a derived chromosomal region. Genet Mol Biol 2012; 35:770-6. [PMID: 23271937 PMCID: PMC3526084 DOI: 10.1590/s1415-47572012005000077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 09/05/2012] [Indexed: 11/23/2022] Open
Abstract
Parodontidae fish show few morphological characteristics for the identification of their representatives and chromosomal analyses have provided reliable features for determining the interrelationships in this family. In this study, the chromosomes of Apareiodon hasemani from the São Francisco River basin, Brazil, were analyzed and showed a karyotype with 2n = 54 meta/submetacentric chromosomes, and a ZZ/ZW sex chromosome system. The study revealed active NORs located on pair 11 and additional 18S rDNA sites on pairs 7 and 22. The 5S rDNA locus was found in pair 14. It showed a pericentric inversion regarding the ancestral condition. The satellite DNA pPh2004 was absent in the chromosomes of A. hasemani, a shared condition with most members of Apareiodon. The WAp probe was able to detect the amplification region of the W chromosome, corroborating the common origin of the system within Parodontidae. These chromosomal data corroborate an origin for the ZW system of Parodontidae and aid in the understanding of the differentiation of sex chromosome systems in Neotropical fishes.
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Affiliation(s)
- Elisangela Bellafronte
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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29
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da Silva EL, Busso AF, Parise-Maltempi PP. Characterization and genome organization of a repetitive element associated with the nucleolus organizer region in Leporinus elongatus (Anostomidae: Characiformes). Cytogenet Genome Res 2012; 139:22-8. [PMID: 23037972 DOI: 10.1159/000342957] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2012] [Indexed: 12/12/2022] Open
Abstract
Chromosome mapping and studies of the genomic organization of repetitive DNA sequences provide valuable insights that enhance our evolutionary and structural understanding of these sequences, as well as identifying chromosomal rearrangements and sex determination. This study investigated the occurrence and organization of repetitive DNA sequences in Leporinus elongatus using restriction enzyme digestion and the mapping of sequences by chromosomal fluorescence in situ hybridization (FISH). A 378-bp fragment with a 54.2% GC content was isolated after digestion with the SmaI restriction enzyme. BLASTN search found no similarity with previously described sequences, so this repetitive sequence was named LeSmaI. FISH experiments were conducted using L. elongatus and other Anostomidae species, i.e. L. macrocephalus, L. obtusidens, L. striatus, L. lacustris, L. friderici, Schizodon borellii, S. isognathus, and Abramites hypselonotus which detected signals that were unique to male and female L. elongatus individuals. Double-FISH using LeSmaI and 18S rDNA showed that LeSmaI was located in a nucleolus organizer region (NOR) in the male and female metaphases of L. elongatus. This report also discusses the role of repetitive DNA associated with NORs in the diversification of Anostomidae species karyotypes.
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Affiliation(s)
- E L da Silva
- Laboratório de Citogenética, Departamento de Biologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista Julio de Mesquita Filho, Rio Claro, Brasil
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30
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de Bello Cioffi M, Kejnovský E, Marquioni V, Poltronieri J, Molina WF, Diniz D, Bertollo LAC. The key role of repeated DNAs in sex chromosome evolution in two fish species with ZW sex chromosome system. Mol Cytogenet 2012; 5:28. [PMID: 22658074 PMCID: PMC3462698 DOI: 10.1186/1755-8166-5-28] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 05/03/2012] [Indexed: 11/10/2022] Open
Abstract
Despite substantial progress, there are still several gaps in our knowledge about the process of sex chromosome differentiation. The degeneration of sex-specific chromosome in some species is well documented, but it is not clear if all species follow the same evolutionary pathway. The accumulation of repetitive DNA sequences, however, is a common feature. To better understand this involvement, fish species emerge as excellent models because they exhibit a wide variety of sex chromosome and sex determining systems. Besides, they have much younger sex chromosomes compared to higher vertebrates, making it possible to follow early steps of differentiation. Here, we analyzed the arrangement of 9 repetitive DNA sequences in the W chromosomes of 2 fish species, namely Leporinus reinhardti and Triportheus auritus, which present well-differentiated ZZ/ZW sex system, but differ in respect to the size of the sex-specific chromosome. Both W chromosomes are almost fully heterochromatic, with accumulation of repeated DNAs in their heterochromatic regions. We found that microsatellites have strongly accumulated on the large W chromosome of L. reinhardti but not on the reduced-size W chromosome of T. auritus and are therefore important players of the W chromosome expansion. The present data highlight that the evolution of the sex chromosomes can diverge even in the same type of sex system, with and without the degeneration of the specific-sex chromosome, being more dynamic than traditionally appreciated.
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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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31
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Cioffi MB, Moreira-Filho O, Almeida-Toledo LF, Bertollo LAC. The contrasting role of heterochromatin in the differentiation of sex chromosomes: an overview from Neotropical fishes. JOURNAL OF FISH BIOLOGY 2012; 80:2125-2139. [PMID: 22551173 DOI: 10.1111/j.1095-8649.2012.03272.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
During the evolutionary process of the sex chromosomes, a general principle that arises is that cessation or a partial restriction of recombination between the sex chromosome pair is necessary. Data from phylogenetically distinct organisms reveal that this phenomenon is frequently associated with the accumulation of heterochromatin in the sex chromosomes. Fish species emerge as excellent models to study this phenomenon because they have much younger sex chromosomes compared to higher vertebrates and many other organisms making it possible to follow their steps of differentiation. In several Neotropical fish species, the heterochromatinization, accompanied by amplification of tandem repeats, represents an important step in the morphological differentiation of simple sex chromosome systems, especially in the ZZ/ZW sex systems. In contrast, multiple sex chromosome systems have no additional increase of heterochromatin in the chromosomes. Thus, the initial stage of differentiation of the multiple sex chromosome systems seems to be associated with proper chromosomal rearrangements, whereas the simple sex chromosome systems have an accumulation of heterochromatin. In this review, attention has been drawn to this contrasting role of heterochromatin in the differentiation of simple and multiple sex chromosomes of Neotropical fishes, highlighting their surprising evolutionary dynamism.
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Affiliation(s)
- M B Cioffi
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil.
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32
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Schemberger MO, Bellafronte E, Nogaroto V, Almeida MC, Schühli GS, Artoni RF, Moreira-Filho O, Vicari MR. Differentiation of repetitive DNA sites and sex chromosome systems reveal closely related group in Parodontidae (Actinopterygii: Characiformes). Genetica 2012; 139:1499-508. [DOI: 10.1007/s10709-012-9649-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 04/09/2012] [Indexed: 11/24/2022]
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33
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Marreta ME, Faldoni FLC, Parise-Maltempi PP. Cytogenetic mapping of the W chromosome in the genus Leporinus (Teleostei, Anostomidae) using a highly repetitive DNA sequence. JOURNAL OF FISH BIOLOGY 2012; 80:630-637. [PMID: 22380557 DOI: 10.1111/j.1095-8649.2011.03199.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The distribution of the Leporinus elongatus LeSpeI repetitive sequence in other Leporinus species was studied in an attempt to elucidate the evolutionary history of sex chromosomes in this genus using chromosome fluorescence in situ hybridization. The presence of fluorescent signals only in species that have differentiated sex chromosomes suggests that this sequence is related to the differentiation of sex chromosomes in this genus. Thus, these data will contribute to a better understanding of chromosome evolution, especially for sex chromosomes, in the Leporinus genus.
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Affiliation(s)
- M E Marreta
- Universidade Estadual Paulista Júlio de Mesquita Filho, Instituto de Biociências, Departamento de Biologia, Avenue 24A, 1515, 13506-900 Rio Claro, SP, Brazil
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Cioffi MB, Martins C, Bertollo LAC. Chromosome spreading of associated transposable elements and ribosomal DNA in the fish Erythrinus erythrinus. Implications for genome change and karyoevolution in fish. BMC Evol Biol 2010; 10:271. [PMID: 20815941 PMCID: PMC2944182 DOI: 10.1186/1471-2148-10-271] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 09/06/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fish, Erythrinus erythrinus, shows an interpopulation diversity, with four karyomorphs differing by chromosomal number, chromosomal morphology and heteromorphic sex chromosomes. Karyomorph A has a diploid number of 2n = 54 and does not have differentiated sex chromosomes. Karyomorph D has 2n = 52 chromosomes in females and 2n = 51 in males, and it is most likely derived from karyomorph A by the differentiation of a multiple X1X2Y sex chromosome system. In this study, we analyzed karyomorphs A and D by means of cytogenetic approaches to evaluate their evolutionary relationship. RESULTS Conspicuous differences in the distribution of the 5S rDNA and Rex3 non-LTR retrotransposon were found between the two karyomorphs, while no changes in the heterochromatin and 18S rDNA patterns were found between them. Rex3 was interstitially dispersed in most chromosomes. It had a compartmentalized distribution in the centromeric regions of only two acrocentric chromosomes in karyomorph A. In comparison, in karyomorph D, Rex3 was found in 22 acrocentric chromosomes in females and 21 in males. All 5S rDNA sites co-localized with Rex3, suggesting that these are associated in the genome. In addition, the origin of the large metacentric Y chromosome in karyomorph D by centric fusion was highlighted by the presence of internal telomeric sites and 5S rDNA/Rex3 sites on this chromosome. CONCLUSION We demonstrated that some repetitive DNAs (5S rDNA, Rex3 retroelement and (TTAGGG)n telomeric repeats) were crucial for the evolutionary divergence inside E. erythrinus. These elements were strongly associated with the karyomorphic evolution of this species. Our results indicate that chromosomal rearrangements and genomic modifications were significant events during the course of evolution of this fish. We detected centric fusions that were associated with the differentiation of the multiple sex chromosomes in karyomorph D, as well as a surprising increase of associated 5S rDNA/Rex3 loci, in contrast to karyomorph A. In this sense, E. erythrinus emerges as an excellent model system for better understanding the evolutionary mechanisms underlying the huge genome diversity in fish. This organism can also contribute to understanding vertebrate genome evolution as a whole.
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Affiliation(s)
- Marcelo B Cioffi
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil.
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35
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Charlesworth D, Mank JE. The birds and the bees and the flowers and the trees: lessons from genetic mapping of sex determination in plants and animals. Genetics 2010; 186:9-31. [PMID: 20855574 PMCID: PMC2940314 DOI: 10.1534/genetics.110.117697] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The ability to identify genetic markers in nonmodel systems has allowed geneticists to construct linkage maps for a diversity of species, and the sex-determining locus is often among the first to be mapped. Sex determination is an important area of study in developmental and evolutionary biology, as well as ecology. Its importance for organisms might suggest that sex determination is highly conserved. However, genetic studies have shown that sex determination mechanisms, and the genes involved, are surprisingly labile. We review studies using genetic mapping and phylogenetic inferences, which can help reveal evolutionary pattern within this lability and potentially identify the changes that have occurred among different sex determination systems. We define some of the terminology, particularly where confusion arises in writing about such a diverse range of organisms, and highlight some major differences between plants and animals, and some important similarities. We stress the importance of studying taxa suitable for testing hypotheses, and the need for phylogenetic studies directed to taxa where the patterns of changes can be most reliably inferred, if the ultimate goal of testing hypotheses regarding the selective forces that have led to changes in such an essential trait is to become feasible.
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Affiliation(s)
- Deborah Charlesworth
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford OX1 3PS, United Kingdom.
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36
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Andreata AA, Ferreira DC, Foresti F, Oliveira C. Molecular cytogenetic study of heterochromatin in Hisonotus leucofrenatus (Teleostei, Loricariidae, Hypoptopomatinae). Hereditas 2010; 147:10-7. [PMID: 20416012 DOI: 10.1111/j.1601-5223.2009.2149.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The fish species Hisonotus leucofrenatus exhibits a large amount of C-band positive segments with different responses after application of the C-banding technique. Type I class named herein appeared to be heavily stained after C-banding in the terminal position of five chromosome pairs and type II class, weakly stained after C-banding in the interstitial or pericentromeric position in nine chromosome pairs and in the supernumerary chromosomes. No variation was observed in type II C-band positive segments, however, type I segments displayed conspicuous polymorphisms, and six cytotypes were detected among the fish analyzed. Chromosomes were also analyzed by CMA(3) and DAPI staining, which showed that type I C-band positive segments comprised both AT-rich and GC-rich DNA, while type II segments were mainly composed of GC-rich sequences. HindIII-digested genomic DNA exhibits fragments of the ladder-like pattern, characteristic of tandemly arrayed repetitive sequences. Two of those fragments corresponding to monomeric and dimeric units of a 78 bp repetitive DNA sequence were cloned and sequenced. The cloned repetitive DNA was used as probe in fluorescent in situ hybridization experiments. The results revealed that these sequences were located in the same position as the type I C-band positive segments. This satellite DNA did not hybridize with DNA from other species of Hisonotus or from other fish of the family Loricariidae, suggesting that this sequence is specific to H. leucofrenatus. The role of these repetitive sequences in the karyotypic evolution of this species is discussed.
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37
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Cioffi MB, Bertollo LAC. Initial steps in XY chromosome differentiation in Hoplias malabaricus and the origin of an X1X2Y sex chromosome system in this fish group. Heredity (Edinb) 2010; 105:554-61. [DOI: 10.1038/hdy.2010.18] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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38
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Hashimoto DT, Laudicina A, Bortolozzi J, Foresti F, Porto-Foresti F. Chromosomal features of nucleolar dominance in hybrids between the Neotropical fish Leporinus macrocephalus and Leporinus elongatus (Characiformes, Anostomidae). Genetica 2009; 137:135-40. [PMID: 19430915 DOI: 10.1007/s10709-009-9366-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Accepted: 04/24/2009] [Indexed: 11/28/2022]
Abstract
In the present study, the chromosomal mechanisms of nucleolar dominance were analyzed in the hybrid lineage "Piaupara," which resulted from crossing the Leporinus macrocephalus female (Piauçu) and L. elongatus male (Piapara) fish. The analyses demonstrated that, in the hybrid, the nucleolar region inherited from L. elongatus presented higher activity, with expression in 100% of the cells, whereas the nucleolar region from L. macrocephalus appeared active at a frequency of 11.6%. The FISH technique with an 18S probe showed that the ribosomal DNA of the nucleolar region was not lost in the hybrid, and the results therefore demonstrated invariable marks in two chromosomes, each originating from one parent. An interesting difference between the nucleolar regions of the parental species was the association of the NOR with heterochromatic blocks (repetitive DNA) in L. elongatus, which could act as a determinative element in the establishment of this process.
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Affiliation(s)
- Diogo Teruo Hashimoto
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista (UNESP), Campus de Bauru, Bauru, SP 17033-360, Brazil
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Oliveira C, Foresti F, Hilsdorf AWS. Genetics of neotropical fish: from chromosomes to populations. FISH PHYSIOLOGY AND BIOCHEMISTRY 2009; 35:81-100. [PMID: 18683061 DOI: 10.1007/s10695-008-9250-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 07/09/2008] [Indexed: 05/26/2023]
Abstract
The Neotropical freshwater fish fauna is very rich--according to the most recent catalogue 71 families and 4,475 species have been described. However, only a small amount of general information is available on the composition of Neotropical marine fishes. In Brazil, 1,298 marine species have been recorded. General analysis of available cytogenetic and population genetic data clearly indicates research has been mainly concentrated on freshwater fishes. Thus, today, cytogenetic information is available for 475 species of Characiformes, 318 species of Siluriformes, 48 species of Gymnotiformes, 199 freshwater species that do not belong to the superorder Ostariophysi, and only 109 species of marine fishes. For the species studied, only about 6% have sex chromosomes and about 5% have supernumerary or B chromosomes. A review of the cytogenetic studies shows that these data have provided valuable information about the relationships between fish groups, the occurrence of cryptic species and species complexes, the mechanism of sex determination and sex chromosome evolution, the distribution of nucleolus organizer regions, the existence supernumerary chromosomes, and the relationship between polyploidy and evolution. In relation to populations in Neotropical marine waters, the studies have shown the presence of cryptic species, which has important implications for fishery management. Different levels of genetic structuring can be found among Neotropical freshwater migratory fish species. This raises important implications for fish population genetic diversity and consequently its sustainable utilization in inland fisheries and aquaculture, specifically for conservation of ichthyo-diversity and survival.
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Affiliation(s)
- C Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil.
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