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Lisachov A, Panthum T, Dedukh D, Singchat W, Ahmad SF, Wattanadilokcahtkun P, Thong T, Srikampa P, Noito K, Rasoarahona R, Kraichak E, Muangmai N, Chatchaiphan S, Sriphairoj K, Hatachote S, Chaiyes A, Jantasuriyarat C, Dokkaew S, Chailertlit V, Suksavate W, Sonongbua J, Prasanpan J, Payungporn S, Han K, Antunes A, Srisapoome P, Koga A, Duengkae P, Na-Nakorn U, Matsuda Y, Srikulnath K. Genome-wide sequence divergence of satellite DNA could underlie meiotic failure in male hybrids of bighead catfish and North African catfish (Clarias, Clariidae). Genomics 2024; 116:110868. [PMID: 38795738 DOI: 10.1016/j.ygeno.2024.110868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/19/2024] [Accepted: 05/23/2024] [Indexed: 05/28/2024]
Abstract
Hybrid sterility, a hallmark of postzygotic isolation, arises from parental genome divergence disrupting meiosis. While chromosomal incompatibility is often implicated, the underlying mechanisms remain unclear. This study investigated meiotic behavior and genome-wide divergence in bighead catfish (C. macrocephalus), North African catfish (C. gariepinus), and their sterile male hybrids (important in aquaculture). Repetitive DNA analysis using bioinformatics and cytogenetics revealed significant divergence in satellite DNA (satDNA) families between parental species. Notably, one hybrid exhibited successful meiosis and spermatozoa production, suggesting potential variation in sterility expression. Our findings suggest that genome-wide satDNA divergence, rather than chromosome number differences, likely contributes to meiotic failure and male sterility in these catfish hybrids.
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Affiliation(s)
- Artem Lisachov
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Dmitrij Dedukh
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov 27721, Czech Republic
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Pish Wattanadilokcahtkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Phanitada Srikampa
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kantika Noito
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Ryan Rasoarahona
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Department of Botany, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Satid Chatchaiphan
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Kednapat Sriphairoj
- Faculty of Natural Resources and Agro-Industry, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand
| | - Sittichai Hatachote
- Faculty of Natural Resources and Agro-Industry, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand
| | - Aingorn Chaiyes
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; School of Agriculture and Cooperatives, Sukhothai Thammathirat Open University, Nonthaburi 11120, Thailand
| | - Chatchawan Jantasuriyarat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Sahabhop Dokkaew
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Visarut Chailertlit
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Pathum Thani Aquatic Animal Genetics Research and Development Center, Aquatic Animal Genetics Research and Development Division, Department of Fisheries, Pathum Thani 12120, Thailand
| | - Warong Suksavate
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Jumaporn Sonongbua
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Faculty of Interdisciplinary Studies, Khon Kaen University, Nong Kom Ko, Mueang Nong Khai District, Nong Khai 43000, Thailand
| | - Jiraboon Prasanpan
- Kalasin Fish Hatchery Farm (Betagro), Buaban, Yangtalad District, Kalasin 46120, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Department of Microbiology, Dankook University, Cheonan 31116, Republic of Korea; Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan 31116, Republic of Korea
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Prapansak Srisapoome
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Uthairat Na-Nakorn
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Yoichi Matsuda
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.
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Dos Santos GE, Crepaldi C, da Silva MJ, Parise-Maltempi PP. Revealing the Satellite DNA Content in Ancistrus sp. (Siluriformes: Loricariidae) by Genomic and Bioinformatic Analysis. Cytogenet Genome Res 2024:1-8. [PMID: 38631304 DOI: 10.1159/000538926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/12/2024] [Indexed: 04/19/2024] Open
Abstract
INTRODUCTION Eukaryotic genomes are composed of simple, repetitive sequences, including satellite DNAs (satDNA), which are noncoding sequences arranged in tandem arrays. These sequences play a crucial role in genomic functions and innovations, influencing processes such as the maintenance of nuclear material, the formation of heterochromatin and the differentiation of sex chromosomes. In this genomic era, advances in next-generation sequencing and bioinformatics tools have facilitated the exhaustive cataloging of repetitive elements in genomes, particularly in non-model species. This study focuses on the satDNA content of Ancistrus sp., a diverse species of fish from the Loricariidae family. The genus Ancistrus shows significant karyotypic evolution, with extensive variability from the ancestral diploid number. METHODS By means of bioinformatic approaches, 40 satDNA families in Ancistrus sp., constituting 5.19% of the genome were identified. Analysis of the abundance and divergence landscape revealed diverse profiles, indicating recent amplification and homogenization of these satDNA sequences. RESULTS The most abundant satellite, AnSat1-142, constitutes 2.1% of the genome, while the least abundant, AnSat40-52, represents 0.0034%. The length of the monomer repeat varies from 16 to 142 base pairs, with an average length of 61 bp. These results contribute to understanding the genomic dynamics and evolution of satDNAs in Ancistrus sp. CONCLUSION The study underscores the variability of satDNAs between fish species and provides valuable information on chromosome organization and the evolution of repetitive elements in non-model organisms.
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Affiliation(s)
- Gabriel Esbrisse Dos Santos
- General and Applied Biology Department, Bioscience Institute/São Paulo State University (UNESP), Rio Claro, Brazil
| | - Carolina Crepaldi
- General and Applied Biology Department, Bioscience Institute/São Paulo State University (UNESP), Rio Claro, Brazil
| | - Marcelo João da Silva
- General and Applied Biology Department, Bioscience Institute/São Paulo State University (UNESP), Rio Claro, Brazil
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Šatović-Vukšić E, Plohl M. Satellite DNAs-From Localized to Highly Dispersed Genome Components. Genes (Basel) 2023; 14:genes14030742. [PMID: 36981013 PMCID: PMC10048060 DOI: 10.3390/genes14030742] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
According to the established classical view, satellite DNAs are defined as abundant non-coding DNA sequences repeated in tandem that build long arrays located in heterochromatin. Advances in sequencing methodologies and development of specialized bioinformatics tools enabled defining a collection of all repetitive DNAs and satellite DNAs in a genome, the repeatome and the satellitome, respectively, as well as their reliable annotation on sequenced genomes. Supported by various non-model species included in recent studies, the patterns of satellite DNAs and satellitomes as a whole showed much more diversity and complexity than initially thought. Differences are not only in number and abundance of satellite DNAs but also in their distribution across the genome, array length, interspersion patterns, association with transposable elements, localization in heterochromatin and/or in euchromatin. In this review, we compare characteristic organizational features of satellite DNAs and satellitomes across different animal and plant species in order to summarize organizational forms and evolutionary processes that may lead to satellitomes' diversity and revisit some basic notions regarding repetitive DNA landscapes in genomes.
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Affiliation(s)
- Eva Šatović-Vukšić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Miroslav Plohl
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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Goes CAG, dos Santos RZ, Aguiar WRC, Alves DCV, Silva DMZDA, Foresti F, Oliveira C, Utsunomia R, Porto-Foresti F. Revealing the Satellite DNA History in Psalidodon and Astyanax Characid Fish by Comparative Satellitomics. Front Genet 2022; 13:884072. [PMID: 35801083 PMCID: PMC9253505 DOI: 10.3389/fgene.2022.884072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/31/2022] [Indexed: 12/02/2022] Open
Abstract
Eukaryotic genomes are usually enriched in repetitive DNA sequences, which can be classified as dispersed or tandemly repeated elements. Satellite DNAs are noncoding monomeric sequences organized in a head-to-tail fashion that are generally located on the subtelomeric and/or pericentromeric heterochromatin. In general, a single species incorporates a diverse group of satellite DNA families, which collection is called satellitome. Here, we characterized three new satellitomes from distinct characid fish (Psalidodon fasciatus, P. bockmanni, and Astyanax lacustris) using a combination of genomic, cytogenetic, and bioinformatic protocols. We also compared our data with the available satellitome of P. paranae. We described 57 satellite DNA (satDNA) families of P. fasciatus (80 variants), 50 of P. bockmanni (77 variants), and 33 of A. lacustris (54 variants). Our analyses demonstrated that several sequences were shared among the analyzed species, while some were restricted to two or three species. In total, we isolated 104 distinctive satDNA families present in the four species, of which 10 were shared among all four. Chromosome mapping revealed that the clustered satDNA was mainly located in the subtelomeric and pericentromeric areas. Although all Psalidodon species demonstrated the same pattern of clusterization of satDNA, the number of clusters per genome was variable, indicating a high dynamism of these sequences. In addition, our results expand the knowledge of the As51 satellite DNA family, revealing that P. bockmanni and P. paranae exhibited an abundant variant of 39 bp, while P. fasciatus showed a variant of 43 bp. The majority of satDNAs in the satellitomes analyzed here presented a common library repetitive sequence in Psalidodon and Astyanax, with abundance variations in each species, as expected for closely related groups. In addition, we concluded that the most abundant satDNA in Psalidodon (As51) passed through a diversification process in this group, resulting in new variants exclusive of Psalidodon.
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Affiliation(s)
- Caio Augusto Gomes Goes
- Laboratório de Genética de Peixes, Faculdade Estadual Paulista “Júlio de Mesquita Filho”, Departamento de Ciências Biológicas, Faculdade de Ciências, Bauru, Brazil
| | - Rodrigo Zeni dos Santos
- Laboratório de Genética de Peixes, Faculdade Estadual Paulista “Júlio de Mesquita Filho”, Departamento de Ciências Biológicas, Faculdade de Ciências, Bauru, Brazil
| | - Weidy Rozendo Clemente Aguiar
- Laboratório de Genética de Peixes, Faculdade Estadual Paulista “Júlio de Mesquita Filho”, Departamento de Ciências Biológicas, Faculdade de Ciências, Bauru, Brazil
| | - Dálete Cássia Vieira Alves
- Instituto de Ciências Biológicas e da Saude, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
| | | | - Fausto Foresti
- Laboratório de Biologia e Genética de Peixes, Faculdade Estadual Paulista “Júlio de Mesquita Filho”, Instituto de Biociências, Botucatu, Brazil
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Faculdade Estadual Paulista “Júlio de Mesquita Filho”, Instituto de Biociências, Botucatu, Brazil
| | - Ricardo Utsunomia
- Instituto de Ciências Biológicas e da Saude, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
| | - Fabio Porto-Foresti
- Laboratório de Genética de Peixes, Faculdade Estadual Paulista “Júlio de Mesquita Filho”, Departamento de Ciências Biológicas, Faculdade de Ciências, Bauru, Brazil
- *Correspondence: Fabio Porto-Foresti,
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Camacho JPM, Cabrero J, López-León MD, Martín-Peciña M, Perfectti F, Garrido-Ramos MA, Ruiz-Ruano FJ. Satellitome comparison of two oedipodine grasshoppers highlights the contingent nature of satellite DNA evolution. BMC Biol 2022; 20:36. [PMID: 35130900 PMCID: PMC8822648 DOI: 10.1186/s12915-021-01216-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The full catalog of satellite DNA (satDNA) within a same genome constitutes the satellitome. The Library Hypothesis predicts that satDNA in relative species reflects that in their common ancestor, but the evolutionary mechanisms and pathways of satDNA evolution have never been analyzed for full satellitomes. We compare here the satellitomes of two Oedipodine grasshoppers (Locusta migratoria and Oedaleus decorus) which shared their most recent common ancestor about 22.8 Ma ago. RESULTS We found that about one third of their satDNA families (near 60 in every species) showed sequence homology and were grouped into 12 orthologous superfamilies. The turnover rate of consensus sequences was extremely variable among the 20 orthologous family pairs analyzed in both species. The satDNAs shared by both species showed poor association with sequence signatures and motives frequently argued as functional, except for short inverted repeats allowing short dyad symmetries and non-B DNA conformations. Orthologous satDNAs frequently showed different FISH patterns at both intra- and interspecific levels. We defined indices of homogenization and degeneration and quantified the level of incomplete library sorting between species. CONCLUSIONS Our analyses revealed that satDNA degenerates through point mutation and homogenizes through partial turnovers caused by massive tandem duplications (the so-called satDNA amplification). Remarkably, satDNA amplification increases homogenization, at intragenomic level, and diversification between species, thus constituting the basis for concerted evolution. We suggest a model of satDNA evolution by means of recursive cycles of amplification and degeneration, leading to mostly contingent evolutionary pathways where concerted evolution emerges promptly after lineages split.
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Affiliation(s)
| | - Josefa Cabrero
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain
| | | | | | - Francisco Perfectti
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.,Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
| | | | - Francisco J Ruiz-Ruano
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden. .,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK.
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Kretschmer R, Goes CAG, Bertollo LAC, Ezaz T, Porto-Foresti F, Toma GA, Utsunomia R, de Bello Cioffi M. Satellitome analysis illuminates the evolution of ZW sex chromosomes of Triportheidae fishes (Teleostei: Characiformes). Chromosoma 2022; 131:29-45. [PMID: 35099570 DOI: 10.1007/s00412-022-00768-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 12/14/2022]
Abstract
Satellites are an abundant source of repetitive DNAs that play an essential role in the chromosomal organization and are tightly linked with the evolution of sex chromosomes. Among fishes, Triportheidae stands out as the only family where almost all species have a homeologous ZZ/ZW sex chromosomes system. While the Z chromosome is typically conserved, the W is always smaller, with variations in size and morphology between species. Here, we report an analysis of the satellitome of Triportheus auritus (TauSat) by integrating genomic and chromosomal data, with a special focus on the highly abundant and female-biased satDNAs. In addition, we investigated the evolutionary trajectories of the ZW sex chromosomes in the Triportheidae family by mapping satDNAs in selected representative species of this family. The satellitome of T. auritus comprised 53 satDNA families of which 24 were also hybridized by FISH. Most satDNAs differed significantly between sexes, with 19 out of 24 being enriched on the W chromosome of T. auritus. The number of satDNAs hybridized into the W chromosomes of T. signatus and T. albus decreased to six and four, respectively, in accordance with the size of their W chromosomes. No TauSat probes produced FISH signals on the chromosomes of Agoniates halecinus. Despite its apparent conservation, our results indicate that each species differs in the satDNA accumulation on the Z chromosome. Minimum spanning trees (MSTs), generated for three satDNA families with different patterns of FISH mapping data, revealed different homogenization rates between the Z and W chromosomes. These results were linked to different levels of recombination between them. The most abundant satDNA family (TauSat01) was exclusively hybridized in the centromeres of all 52 chromosomes of T. auritus, and its putative role in the centromere evolution was also highlighted. Our results identified a high differentiation of both ZW chromosomes regarding satellites composition, highlighting their dynamic role in the sex chromosomes evolution.
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Affiliation(s)
- Rafael Kretschmer
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | | | - Gustavo Akira Toma
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Ricardo Utsunomia
- Instituto de Ciências Biológicas e da Saúde, ICBS, Universidade Federal Rural do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil.
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7
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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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Heitkam T, Schulte L, Weber B, Liedtke S, Breitenbach S, Kögler A, Morgenstern K, Brückner M, Tröber U, Wolf H, Krabel D, Schmidt T. Comparative Repeat Profiling of Two Closely Related Conifers ( Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs. Front Genet 2021; 12:683668. [PMID: 34322154 PMCID: PMC8312256 DOI: 10.3389/fgene.2021.683668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/25/2021] [Indexed: 12/26/2022] Open
Abstract
In eukaryotic genomes, cycles of repeat expansion and removal lead to large-scale genomic changes and propel organisms forward in evolution. However, in conifers, active repeat removal is thought to be limited, leading to expansions of their genomes, mostly exceeding 10 giga base pairs. As a result, conifer genomes are largely littered with fragmented and decayed repeats. Here, we aim to investigate how the repeat landscapes of two related conifers have diverged, given the conifers' accumulative genome evolution mode. For this, we applied low-coverage sequencing and read clustering to the genomes of European and Japanese larch, Larix decidua (Lamb.) Carrière and Larix kaempferi (Mill.), that arose from a common ancestor, but are now geographically isolated. We found that both Larix species harbored largely similar repeat landscapes, especially regarding the transposable element content. To pin down possible genomic changes, we focused on the repeat class with the fastest sequence turnover: satellite DNAs (satDNAs). Using comparative bioinformatics, Southern, and fluorescent in situ hybridization, we reveal the satDNAs' organizational patterns, their abundances, and chromosomal locations. Four out of the five identified satDNAs are widespread in the Larix genus, with two even present in the more distantly related Pseudotsuga and Abies genera. Unexpectedly, the EulaSat3 family was restricted to L. decidua and absent from L. kaempferi, indicating its evolutionarily young age. Taken together, our results exemplify how the accumulative genome evolution of conifers may limit the overall divergence of repeats after speciation, producing only few repeat-induced genomic novelties.
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Affiliation(s)
- Tony Heitkam
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Luise Schulte
- Institute of Botany, Technische Universität Dresden, Dresden, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Beatrice Weber
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Susan Liedtke
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Sarah Breitenbach
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Anja Kögler
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Kristin Morgenstern
- Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, Tharandt, Germany
| | | | - Ute Tröber
- Staatsbetrieb Sachsenforst, Pirna, Germany
| | - Heino Wolf
- Staatsbetrieb Sachsenforst, Pirna, Germany
| | - Doris Krabel
- Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, Tharandt, Germany
| | - Thomas Schmidt
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
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9
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The B Chromosomes of Prochilodus lineatus (Teleostei, Characiformes) Are Highly Enriched in Satellite DNAs. Cells 2021; 10:cells10061527. [PMID: 34204462 PMCID: PMC8235050 DOI: 10.3390/cells10061527] [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: 05/17/2021] [Revised: 06/07/2021] [Accepted: 06/11/2021] [Indexed: 12/18/2022] Open
Abstract
B or supernumerary chromosomes are dispensable elements that are widely present in numerous eukaryotes. Due to their non-recombining nature, there is an evident tendency for repetitive DNA accumulation in these elements. Thus, satellite DNA plays an important role in the evolution and diversification of B chromosomes and can provide clues regarding their origin. The characiform Prochilodus lineatus was one of the first discovered fish species bearing B chromosomes, with all populations analyzed so far showing one to nine micro-B chromosomes and exhibiting at least three morphological variants (Ba, Bsm, and Bm). To date, a single satellite DNA is known to be located on the B chromosomes of this species, but no information regarding the differentiation of the proposed B-types is available. Here, we characterized the satellitome of P. lineatus and mapped 35 satellite DNAs against the chromosomes of P. lineatus, of which six were equally located on all B-types and this indicates a similar genomic content. In addition, we describe, for the first time, an entire population without B chromosomes.
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10
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Montiel EE, Panzera F, Palomeque T, Lorite P, Pita S. Satellitome Analysis of Rhodnius prolixus, One of the Main Chagas Disease Vector Species. Int J Mol Sci 2021; 22:6052. [PMID: 34205189 PMCID: PMC8199985 DOI: 10.3390/ijms22116052] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022] Open
Abstract
The triatomine Rhodnius prolixus is the main vector of Chagas disease in countries such as Colombia and Venezuela, and the first kissing bug whose genome has been sequenced and assembled. In the repetitive genome fraction (repeatome) of this species, the transposable elements represented 19% of R. prolixus genome, being mostly DNA transposon (Class II elements). However, scarce information has been published regarding another important repeated DNA fraction, the satellite DNA (satDNA), or satellitome. Here, we offer, for the first time, extended data about satellite DNA families in the R. prolixus genome using bioinformatics pipeline based on low-coverage sequencing data. The satellitome of R. prolixus represents 8% of the total genome and it is composed by 39 satDNA families, including four satDNA families that are shared with Triatoma infestans, as well as telomeric (TTAGG)n and (GATA)n repeats, also present in the T. infestans genome. Only three of them exceed 1% of the genome. Chromosomal hybridization with these satDNA probes showed dispersed signals over the euchromatin of all chromosomes, both in autosomes and sex chromosomes. Moreover, clustering analysis revealed that most abundant satDNA families configured several superclusters, indicating that R. prolixus satellitome is complex and that the four most abundant satDNA families are composed by different subfamilies. Additionally, transcription of satDNA families was analyzed in different tissues, showing that 33 out of 39 satDNA families are transcribed in four different patterns of expression across samples.
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Affiliation(s)
- Eugenia E. Montiel
- Department of Experimental Biology, Genetics, University of Jaén. Paraje las Lagunillas sn., 23071 Jaén, Spain; (E.E.M.); (T.P.)
| | - Francisco Panzera
- Evolutionary Genetic Section, Faculty of Science, University of the Republic, Iguá 4225, Montevideo 11400, Uruguay;
| | - Teresa Palomeque
- Department of Experimental Biology, Genetics, University of Jaén. Paraje las Lagunillas sn., 23071 Jaén, Spain; (E.E.M.); (T.P.)
| | - Pedro Lorite
- Department of Experimental Biology, Genetics, University of Jaén. Paraje las Lagunillas sn., 23071 Jaén, Spain; (E.E.M.); (T.P.)
| | - Sebastián Pita
- Evolutionary Genetic Section, Faculty of Science, University of the Republic, Iguá 4225, Montevideo 11400, Uruguay;
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11
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Goes CAG, Silva DMZDA, Utsunomia R, Yasui GS, Artoni RF, Foresti F, Porto-Foresti F. Establishment of rapid and non-invasive protocols to identify B-carrying individuals of Psalidodon paranae. Genet Mol Biol 2021; 44:e20200003. [PMID: 33769429 PMCID: PMC7995683 DOI: 10.1590/1678-4685-gmb-2020-0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 02/12/2021] [Indexed: 11/23/2022] Open
Abstract
Supernumerary, or B, chromosomes are present in several eukaryotes, including characid fish of the genus Psalidodon. Notably, Psalidodon paranae carries the most studied B chromosome variant, a macro-B chromosome. The origin of this element was determined to be an isochromosome; however, data regarding its inheritance remain unavailable due to methodological barriers such as the lack of an efficient, non-invasive, and rapid protocol for identifying B-carrying individuals that would enable the design of efficient crossing experiments. Thus, in this study, we primarily aimed was to develop two non-invasive and fast (approximately 2 h) methods to identify the presence of B chromosomes in live specimens of P. paranae based on satellite DNA (satDNA) sequences known to be present in this element. The methods include fluorescence in situ hybridization in interphase nuclei and relative gene quantification of satDNAs using quantitative polymerase chain reaction. Our results reveal the efficiency of quick-fluorescence in situ hybridization and quantitative polymerase chain reaction for identifying B-carrying individuals using the proposed satDNA sequences and open up new possibilities to study B chromosomes.
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Affiliation(s)
- Caio Augusto Gomes Goes
- Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Faculdade de Ciências, Bauru, SP, Brazil
| | | | - Ricardo Utsunomia
- Universidade Federal Rural do Rio de Janeiro, Instituto de Ciências Biológicas e da Saúde, ICBS, Seropédica, RJ, Brazil
| | - George Shigueki Yasui
- Centro nacional de Pesquisa e Conservação da Biota Aquática Continental (CEPTA-ICMBIO), Pirassununga, SP, Brazil
| | - Roberto Ferreira Artoni
- Universidade Estadual de Ponta Grossa, Setor de Ciências Biológicas e da Saúde, Ponta Grossa, PR, Brazil
| | - Fausto Foresti
- Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Instituto de Biociências, Botucatu, SP, Brazil
| | - Fábio Porto-Foresti
- Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Faculdade de Ciências, Bauru, SP, Brazil
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12
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dos Santos RZ, Calegari RM, Silva DMZDA, Ruiz-Ruano FJ, Melo S, Oliveira C, Foresti F, Uliano-Silva M, Porto-Foresti F, Utsunomia R. A Long-Term Conserved Satellite DNA That Remains Unexpanded in Several Genomes of Characiformes Fish Is Actively Transcribed. Genome Biol Evol 2021; 13:evab002. [PMID: 33502491 PMCID: PMC8210747 DOI: 10.1093/gbe/evab002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2021] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic genomes contain large amounts of repetitive DNA sequences, such as tandemly repeated satellite DNAs (satDNAs). These sequences are highly dynamic and tend to be genus- or species-specific due to their particular evolutionary pathways, although there are few unusual cases of conserved satDNAs over long periods of time. Here, we used multiple approaches to reveal that an satDNA named CharSat01-52 originated in the last common ancestor of Characoidei fish, a superfamily within the Characiformes order, ∼140-78 Ma, whereas its nucleotide composition has remained considerably conserved in several taxa. We show that 14 distantly related species within Characoidei share the presence of this satDNA, which is highly amplified and clustered in subtelomeric regions in a single species (Characidium gomesi), while remained organized as small clusters in all the other species. Defying predictions of the molecular drive of satellite evolution, CharSat01-52 shows similar values of intra- and interspecific divergence. Although we did not provide evidence for a specific functional role of CharSat01-52, its transcriptional activity was demonstrated in different species. In addition, we identified short tandem arrays of CharSat01-52 embedded within single-molecule real-time long reads of Astyanax paranae (536 bp-3.1 kb) and A. mexicanus (501 bp-3.9 kb). Such arrays consisted of head-to-tail repeats and could be found interspersed with other sequences, inverted sequences, or neighbored by other satellites. Our results provide a detailed characterization of an old and conserved satDNA, challenging general predictions of satDNA evolution.
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Affiliation(s)
- Rodrigo Zeni dos Santos
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | - Rodrigo Milan Calegari
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | | | - Francisco J Ruiz-Ruano
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology
Centre, Uppsala University, Uppsala, Sweden
| | - Silvana Melo
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | - Fausto Foresti
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | | | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | - Ricardo Utsunomia
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, ICBS,
Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janerio,
Brazil
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13
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Marta A, Dedukh D, Bartoš O, Majtánová Z, Janko K. Cytogenetic Characterization of Seven Novel satDNA Markers in Two Species of Spined Loaches ( Cobitis) and Their Clonal Hybrids. Genes (Basel) 2020; 11:genes11060617. [PMID: 32512717 PMCID: PMC7348982 DOI: 10.3390/genes11060617] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 01/11/2023] Open
Abstract
Interspecific hybridization is a powerful evolutionary force. However, the investigation of hybrids requires the application of methodologies that provide efficient and indubitable identification of both parental subgenomes in hybrid individuals. Repetitive DNA, and especially the satellite DNA sequences (satDNA), can rapidly diverge even between closely related species, hence providing a useful tool for cytogenetic investigations of hybrids. Recent progress in whole-genome sequencing (WGS) offers unprecedented possibilities for the development of new tools for species determination, including identification of species-specific satDNA markers. In this study, we focused on spined loaches (Cobitis, Teleostei), a group of fishes with frequent interspecific hybridization. Using the WGS of one species, C. elongatoides, we identified seven satDNA markers, which were mapped by fluorescence in situ hybridization on mitotic and lampbrush chromosomes of C. elongatoides, C. taenia and their triploid hybrids (C. elongatoides × 2C. taenia). Two of these markers were chromosome-specific in both species, one had centromeric localization in multiple chromosomes and four had variable patterns between tested species. Our study provided a novel set of cytogenetic markers for Cobitis species and demonstrated that NGS-based development of satDNA cytogenetic markers may provide a very efficient and easy tool for the investigation of hybrid genomes, cell ploidy, and karyotype evolution.
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Affiliation(s)
- Anatolie Marta
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
- Department of Zoology, Faculty of Science, Charles University in Prague, 128 00 Prague, Czech Republic
- Institute of Zoology, Academy of Science of Moldova, MD-2028, Academiei 1, 2001 Chisinau, Moldova
- Correspondence:
| | - Dmitry Dedukh
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
| | - Oldřich Bartoš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
- Department of Zoology, Faculty of Science, Charles University in Prague, 128 00 Prague, Czech Republic
| | - Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
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14
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Goes CAG, Daniel SN, Piva LH, Yasui GS, Artoni RF, Hashimoto DT, Foresti F, Porto-Foresti F. Cytogenetic markers as a tool for characterization of hybrids of Astyanax Baird & Girard, 1854 and Hyphessobrycon Eigenmann, 1907. COMPARATIVE CYTOGENETICS 2020; 14:231-242. [PMID: 32537093 PMCID: PMC7270076 DOI: 10.3897/compcytogen.v14i2.49513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
Astyanax Baird et Girard, 1854, is one of the largest genera in the family Characidae and comprises 177 valid species. This genus has been the focus of cytogenetic studies primarily owing to the presence of B chromosomes and high karyotypic diversity among different populations. The intense genetic variability in Astyanax is one of the factors responsible for the occurrence of species complexes, which are groups (1) with certain difficulties in establishing common genetic pools or (2) belonging to different cryptic species. To evaluate cytogenetic marker inheritance and the possibility of the identification of these hybrids, this study aimed to describe cytogenetic hybrids from three strains of species of the genera Astyanax and Hyphessobrycon Eigenmann, 1908. A. lacustris Lütken, 1875, A. schubarti Britski, 1964, A. fasciatus Cuvier, 1819, and H. anisitsi Eigenmann, 1907 were used to generate three hybrid lineages. The diploid number, heterochromatin sites, and ribosomal genes (18S and 5S rDNA) of the parental strains and the hybrids were analyzed. The results indicated that the three hybrid lineages had cytogenetic markers of both parents, presenting Mendelian inheritance. However, differences in distribution of heterochromatic blocks were observed between the hybrids and the parent strains. Our results allowed the identification of the hybrid strains based on the cytogenetic markers applied, reinforcing the efficiency of cytogenetic markers as tools for identification and indicating that such events may increase the karyotypic diversity in the genera Astyanax and Hyphessobrycon.
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Affiliation(s)
- Caio Augusto Gomes Goes
- Universidade Estadual Paulista (UNESP) “Júlio de Mesquita Filho”, Faculdade de Ciências, Edmundo Carrijo Coube Avenue, Bauru, SP, BrazilUniversidade Estadual PaulistaBauruBrazil
| | - Sandro Natal Daniel
- Universidade Estadual Paulista (UNESP) “Júlio de Mesquita Filho”, Faculdade de Ciências, Edmundo Carrijo Coube Avenue, Bauru, SP, BrazilUniversidade Estadual PaulistaBauruBrazil
| | - Lucas Henrique Piva
- Centro nacional de Pesquisa e Conservação da Biota Aquática Continental (CEPTA-ICMBIO), Prefeito Euberto Nemésio Pereira Godói Highway, Pirassununga, SP, BrazilCentro nacional de Pesquisa e Conservação da Biota Aquática ContinentalPirassunungaBrazil
| | - George Shigueki Yasui
- Centro nacional de Pesquisa e Conservação da Biota Aquática Continental (CEPTA-ICMBIO), Prefeito Euberto Nemésio Pereira Godói Highway, Pirassununga, SP, BrazilCentro nacional de Pesquisa e Conservação da Biota Aquática ContinentalPirassunungaBrazil
| | - Roberto Ferreira Artoni
- Universidade Estadual de Ponta Grossa, Setor de Ciências Biológicas e da Saúde, Santos Andrade Square, Ponta Grossa, PR, BrazilUniversidade Estadual de Ponta GrossaPonta GrossaBrazil
| | - Diogo Teruo Hashimoto
- Universidade Estadual Paulista (UNESP) “Júlio de Mesquita Filho”, Centro de Aquicultura da UNESP, Prof. Paulo Donato Castelane Acess way, Jaboticabal, SP, BrazilUniversidade Estadual PaulistaJaboticabalBrazil
| | - Fausto Foresti
- Universidade Estadual Paulista (UNESP) “Júlio de Mesquita Filho”, Instituto de Biociências, Prof. Montenegro Avenue, Botucatu, SP, BrazilUniversidade Estadual PaulistaBotucatuBrazil
| | - Fábio Porto-Foresti
- Universidade Estadual Paulista (UNESP) “Júlio de Mesquita Filho”, Faculdade de Ciências, Edmundo Carrijo Coube Avenue, Bauru, SP, BrazilUniversidade Estadual PaulistaBauruBrazil
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15
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Palacios-Gimenez OM, Milani D, Song H, Marti DA, López-León MD, Ruiz-Ruano FJ, Camacho JPM, Cabral-de-Mello DC. Eight Million Years of Satellite DNA Evolution in Grasshoppers of the Genus Schistocerca Illuminate the Ins and Outs of the Library Hypothesis. Genome Biol Evol 2020; 12:88-102. [PMID: 32211863 PMCID: PMC7093836 DOI: 10.1093/gbe/evaa018] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2020] [Indexed: 12/21/2022] Open
Abstract
Satellite DNA (satDNA) is an abundant class of tandemly repeated noncoding sequences, showing high rate of change in sequence, abundance, and physical location. However, the mechanisms promoting these changes are still controversial. The library model was put forward to explain the conservation of some satDNAs for long periods, predicting that related species share a common collection of satDNAs, which mostly experience quantitative changes. Here, we tested the library model by analyzing three satDNAs in ten species of Schistocerca grasshoppers. This group represents a valuable material because it diversified during the last 7.9 Myr across the American continent from the African desert locust (Schistocerca gregaria), and this thus illuminates the direction of evolutionary changes. By combining bioinformatic and cytogenetic, we tested whether these three satDNA families found in S. gregaria are also present in nine American species, and whether differential gains and/or losses have occurred in the lineages. We found that the three satDNAs are present in all species but display remarkable interspecies differences in their abundance and sequences while being highly consistent with genus phylogeny. The number of chromosomal loci where satDNA is present was also consistent with phylogeny for two satDNA families but not for the other. Our results suggest eminently chance events for satDNA evolution. Several evolutionary trends clearly imply either massive amplifications or contractions, thus closely fitting the library model prediction that changes are mostly quantitative. Finally, we found that satDNA amplifications or contractions may influence the evolution of monomer consensus sequences and by chance playing a major role in driftlike dynamics.
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Affiliation(s)
- Octavio M Palacios-Gimenez
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden
- Department of Organismal Biology, Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Univ Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Hojun Song
- Department of Entomology, Texas A&M University
| | - Dardo A Marti
- Laboratorio de Genética Evolutiva, IBS, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, CONICET, Posadas, Argentina
| | - Maria D López-León
- Departamento de Genética, Facultad de Ciencias, UGR - Univ de Granada, Spain
| | - Francisco J Ruiz-Ruano
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden
- Department of Organismal Biology, Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | | | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Univ Estadual Paulista, Rio Claro, São Paulo, Brazil
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16
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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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17
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Louzada S, Lopes M, Ferreira D, Adega F, Escudeiro A, Gama-Carvalho M, Chaves R. Decoding the Role of Satellite DNA in Genome Architecture and Plasticity-An Evolutionary and Clinical Affair. Genes (Basel) 2020; 11:E72. [PMID: 31936645 PMCID: PMC7017282 DOI: 10.3390/genes11010072] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 12/29/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
Repetitive DNA is a major organizational component of eukaryotic genomes, being intrinsically related with their architecture and evolution. Tandemly repeated satellite DNAs (satDNAs) can be found clustered in specific heterochromatin-rich chromosomal regions, building vital structures like functional centromeres and also dispersed within euchromatin. Interestingly, despite their association to critical chromosomal structures, satDNAs are widely variable among species due to their high turnover rates. This dynamic behavior has been associated with genome plasticity and chromosome rearrangements, leading to the reshaping of genomes. Here we present the current knowledge regarding satDNAs in the light of new genomic technologies, and the challenges in the study of these sequences. Furthermore, we discuss how these sequences, together with other repeats, influence genome architecture, impacting its evolution and association with disease.
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Affiliation(s)
- Sandra Louzada
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Mariana Lopes
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Daniela Ferreira
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Filomena Adega
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Ana Escudeiro
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Margarida Gama-Carvalho
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
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18
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Serrano-Freitas ÉA, Silva DMZA, Ruiz-Ruano FJ, Utsunomia R, Araya-Jaime C, Oliveira C, Camacho JPM, Foresti F. Satellite DNA content of B chromosomes in the characid fish Characidium gomesi supports their origin from sex chromosomes. Mol Genet Genomics 2019; 295:195-207. [PMID: 31624915 DOI: 10.1007/s00438-019-01615-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 10/01/2019] [Indexed: 12/28/2022]
Abstract
The origin of supernumerary (B) chromosomes is clearly conditioned by their ancestry from the standard (A) chromosomes. Sequence similarity between A and B chromosomes is thus crucial to determine B chromosome origin. For this purpose, we compare here the DNA sequences from A and B chromosomes in the characid fish Characidium gomesi using two main approaches. First, we found 59 satellite DNA (satDNA) families constituting the satellitome of this species and performed FISH analysis for 18 of them. This showed the presence of six satDNAs on the B chromosome: one shared with sex chromosomes and autosomes, two shared with sex chromosomes, one shared with autosomes and two being B-specific. This indicated that B chromosomes most likely arose from the sex chromosomes. Our second approach consisted of the analysis of five repetitive DNA families: 18S and 5S ribosomal DNA (rDNA), the H3 histone gene, U2 snDNA and the most abundant satDNA (CgoSat01-184) on DNA obtained from microdissected B chromosomes and from B-lacking genomes. PCR and sequence analysis of these repetitive sequences was successful for three of them (5S rDNA, H3 histone gene and CgoSat01-184), and sequence comparison revealed that DNA sequences obtained from the B chromosomes displayed higher identity with C. gomesi genomic DNA than with those obtained from other Characidium species. Taken together, our results support the intraspecific origin of B chromosomes in C. gomesi and point to sex chromosomes as B chromosome ancestors, which raises interesting prospects for future joint research on the genetic content of sex and B chromosomes in this species.
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Affiliation(s)
- Érica A Serrano-Freitas
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil.,Centro de Ciências Biológicas e da Saúde, Fundação Educacional de Penápolis, Funepe, Penápolis, SP, 16303-180, Brazil
| | - Duílio M Z A Silva
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil.
| | - Francisco J Ruiz-Ruano
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.,Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236, Uppsala, Sweden
| | - Ricardo Utsunomia
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, ICBS, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brazil
| | - Cristian Araya-Jaime
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, 1720256, La Serena, Chile.,Laboratorio de Genética y Citogenética Vegetal, Departamento de Biología, Universidad de La Serena, 1720256, La Serena, Chile
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | | | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
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19
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Rodrigues PHDM, Dos Santos RZ, Silva DMZDA, Goes CAG, Oliveira C, Foresti F, Porto-Foresti F, Utsunomia R. Chromosomal and Genomic Dynamics of Satellite DNAs in Characidae (Characiformes, Teleostei) Species. Zebrafish 2019; 16:408-414. [PMID: 31145041 DOI: 10.1089/zeb.2019.1738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Satellite DNAs (satDNAs) are tandemly repeated DNA sequences with great abundance in eukaryotic genomes. A single species may carry up to hundreds of satDNA families, which is collectively called as "satellitome," each showing its own dynamics and evolution rates. In this context, all live species contain a satDNA library that may be partially or totally shared with other related species/populations. In the late few years, next-generation sequencing (NGS) and novel bioinformatic tools facilitated the massive characterization of these sequences at low costs, and consequently, comparing satDNAs between species. In this study, we characterized two novel satDNAs (MsaSat03-80 and MsaSat04-142) in three characid fish (Astyanax paranae and Astyanax fasciatus and two populations of Moenkhausia sanctaefilomenae) and mapped their chromosomal location to unveil the evolutionary dynamics of satDNA repeats in those species. Our results evidenced that MsaSat03 is present in the genomes of all analyzed species, but is clustered only in the chromosomes of M. sanctaefilomenae, exhibiting a conserved number and location of sites. Conversely, MsaSat04 sequences is restricted to M. sanctaefilomenae and shows a differential distribution between the two analyzed populations. Altogether, our analyses point to a complex history of satDNA families in characid fish and the utility of NGS data for comparative satDNA analysis.
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Affiliation(s)
| | - Rodrigo Zeni Dos Santos
- 1Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista-UNESP, Bauru, Brazil
| | | | - Caio Augusto Gomes Goes
- 1Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista-UNESP, Bauru, Brazil
| | - Claudio Oliveira
- 2Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista-UNESP, Botucatu, Brazil
| | - Fausto Foresti
- 2Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista-UNESP, Botucatu, Brazil
| | - Fábio Porto-Foresti
- 1Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista-UNESP, Bauru, Brazil
| | - Ricardo Utsunomia
- 1Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista-UNESP, Bauru, Brazil.,2Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista-UNESP, Botucatu, Brazil
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20
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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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21
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Pita S, Díaz-Viraqué F, Iraola G, Robello C. The Tritryps Comparative Repeatome: Insights on Repetitive Element Evolution in Trypanosomatid Pathogens. Genome Biol Evol 2019; 11:546-551. [PMID: 30715360 PMCID: PMC6390901 DOI: 10.1093/gbe/evz017] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2019] [Indexed: 01/01/2023] Open
Abstract
The major human pathogens Trypanosoma cruzi, Trypanosoma brucei, and Leishmania major are collectively known as the Tritryps. The initial comparative analysis of their genomes has uncovered that Tritryps share a great number of genes, but repetitive DNA seems to be extremely variable between them. However, the in-depth characterization of repetitive DNA in these pathogens has been in part neglected, mainly due to the well-known technical challenges of studying repetitive sequences from de novo assemblies using short reads. Here, we compared the repetitive DNA repertories between the Tritryps genomes using genome-wide, low-coverage Illumina sequencing coupled to RepeatExplorer analysis. Our work demonstrates that this extensively implemented approach for studying higher eukaryote repeatomes is also useful for protozoan parasites like trypanosomatids, as we recovered previously observed differences in the presence and amount of repetitive DNA families. Additionally, our estimations of repetitive DNA abundance were comparable to those obtained from enhanced-quality assemblies using longer reads. Importantly, our methodology allowed us to describe a previously undescribed transposable element in Leishmania major (TATE element), highlighting its potential to accurately recover distinctive features from poorly characterized repeatomes. Together, our results support the application of this low-cost, low-coverage sequencing approach for the extensive characterization of repetitive DNA evolutionary dynamics in trypanosomatid and other protozoan genomes.
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Affiliation(s)
- Sebastián Pita
- Laboratory of Host Pathogen Interactions, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Florencia Díaz-Viraqué
- Laboratory of Host Pathogen Interactions, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur Montevideo, Montevideo, Uruguay.,Centro de Biología Integrativa, Universidad Mayor, Santiago de Chile, Chile
| | - Carlos Robello
- Laboratory of Host Pathogen Interactions, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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22
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Cacheux L, Ponger L, Gerbault-Seureau M, Loll F, Gey D, Richard FA, Escudé C. The Targeted Sequencing of Alpha Satellite DNA in Cercopithecus pogonias Provides New Insight Into the Diversity and Dynamics of Centromeric Repeats in Old World Monkeys. Genome Biol Evol 2018; 10:1837-1851. [PMID: 29860303 PMCID: PMC6061836 DOI: 10.1093/gbe/evy109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2018] [Indexed: 02/06/2023] Open
Abstract
Alpha satellite is the major repeated DNA element of primate centromeres. Specific evolutionary mechanisms have led to a great diversity of sequence families with peculiar genomic organization and distribution, which have till now been studied mostly in great apes. Using high throughput sequencing of alpha satellite monomers obtained by enzymatic digestion followed by computational and cytogenetic analysis, we compare here the diversity and genomic distribution of alpha satellite DNA in two related Old World monkey species, Cercopithecus pogonias and Cercopithecus solatus, which are known to have diverged about 7 Ma. Two main families of monomers, called C1 and C2, are found in both species. A detailed analysis of our data sets revealed the existence of numerous subfamilies within the centromeric C1 family. Although the most abundant subfamily is conserved between both species, our fluorescence in situ hybridization (FISH) experiments clearly show that some subfamilies are specific for each species and that their distribution is restricted to a subset of chromosomes, thereby pointing to the existence of recurrent amplification/homogenization events. The pericentromeric C2 family is very abundant on the short arm of all acrocentric chromosomes in both species, pointing to specific mechanisms that lead to this distribution. Results obtained using two different restriction enzymes are fully consistent with a predominant monomeric organization of alpha satellite DNA that coexists with higher order organization patterns in the C. pogonias genome. Our study suggests a high dynamics of alpha satellite DNA in Cercopithecini, with recurrent apparition of new sequence variants and interchromosomal sequence transfer.
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Affiliation(s)
- Lauriane Cacheux
- Département Adaptations du Vivant, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
- Département Origines et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Loïc Ponger
- Département Adaptations du Vivant, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Michèle Gerbault-Seureau
- Département Origines et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - François Loll
- Département Adaptations du Vivant, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Delphine Gey
- Service de Systématique Moléculaire, UMS 2700 CNRS, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Florence Anne Richard
- Département Origines et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
- Université Versailles St-Quentin, Montigny-le-Bretonneux, France
| | - Christophe Escudé
- Département Adaptations du Vivant, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
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23
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Lower SS, McGurk MP, Clark AG, Barbash DA. Satellite DNA evolution: old ideas, new approaches. Curr Opin Genet Dev 2018; 49:70-78. [PMID: 29579574 PMCID: PMC5975084 DOI: 10.1016/j.gde.2018.03.003] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/02/2018] [Accepted: 03/08/2018] [Indexed: 12/22/2022]
Abstract
A substantial portion of the genomes of most multicellular eukaryotes consists of large arrays of tandemly repeated sequence, collectively called satellite DNA. The processes generating and maintaining different satellite DNA abundances across lineages are important to understand as satellites have been linked to chromosome mis-segregation, disease phenotypes, and reproductive isolation between species. While much theory has been developed to describe satellite evolution, empirical tests of these models have fallen short because of the challenges in assessing satellite repeat regions of the genome. Advances in computational tools and sequencing technologies now enable identification and quantification of satellite sequences genome-wide. Here, we describe some of these tools and how their applications are furthering our knowledge of satellite evolution and function.
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Affiliation(s)
- Sarah Sander Lower
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14853, United States
| | - Michael P McGurk
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14853, United States
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14853, United States
| | - Daniel A Barbash
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14853, United States.
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24
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García-Souto D, Pérez-García C, Pasantes JJ. Are Pericentric Inversions Reorganizing Wedge Shell Genomes? Genes (Basel) 2017; 8:genes8120370. [PMID: 29215567 PMCID: PMC5748688 DOI: 10.3390/genes8120370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 11/27/2022] Open
Abstract
Wedge shells belonging to the Donacidae family are the dominant bivalves in exposed beaches in almost all areas of the world. Typically, two or more sympatric species of wedge shells differentially occupy intertidal, sublittoral, and offshore coastal waters in any given locality. A molecular cytogenetic analysis of two sympatric and closely related wedge shell species, Donax trunculus and Donax vittatus, was performed. Results showed that the karyotypes of these two species were both strikingly different and closely alike; whilst metacentric and submetacentric chromosome pairs were the main components of the karyotype of D. trunculus, 10–11 of the 19 chromosome pairs were telocentric in D. vittatus, most likely as a result of different pericentric inversions. GC-rich heterochromatic bands were present in both species. Furthermore, they showed coincidental 45S ribosomal RNA (rRNA), 5S rRNA and H3 histone gene clusters at conserved chromosomal locations, although D. trunculus had an additional 45S rDNA cluster. Intraspecific pericentric inversions were also detected in both D. trunculus and D. vittatus. The close genetic similarity of these two species together with the high degree of conservation of the 45S rRNA, 5S rRNA and H3 histone gene clusters, and GC-rich heterochromatic bands indicate that pericentric inversions contribute to the karyotype divergence in wedge shells.
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Affiliation(s)
- Daniel García-Souto
- Dpto. Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain.
| | | | - Juan J Pasantes
- Dpto. Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain.
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