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Tunjić-Cvitanić M, García-Souto D, Pasantes JJ, Šatović-Vukšić E. Dominance of transposable element-related satDNAs results in great complexity of "satDNA library" and invokes the extension towards "repetitive DNA library". MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:236-251. [PMID: 38827134 PMCID: PMC11136912 DOI: 10.1007/s42995-024-00218-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 02/26/2024] [Indexed: 06/04/2024]
Abstract
Research on bivalves is fast-growing, including genome-wide analyses and genome sequencing. Several characteristics qualify oysters as a valuable model to explore repetitive DNA sequences and their genome organization. Here we characterize the satellitomes of five species in the family Ostreidae (Crassostrea angulata, C. virginica, C. hongkongensis, C. ariakensis, Ostrea edulis), revealing a substantial number of satellite DNAs (satDNAs) per genome (ranging between 33 and 61) and peculiarities in the composition of their satellitomes. Numerous satDNAs were either associated to or derived from transposable elements, displaying a scarcity of transposable element-unrelated satDNAs in these genomes. Due to the non-conventional satellitome constitution and dominance of Helitron-associated satDNAs, comparative satellitomics demanded more in-depth analyses than standardly employed. Comparative analyses (including C. gigas, the first bivalve species with a defined satellitome) revealed that 13 satDNAs occur in all six oyster genomes, with Cg170/HindIII satDNA being the most abundant in all of them. Evaluating the "satDNA library model" highlighted the necessity to adjust this term when studying tandem repeat evolution in organisms with such satellitomes. When repetitive sequences with potential variation in the organizational form and repeat-type affiliation are examined across related species, the introduction of the terms "TE library" and "repetitive DNA library" becomes essential. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-024-00218-0.
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Affiliation(s)
| | - Daniel García-Souto
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Juan J. Pasantes
- Centro de Investigación Mariña, Dpto de Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, 36310 Vigo, Spain
| | - Eva Šatović-Vukšić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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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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Tunjić-Cvitanić M, Pasantes JJ, García-Souto D, Cvitanić T, Plohl M, Šatović-Vukšić E. Satellitome Analysis of the Pacific Oyster Crassostrea gigas Reveals New Pattern of Satellite DNA Organization, Highly Scattered across the Genome. Int J Mol Sci 2021; 22:ijms22136798. [PMID: 34202698 PMCID: PMC8268682 DOI: 10.3390/ijms22136798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/22/2022] Open
Abstract
Several features already qualified the invasive bivalve species Crassostrea gigas as a valuable non-standard model organism in genome research. C. gigas is characterized by the low contribution of satellite DNAs (satDNAs) vs. mobile elements and has an extremely low amount of heterochromatin, predominantly built of DNA transposons. In this work, we have identified 52 satDNAs composing the satellitome of C. gigas and constituting about 6.33% of the genome. Satellitome analysis reveals unusual, highly scattered organization of relatively short satDNA arrays across the whole genome. However, peculiar chromosomal distribution and densities are specific for each satDNA. The inspection of the organizational forms of the 11 most abundant satDNAs shows association with constitutive parts of Helitron mobile elements. Nine of the inspected satDNAs are dominantly found in mobile element-associated form, two mostly appear standalone, and only one is present exclusively as Helitron-associated sequence. The Helitron-related satDNAs appear in more chromosomes than other satDNAs, indicating that these mobile elements could be leading satDNA propagation in C. gigas. No significant accumulation of satDNAs on certain chromosomal positions was detected in C. gigas, thus establishing a novel pattern of satDNA organization on the genome level.
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Affiliation(s)
- Monika Tunjić-Cvitanić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.T.-C.); (M.P.)
| | - Juan J. Pasantes
- Centro de Investigación Mariña, Universidade de Vigo, Dpto de Bioquímica, Xenética e Inmunoloxía, 36310 Vigo, Spain;
| | - Daniel García-Souto
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain;
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Tonči Cvitanić
- Rimac Automobili d.o.o., Ljubljanska ulica 7, 10431 Sveta Nedelja, Croatia;
| | - Miroslav Plohl
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.T.-C.); (M.P.)
| | - Eva Šatović-Vukšić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.T.-C.); (M.P.)
- Correspondence:
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Tunjić Cvitanić M, Vojvoda Zeljko T, Pasantes JJ, García-Souto D, Gržan T, Despot-Slade E, Plohl M, Šatović E. Sequence Composition Underlying Centromeric and Heterochromatic Genome Compartments of the Pacific Oyster Crassostrea gigas. Genes (Basel) 2020; 11:genes11060695. [PMID: 32599860 PMCID: PMC7348941 DOI: 10.3390/genes11060695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/10/2020] [Accepted: 06/22/2020] [Indexed: 02/07/2023] Open
Abstract
Segments of the genome enriched in repetitive sequences still present a challenge and are omitted in genome assemblies. For that reason, the exact composition of DNA sequences underlying the heterochromatic regions and the active centromeres are still unexplored for many organisms. The centromere is a crucial region of eukaryotic chromosomes responsible for the accurate segregation of genetic material. The typical landmark of centromere chromatin is the rapidly-evolving variant of the histone H3, CenH3, while DNA sequences packed in constitutive heterochromatin are associated with H3K9me3-modified histones. In the Pacific oyster Crassostrea gigas we identified its centromere histone variant, Cg-CenH3, that shows stage-specific distribution in gonadal cells. In order to investigate the DNA composition of genomic regions associated with the two specific chromatin types, we employed chromatin immunoprecipitation followed by high-throughput next-generation sequencing of the Cg-CenH3- and H3K9me3-associated sequences. CenH3-associated sequences were assigned to six groups of repetitive elements, while H3K9me3-associated-ones were assigned only to three. Those associated with CenH3 indicate the lack of uniformity in the chromosomal distribution of sequences building the centromeres, being also in the same time dispersed throughout the genome. The heterochromatin of C. gigas exhibited general paucity and limited chromosomal localization as predicted, with H3K9me3-associated sequences being predominantly constituted of DNA transposons.
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Affiliation(s)
- Monika Tunjić Cvitanić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
| | - Tanja Vojvoda Zeljko
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
| | - Juan J. Pasantes
- Departamento de Bioquímica, Xenética e Inmunoloxía, Centro de Investigación Mariña (CIM), Universidade de Vigo, 36310 Vigo, Spain; (J.J.P.); (D.G.-S.)
| | - Daniel García-Souto
- Departamento de Bioquímica, Xenética e Inmunoloxía, Centro de Investigación Mariña (CIM), Universidade de Vigo, 36310 Vigo, Spain; (J.J.P.); (D.G.-S.)
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Praza do Obradoiro, 0, 15705 Santiago de Compostela, Spain
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Tena Gržan
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
| | - Evelin Despot-Slade
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
| | - Miroslav Plohl
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
- Correspondence: (M.P.); (E.Š.)
| | - Eva Šatović
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
- Correspondence: (M.P.); (E.Š.)
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Garrido-Ramos MA. Satellite DNA: An Evolving Topic. Genes (Basel) 2017; 8:genes8090230. [PMID: 28926993 PMCID: PMC5615363 DOI: 10.3390/genes8090230] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022] Open
Abstract
Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes. The whole of the historical and current approaches to the topic gives us a broad view of the function and evolution of satellite DNA and its role in chromosomal evolution. Currently, we have extensive information on the molecular, chromosomal, biological, and population factors that affect the evolutionary fate of satellite DNA, knowledge that gives rise to a series of hypotheses that get on well with each other about the origin, spreading, and evolution of satellite DNA. In this paper, I review these hypotheses from a methodological, conceptual, and historical perspective and frame them in the context of chromosomal organization and evolution.
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Affiliation(s)
- Manuel A Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
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Satović E, Vojvoda Zeljko T, Luchetti A, Mantovani B, Plohl M. Adjacent sequences disclose potential for intra-genomic dispersal of satellite DNA repeats and suggest a complex network with transposable elements. BMC Genomics 2016; 17:997. [PMID: 27919246 PMCID: PMC5139131 DOI: 10.1186/s12864-016-3347-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/25/2016] [Indexed: 11/14/2022] Open
Abstract
Background Satellite DNA (satDNA) sequences are typically arranged as arrays of tandemly repeated monomers. Due to the similarity among monomers, their organizational pattern and abundance, satDNAs are hardly accessible to structural and functional studies and still represent the most obscure genome component. Although many satDNA arrays of diverse length and even single monomers exist in the genome, surprisingly little is known about transition from satDNAs to other sequences. Studying satDNA monomers at junctions and identifying DNA sequences adjacent to them can help to understand the processes that (re)distribute satDNAs and significance that evolution of these sequence elements might have in creating the genomic landscape. Results We explored sets of randomly selected satDNA-harboring genomic fragments in four mollusc species to examine satDNA transition sites, and the nature of adjacent sequences. All examined junctions are characterized by abrupt transitions from satDNAs to other sequences. Among them, junctions of only one examined satDNA mapped non-randomly (within the palindrome), indicating that well-defined sequence feature is not a necessary prerequisite in the junction formation. In the studied sample, satDNA flanking sequences can be roughly classified into two groups. The first group is composed of anonymous DNA sequences which occasionally include short segments of transposable elements (TEs) as well as segments of other satDNA sequences. In the second group, satDNA repeats and the array flanking sequences are identified as parts of TEs of the Helitron superfamily. There, some array flanking regions hold fragmented satDNA monomers alternating with anonymous sequences of comparable length as missing monomer parts, suggesting a process of sequence reorganization by a mechanism able to excise short monomer parts and replace them with unrelated sequences. Conclusions The observed architecture of satDNA transition sites can be explained as a result of insertion and/or recombination events involving short arrays of satDNA monomers and TEs, in combination with hypothetical transposition-related ability of satDNA monomers to be shuffled independently in the genome. We conclude that satDNAs and TEs can form a complex network of sequences which essentially share the propagation mechanisms and in synergy shape the genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3347-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eva Satović
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Andrea Luchetti
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali-Università di Bologna, Bologna, Italy
| | - Barbara Mantovani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali-Università di Bologna, Bologna, Italy
| | - Miroslav Plohl
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia.
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Meštrović N, Mravinac B, Pavlek M, Vojvoda-Zeljko T, Šatović E, Plohl M. Structural and functional liaisons between transposable elements and satellite DNAs. Chromosome Res 2016; 23:583-96. [PMID: 26293606 DOI: 10.1007/s10577-015-9483-7] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Transposable elements (TEs) and satellite DNAs (satDNAs) are typically identified as major repetitive DNA components in eukaryotic genomes. TEs are DNA segments able to move throughout a genome while satDNAs are tandemly repeated sequences organized in long arrays. Both classes of repetitive sequences are extremely diverse, and many TEs and satDNAs exist within a genome. Although they differ in structure, genomic organization, mechanisms of spread, and evolutionary dynamics, TEs and satDNAs can share sequence similarity and organizational patterns, thus indicating that complex mutual relationships can determine their evolution, and ultimately define roles they might have on genome architecture and function. Motivated by accumulating data about sequence elements that incorporate features of both TEs and satDNAs, here we present an overview of their structural and functional liaisons.
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Affiliation(s)
| | | | - Martina Pavlek
- Ruđer Bošković Institute, Bijenička 54, HR-10000, Zagreb, Croatia
| | | | - Eva Šatović
- Ruđer Bošković Institute, Bijenička 54, HR-10000, Zagreb, Croatia
| | - Miroslav Plohl
- Ruđer Bošković Institute, Bijenička 54, HR-10000, Zagreb, Croatia.
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