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  1. Book: Repetitive DNA

    Garrido-Ramos, Manuel A.

    1 table

    (Genome dynamics ; 7)

    2012  

    Author's details vol. ed. Manuel A. Garrido-Ramos
    Series title Genome dynamics ; 7
    Collection
    Keywords DNA / genetics ; Repetitive Sequences, Nucleic Acid ; Genomics / methods ; Repetitive DNS
    Subject Repetitive Sequenz ; Multiple DNS ; Repetitive DNA
    Language English
    Size VIII, 230 S. : Ill., graph. Darst.
    Publisher Karger
    Publishing place Basel u.a.
    Publishing country Switzerland
    Document type Book
    HBZ-ID HT017302274
    ISBN 978-3-318-02149-3 ; 3-318-02149-0 ; 9783318021509 ; 3318021504
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2012 A 2907 order for loan Magazin

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  2. Article: The Genomics of Plant Satellite DNA.

    Garrido-Ramos, Manuel A

    Progress in molecular and subcellular biology

    2021  Volume 60, Page(s) 103–143

    Abstract: The twenty-first century began with a certain indifference to the research of satellite DNA (satDNA). Neither genome sequencing projects were able to accurately encompass the study of satDNA nor classic methodologies were able to go further in ... ...

    Abstract The twenty-first century began with a certain indifference to the research of satellite DNA (satDNA). Neither genome sequencing projects were able to accurately encompass the study of satDNA nor classic methodologies were able to go further in undertaking a better comprehensive study of the whole set of satDNA sequences of a genome. Nonetheless, knowledge of satDNA has progressively advanced during this century with the advent of new analytical techniques. The enormous advantages that genome-wide approaches have brought to its analysis have now stimulated a renewed interest in the study of satDNA. At this point, we can look back and try to assess more accurately many of the key questions that were left unsolved in the past about this enigmatic and important component of the genome. I review here the understanding gathered on plant satDNAs over the last few decades with an eye on the near future.
    MeSH term(s) Chromosome Mapping ; DNA, Plant/genetics ; DNA, Satellite/genetics ; Evolution, Molecular ; Genomics
    Chemical Substances DNA, Plant ; DNA, Satellite
    Language English
    Publishing date 2021-08-13
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 0079-6484
    ISSN 0079-6484
    DOI 10.1007/978-3-030-74889-0_5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Bread wheat satellitome: a complex scenario in a huge genome.

    Gálvez-Galván, Ana / Garrido-Ramos, Manuel A / Prieto, Pilar

    Plant molecular biology

    2024  Volume 114, Issue 1, Page(s) 8

    Abstract: In bread wheat (Triticum aestivum L.), chromosome associations during meiosis are extremely regulated and initiate at the telomeres and subtelomeres, which are enriched in satellite DNA (satDNA). We present the study and characterization of the bread ... ...

    Abstract In bread wheat (Triticum aestivum L.), chromosome associations during meiosis are extremely regulated and initiate at the telomeres and subtelomeres, which are enriched in satellite DNA (satDNA). We present the study and characterization of the bread wheat satellitome to shed light on the molecular organization of wheat subtelomeres. Our results revealed that the 2.53% of bread wheat genome is composed by satDNA and subtelomeres are particularly enriched in such DNA sequences. Thirty-four satellite DNA (21 for the first time in this work) have been identified, analyzed and cytogenetically validated. Many of the satDNAs were specifically found at particular subtelomeric chromosome regions revealing the asymmetry in subtelomere organisation among the wheat subgenomes, which might play a role in proper homologous recognition and pairing during meiosis. An integrated physical map of the wheat satellitome was also constructed. To the best of our knowledge, our results show that the combination of both cytogenetics and genome research allowed the first comprehensive analysis of the wheat satellitome, shedding light on the complex wheat genome organization, especially on the polymorphic nature of subtelomeres and their putative implication in chromosome recognition and pairing during meiosis.
    MeSH term(s) Genome, Plant ; Triticum/genetics ; DNA, Satellite ; Bread ; Base Sequence
    Chemical Substances DNA, Satellite
    Language English
    Publishing date 2024-01-30
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 778032-1
    ISSN 1573-5028 ; 0167-4412
    ISSN (online) 1573-5028
    ISSN 0167-4412
    DOI 10.1007/s11103-023-01404-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3458: Show issues Location:
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  4. Article: Satellite DNA: An Evolving Topic.

    Garrido-Ramos, Manuel A

    Genes

    2017  Volume 8, Issue 9

    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 ... ...

    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.
    Language English
    Publishing date 2017-09-18
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes8090230
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Comparison between the Gametophyte and the Sporophyte Transcriptomes of the Endangered Fern

    Martín-Blázquez, Rubén / Bakkali, Mohammed / Ruiz-Estévez, Mercedes / Garrido-Ramos, Manuel A

    Genes

    2023  Volume 14, Issue 1

    Abstract: Genomic resources are essential to understanding the evolution and functional biology of organisms. Nevertheless, generating genomic resources from endangered species may be challenging due to the scarcity of available specimens and sampling difficulties. ...

    Abstract Genomic resources are essential to understanding the evolution and functional biology of organisms. Nevertheless, generating genomic resources from endangered species may be challenging due to the scarcity of available specimens and sampling difficulties. In this study, we compare the transcriptomes of the sporophyte and the gametophyte of the endangered fern
    MeSH term(s) Ferns/genetics ; Transcriptome/genetics ; Germ Cells, Plant/physiology ; Genomics ; High-Throughput Nucleotide Sequencing
    Language English
    Publishing date 2023-01-07
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14010166
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Satellite DNA in Plants: More than Just Rubbish.

    Garrido-Ramos, Manuel A

    Cytogenetic and genome research

    2015  Volume 146, Issue 2, Page(s) 153–170

    Abstract: For decades, satellite DNAs have been the hidden part of genomes. Initially considered as junk DNA, there is currently an increasing appreciation of the functional significance of satellite DNA repeats and of their sequences. Satellite DNA families ... ...

    Abstract For decades, satellite DNAs have been the hidden part of genomes. Initially considered as junk DNA, there is currently an increasing appreciation of the functional significance of satellite DNA repeats and of their sequences. Satellite DNA families accumulate in the heterochromatin in different parts of the eukaryotic chromosomes, mainly in pericentromeric and subtelomeric regions, but they also span the functional centromere. Tandem repeat sequences may spread from subtelomeric to interstitial loci, leading to the formation of chromosome-specific loci or to the accumulation in equilocal sites in different chromosomes. They also appear as the main components of the heterochromatin in the sex-specific region of sex chromosomes. Satellite DNA, required for chromosome organization, also plays a role in pairing and segregation. Some satellite repeats are transcribed and can participate in the formation and maintenance of heterochromatin structure and in the modulation of gene expression. In addition to the identification of the different satellite DNA families, their characteristics and location, we are interested in determining their impact on the genomes, by identifying the mechanisms leading to their appearance and amplification as well as in understanding how they change over time, the factors affecting these changes, and the influence exerted by the evolutionary history of the organisms. On the other hand, satellite DNA sequences are rapidly evolving sequences that may cause reproductive barriers between organisms and promote speciation. The accumulation of experimental data collected in recent years and the emergence of new approaches based on next-generation sequencing and high-throughput genome analysis are opening new perspectives that are changing our understanding of satellite DNA. This review examines recent data to provide a timely update on the overall information gathered about this part of the genome, focusing on the advances in the knowledge of its origin, its evolution, and its potential functional roles.
    MeSH term(s) Centromere/genetics ; Chromosomes, Plant/genetics ; DNA, Plant/genetics ; DNA, Satellite/genetics ; Evolution, Molecular ; Genome, Plant/genetics ; Heterochromatin/genetics ; Phylogeny ; Plants/classification ; Plants/genetics ; Telomere/genetics
    Chemical Substances DNA, Plant ; DNA, Satellite ; Heterochromatin
    Language English
    Publishing date 2015-07-18
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2087824-2
    ISSN 1424-859X ; 1424-8581
    ISSN (online) 1424-859X
    ISSN 1424-8581
    DOI 10.1159/000437008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 512: Show issues Location:
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    ab Jg. 2022: Lesesaal (EG)

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  7. Article ; Online: Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia).

    Sales-Oliveira, Vanessa C / Dos Santos, Rodrigo Zeni / Goes, Caio Augusto Gomes / Calegari, Rodrigo Milan / Garrido-Ramos, Manuel A / Altmanová, Marie / Ezaz, Tariq / Liehr, Thomas / Porto-Foresti, Fabio / Utsunomia, Ricardo / Cioffi, Marcelo B

    BMC biology

    2024  Volume 22, Issue 1, Page(s) 47

    Abstract: Background: Crocodilians are one of the oldest extant vertebrate lineages, exhibiting a combination of evolutionary success and morphological resilience that has persisted throughout the history of life on Earth. This ability to endure over such a long ... ...

    Abstract Background: Crocodilians are one of the oldest extant vertebrate lineages, exhibiting a combination of evolutionary success and morphological resilience that has persisted throughout the history of life on Earth. This ability to endure over such a long geological time span is of great evolutionary importance. Here, we have utilized the combination of genomic and chromosomal data to identify and compare the full catalogs of satellite DNA families (satDNAs, i.e., the satellitomes) of 5 out of the 8 extant Alligatoridae species. As crocodilian genomes reveal ancestral patterns of evolution, by employing this multispecies data collection, we can investigate and assess how satDNA families evolve over time.
    Results: Alligators and caimans displayed a small number of satDNA families, ranging from 3 to 13 satDNAs in A. sinensis and C. latirostris, respectively. Together with little variation both within and between species it highlighted long-term conservation of satDNA elements throughout evolution. Furthermore, we traced the origin of the ancestral forms of all satDNAs belonging to the common ancestor of Caimaninae and Alligatorinae. Fluorescence in situ experiments showed distinct hybridization patterns for identical orthologous satDNAs, indicating their dynamic genomic placement.
    Conclusions: Alligators and caimans possess one of the smallest satDNA libraries ever reported, comprising only four sets of satDNAs that are shared by all species. Besides, our findings indicated limited intraspecific variation in satellite DNA, suggesting that the majority of new satellite sequences likely evolved from pre-existing ones.
    MeSH term(s) Animals ; DNA, Satellite/genetics ; Alligators and Crocodiles/genetics ; Chromosomes ; Genomics ; Evolution, Molecular
    Chemical Substances DNA, Satellite
    Language English
    Publishing date 2024-02-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 2133020-7
    ISSN 1741-7007 ; 1741-7007
    ISSN (online) 1741-7007
    ISSN 1741-7007
    DOI 10.1186/s12915-024-01847-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Comparison between the Gametophyte and the Sporophyte Transcriptomes of the Endangered Fern Vandenboschia speciosa

    Martín-Blázquez, Rubén / Bakkali, Mohammed / Ruiz-Estévez, Mercedes / Garrido-Ramos, Manuel A.

    Genes (Basel). 2023 Jan. 07, v. 14, no. 1

    2023  

    Abstract: Genomic resources are essential to understanding the evolution and functional biology of organisms. Nevertheless, generating genomic resources from endangered species may be challenging due to the scarcity of available specimens and sampling difficulties. ...

    Abstract Genomic resources are essential to understanding the evolution and functional biology of organisms. Nevertheless, generating genomic resources from endangered species may be challenging due to the scarcity of available specimens and sampling difficulties. In this study, we compare the transcriptomes of the sporophyte and the gametophyte of the endangered fern Vandenboschia speciosa. After Illumina sequencing and de novo transcriptome assembly of the gametophyte, annotation proved the existence of cross-species contamination in the gametophyte sample. Thus, we developed an in silico decontamination step for the gametophyte sequences. Once the quality check of the decontaminated reads passed, we produced a de novo assembly with the decontaminated gametophyte reads (with 43,139 contigs) and another combining the sporophyte and in silico decontaminated gametophyte reads (with 42,918 contigs). A comparison of the enriched GO terms from the top 1000 most expressed transcripts from both tissues showed that the gametophyte GO term set was enriched in sequences involved in development, response to stress, and plastid organization, while the sporophyte GO term set had a larger representation of more general metabolic functions. This study complements the available genomic resources on the life cycle of the endangered fern Vandenboschia speciosa.
    Keywords computer simulation ; decontamination ; endangered species ; evolution ; ferns and fern allies ; gametophytes ; genomics ; sporophytes ; stress response ; transcriptome
    Language English
    Dates of publication 2023-0107
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14010166
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: De Novo Sporophyte Transcriptome Assembly and Functional Annotation in the Endangered Fern Species

    Bakkali, Mohammed / Martín-Blázquez, Rubén / Ruiz-Estévez, Mercedes / Garrido-Ramos, Manuel A

    Genes

    2021  Volume 12, Issue 7

    Abstract: We sequenced the sporophyte transcriptome of Killarney fern ( ...

    Abstract We sequenced the sporophyte transcriptome of Killarney fern (
    MeSH term(s) Endangered Species ; Ferns/genetics ; Ferns/growth & development ; Ferns/metabolism ; Gene Expression Regulation, Plant ; Genome, Plant ; Genomics ; Germ Cells, Plant/metabolism ; Molecular Sequence Annotation ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Transcriptome
    Chemical Substances Plant Proteins
    Language English
    Publishing date 2021-06-30
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12071017
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Transposable element landscapes illuminate past evolutionary events in the endangered fern

    Ruiz-Ruano, Francisco J / Navarro-Domínguez, Beatriz / Camacho, Juan Pedro M / Garrido-Ramos, Manuel A

    Genome

    2021  Volume 65, Issue 2, Page(s) 95–103

    Abstract: Vandenboschia ... ...

    Abstract Vandenboschia speciosa
    MeSH term(s) DNA Transposable Elements/genetics ; Evolution, Molecular ; Ferns/genetics ; Genome, Plant ; Retroelements
    Chemical Substances DNA Transposable Elements ; Retroelements
    Language English
    Publishing date 2021-09-23
    Publishing country Canada
    Document type Journal Article
    ZDB-ID 639031-6
    ISSN 1480-3321 ; 0831-2796
    ISSN (online) 1480-3321
    ISSN 0831-2796
    DOI 10.1139/gen-2021-0022
    Database MEDical Literature Analysis and Retrieval System OnLINE

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