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Plant Genomic and Cytogenetic Databases

  • Book
  • © 2023

Overview

Editors:
  1. Sònia Garcia

    1. Botanical Institute of Barcelona IBB (CSIC-Barcelona City Council), Barcelona, Spain

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    You can also search for this editor in PubMed   Google Scholar

  2. Neus Nualart

    1. Botanical Institute of Barcelona, IBB (CSIC-Barcelona City Council), Barcelona, Spain

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2703)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Genomic Databases

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. The Plant Phenomics and Genomics Research Data Repository: An On-Premise Approach for FAIR-Compliant Data Acquisition

      • Daniel Arend, Uwe Scholz, Matthias Lange
      Pages 3-22

    3. Investigating Pangenome Graphs Using Wheat Panache

      • Philipp E. Bayer, David Edwards
      Pages 23-29

    4. InpactorDB: A Plant LTR Retrotransposon Reference Library

      • Simon Orozco-Arias, Simon Gaviria-Orrego, Reinel Tabares-Soto, Gustavo Isaza, Romain Guyot
      Pages 31-44

    5. TEMM: A Curated Data Resource for Transposon Element-Based Molecular Markers in Plants

      • Asmaa H. Hassan, Morad M. Mokhtar, Achraf El Allali
      Pages 45-57

    6. PlanTEnrichment: A How-to Guide on Rapid Identification of Transposable Elements Associated with Regions of Interest in Select Plant Genomes

      • Doğa Eskier, Alirıza Arıbaş, Gökhan Karakülah
      Pages 59-70

    7. CicerSpTEdb2.0: An Upgrade of Cicer Species Transposable Elements Database

      • Morad M. Mokhtar, Ahmed S. Fouad, Haytham M. Abd-Elhalim, Achraf El Allali
      Pages 71-82

    8. “BIFloraExplorer”: A Taxonomic, Genetic, and Ecological Data Resource for the Vascular Plants of Britain and Ireland

      • Marie C. Henniges, Andrew R. Leitch, Ilia J. Leitch
      Pages 83-90

    9. PEATmoss: A Gene Expression Atlas for Bryophytes

      • Noe Fernandez-Pozo
      Pages 91-107

  3. Cytogenetics and Chromosome-Related Databases

    1. Front Matter

      Pages 109-109
      Download chapter PDF

    2. The Plant DNA C-Values Database: A One-Stop Shop for Plant Genome Size Data

      • Marie C. Henniges, Emmeline Johnston, Jaume Pellicer, Oriane Hidalgo, Michael D. Bennett, Ilia J. Leitch
      Pages 111-122

    3. The Chromosome Counts Database (CCDB)

      • Anna Rice, Itay Mayrose
      Pages 123-129

    4. CromoCat: Chromosome Database of the Vascular Flora of the Catalan Countries—25 years

      • Joan Simon, Maria Bosch, Cèsar Blanché
      Pages 131-160

    5. An Overview to the Index to Chromosome Numbers in Asteraceae Database: Revisiting Base Chromosome Numbers, Polyploidy, Descending Dysploidy, and Hybridization

      • John C. Semple, Kuniaki Watanabe
      Pages 161-171

    6. DCDB: Chromosome Database of Tribe Delphinieae (Ranunculaceae): Structure, Exploitation, and Recent Development

      • Maria Bosch, Jordi López-Pujol, Cèsar Blanché, Joan Simon
      Pages 173-192

    7. Chilean Plants Cytogenetic Database: An Online Resource for Embryophytes of the Southern Cone

      • Pedro Jara-Seguel, Jonathan Urrutia-Estrada
      Pages 193-200

    8. The Data Portal “Chromosome Numbers of the Flora of Germany”: Progress After Five Years, Recent Developments, and Future Strategies

      • Thomas Gregor, Stefan Dressler, Sebastian Klemm, Christiane M. Ritz, Marco Schmidt, Karsten Wesche et al.
      Pages 201-209

    9. South American Plant Chromosome Numbers Databases: The Information We Have and the Information We Lack on the Most Plant-Diverse Continent

      • Mariela A. Sader, Lucas A. Costa, Gustavo Souza, Juan D. Urdampilleta, Joan Simon, Magdalena Vaio
      Pages 211-225

    10. First Update to B-Chrom: A Database on B-Chromosomes

      • María Luisa Gutiérrez, Roi Rodríguez-González, Inés Fuentes, Francisco Gálvez-Prada, Aleš Kovařík, Sònia Garcia
      Pages 227-236
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Keywords

About this book

This volume discusses the latest online plant genomics and cytogenetic resources used by plant evolutionary biologists and plant breeders. The chapters in this book are organized into two parts. Part One looks at plant genomic databases, and covers topics such as plant phenomics and genomics research data repositories, InpactorDB, PlanTEenrichment, and PEATmoss, among others. Part Two looks at cytogenetics and chromosome-related databases, and covers resources such as the Plant DNA C-values database, the Delphineae Chromosome Database (DCDB), B-chrom, a Database on B-chromosomes, and the Plant Ribosomal DNA Database. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective databases and offers explicit directions on how to access and get the most of these resources. 

Cutting-edge and comprehensive, Plant Genomic and Cytogenetic Databases is a valuable instrument for any plant science researcher who is interested in learning more about the wealth of information that is available through the use of these databases.


Editors and Affiliations

  • Botanical Institute of Barcelona IBB (CSIC-Barcelona City Council), Barcelona, Spain

    Sònia Garcia

  • Botanical Institute of Barcelona, IBB (CSIC-Barcelona City Council), Barcelona, Spain

    Neus Nualart

Bibliographic Information

  • Book Title: Plant Genomic and Cytogenetic Databases

  • Editors: Sònia Garcia, Neus Nualart

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-3389-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-3388-5Published: 31 August 2023

  • Softcover ISBN: 978-1-0716-3391-5Due: 01 October 2023

  • eBook ISBN: 978-1-0716-3389-2Published: 30 August 2023

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 249

  • Number of Illustrations: 4 b/w illustrations, 72 illustrations in colour

  • Topics: Plant Genetics and Genomics, Bioinformatics

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