Plant Genomic and Cytogenetic Databases

ISBN-13: 9781071633885 / Angielski / Twarda / 2023

Opis

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.

Spis treści

Preface…
Table of Contents…
Contributing Authors…

Part I Genomic Databases

1. The Plant Phenomics and Genomics Research Data Repository: An On-Premise Approach for FAIR Compliant Data Acquisition
Daniel Arend, Uwe Scholz, and Matthias Lange

2. Investigating Pangenome Graphs using Wheat Panache
Philipp E. Bayer and David Edwards

3. InpactorDB: A Plant LTR Retrotransposon Reference Library
Simon Orozco-Arias, Simon Gaviria-Orrego, Reinel Tabares-Soto, Gustavo Isaza, and Romain Guyot

4. TEMM: A Curated Data Resource for Transposon Element-Based Molecular Markers in Plants
Asmaa H. Hassan, Morad M. Mokhtar, and Achraf El Allali

5. PlanTEnrichment: A How-To Guide on Rapid Identification of TEs Associated with Regions of Interest in Select Plant Genomes
Doğa Eskier, Alirıza Arıbaş, and Gökhan Karakülah

6. CicerSpTEdb2.0: An Upgrade of Cicer Species Transposable Elements Database
Morad M. Mokhtar, Ahmed S. Fouad, Haytham M. Abd-Elhalim, and Achraf El Allali

7. ‘BIFloraExplorer’: A Taxonomic, Genetic, and Ecological Data Resource for the Vascular Plants of Britain and Ireland
Marie C. Henniges, Andrew Leitch, and Ilia J. Leitch

8. PEATmoss: A Gene Expression Atlas for Bryophytes
Noe Fernandez-Pozo

Part II Cytogenetics and Chromosome-Related Databases

9. 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, and Ilia J. Leitch

10. The Chromosome Counts Database (CCDB)
Anna Rice and Itay Mayrose

11. CromoCat: Chromosome Database of the Vascular Flora of the Catalan Countries - 25 Years
Joan Simon, Maria Bosch, and Cèsar Blanché

12. An Overview to the Index to Chromosome Numbers in Asteraceae Database: Revisiting Base Chromosome Numbers, Polyploidy, Descending Dysploidy, and Hybridization
John C. Semple and Kuniaki Watanabe

13. DCDB: Chromosome Database of Tribe Delphinieae (Ranunculaceae): Structure, Exploitation, and Recent Development
Maria Bosch, Jordi López-Pujol, Cèsar Blanché, and Joan Simon

14. Chilean Plants Cytogenetic Database: An Online Resource for Embryophytes of the Southern Cone
Pedro Jara-Seguel and Jonathan Urrutia-Estrada

15. 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, Jens Wesenberg, Georg Zizka, and Juraj Paule

16. 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, and Magdalena Vaio

17. First Update to B-Chrom: A Database on B-Chromosomes
María Luisa Gutiérrez, Roi Rodríguez González, Inés Fuentes, Francisco Gálvez-Prada, Ales Kovarik, and Sònia Garcia

18. Release 4.0 of the Plant rDNA Database: A Database on Plant Ribosomal DNA loci Number, Their Position, and Organization - An Information Source for Comparative Cytogenetics
Roi Rodríguez González, Maria Luisa Gutiérrez, Inés Fuentes, Francisco Gálvez-Prada, Jana Sochorova, Ales Kovarik, and Sònia Garcia

Subject Index List…