Abstract
The advancements in research in the field of plant cytogenetics and genomics in recent decades have led to a significant increase in publications. To simplify access to the widely dispersed data, there has been a rise in the number of online databases, repositories, and analytical tools. This chapter presents a comprehensive overview of these resources, which can be beneficial to researchers in these areas. It includes, among others, databases on chromosome numbers, special chromosomes (such as B chromosomes or sex chromosomes), some of which are taxon-specific; genome sizes, cytogenetics; and online applications and tools for genomic analysis and visualization.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Rice A, Glick L, Abadi S et al (2015) The Chromosome Counts Database (CCDB)–a community resource of plant chromosome numbers. New Phytol 206(1):19–26. https://doi.org/10.1111/nph.13191
Kluyver TA, Osborne CP (2013) Taxonome: a software package for linking biological species data. Ecol Evol 3(5):1262–1265. https://doi.org/10.1002/ece3.529
D’Ambrosio U, Alonso-Lifante MP, Barros K et al (2017) B-chrom: a database on B-chromosomes of plants, animals and fungi. New Phytol 216:635–642. https://doi.org/10.1111/nph.14723
Baránková S, Pascual-Díaz JP, Sultana N et al (2020) Sex-chrom, a database on plant sex chromosomes. New Phytol 227:1594–1604. https://doi.org/10.1111/nph.16635
Garcia S, Janousek B, Pascual-Díaz JP et al (2023) Sex-chrom v. 2.0: a database of green plant species with sex chromosomes. Chromosoma, 132:55–58. https://doi.org/10.1007/s00412-023-00786-7
Goldblatt P, Lowry PP (2011) The Index to Plant Chromosome Numbers (IPCN): three decades of publication by the Missouri Botanical Garden come to an end. Ann Miss Bot Gard 98(2):226–227. https://doi.org/10.3417/2011027
Paule J, Gregor T, Schmidt M et al (2017) Chromosome numbers of the flora of Germany—a new online database of georeferenced chromosome counts and flow cytometric ploidy estimates. Plant Syst Evol 303(8):1123–1129. https://doi.org/10.1007/s00606-016-1362-y
Marhold K (2007) Chromosome number survey of the ferns and flowering plants of Slovakia. Veda, Bratislava
Semple JC, Watanabe K (2009) A review of chromosome numbers in Asteraceae with hypotheses on chromosomal base number evolution. In: Funk VA, Susanna A, Stuessy T, Bayer R (eds) Systematic, evolution, and biogeography of Compositae. International Association for Plant Taxonomy, Vienna, pp 61–72
Španiel S, Kempa M, Salmerón-Sánchez E et al (2015) AlyBase: database of names, chromosome numbers, and ploidy levels of Alysseae (Brassicaceae), with a new generic concept of the tribe. Plant Syst Evol 301(10):2463–2491. https://doi.org/10.1007/s00606-015-1257-3
Schuhwerk F (1996) Published chromosome counts in Hieracium. http://www.botanischestaatssammlung.de/projects/chrzlit.html. Accessed 29 Aug 2021
Hinsley SR (2009) Chromosome counts for Malvaceae. http://www.malvaceae.info/Biology/Chromosomes.php. Accessed 3 Sept 2021
Bennett MD, Leitch IJ (2001) Plant DNA C-values database (release 1.0, Sept. 2001). https://cvalues.science.kew.org/. Accessed 3 Sept 2021
Pellicer J, Leitch IJ (2019) The Plant DNA C-values database release (7.1): an updated online repository of plant genome size data for comparative studies. New Phytol 226(2):301–305. https://doi.org/10.1111/nph.16261
Siljak-Yakovlev S, Muratović E, Bogunić F et al (2020) Genome size of Balkan flora: a database (GeSDaBaF) and C-values for 51 taxa of which 46 are novel. Plant Syst Evol 306(2):1–15. https://doi.org/10.1007/s00606-020-01670-y
Garnatje T, Canela MÁ, Garcia S et al (2011) GSAD: a genome size database in the Asteraceae. Cytometry A 79A:401–404. https://doi.org/10.1002/cyto.a.21056
Vitales D, Fernández P, Garnatje T et al (2019) Progress in the study of genome size evolution in Asteraceae: analysis of the last update. Database 2019:baz098. https://doi.org/10.1093/database/baz098
Loureiro J, Rodriguez E, Santos C et al (2008) FLOWer: a plant DNA flow cytometry database (release 1.0, May 2008). In: Doležel J, Greilhuber J, Sud J (eds) Flow cytometry with plant cells - analysis of genes, chromosomes and genomes. Wiley-VCH, Berlin, pp 423–438
Garcia S, Garnatje T, Kovařík A (2012) Plant rDNA database: ribosomal DNA loci information goes online. Chromosoma 121(4):389–394. https://doi.org/10.1007/s00412-012-0368-7
Vitales D, D’Ambrosio U, Gálvez F et al (2017) Third release of the plant rDNA database with updated content and information on telomere composition and sequenced plant genomes. Plant Syst Evol 303(8):1115–1121. https://doi.org/10.1007/s00606-017-1440-9
Jara-Seguel P, Urrutia-Estrada J (2018) Chilean Plants Cytogenetic Database: coverage, features and usages. Base de Datos Citogenéticos de Plantas Chilenas: Cobertura, Características y usos. J Basic Appl Genet 29(1):65–69
Jha S, Raina SN, Ohri D et al (2019) A new online database on genome-related information of Indian plants. Plant Syst Evol 305(9):837–843. https://doi.org/10.1007/00606-019-01602-5
Roa F, de Campos Telles MP (2017) The Cerrado (Brazil) plant cytogenetics database. Comp Cytogen 11(2):285. https://doi.org/10.3897/CompCytogen.v11i2.11395
Albers F, Meve U (2001) A karyological survey of Asclepiadoideae, Periplocoideae, and Secamonoideae, and evolutionary considerations within Apocynaceae sl. Ann Miss Bot Gar 88(4):624–656. https://doi.org/10.2307/3298637
Šmarda P, Knápek O, Březinová A et al (2019) Genome sizes and genomic guanine+cytosine (GC) contents of the Czech vascular flora with new estimates for 1700 species. Preslia 91(2):117–142. https://doi.org/10.23855/preslia.2019.117
Bosch M, Simon J, López J et al (2016) DCDB: an updated on-line database of chromosome numbers of tribe Delphinieae (Ranunculaceae). Fl Medit 26:191–201. https://doi.org/10.7320/FlMedit26.191
Bedini G, Garbari F, Peruzzi L (2010) Chorobase.it - Chromosome numbers for the Italian flora. http://www.biologia.unipi.it/chrobase/. Accessed 3 Sept 2021
Kučera J, Valko I, Marhold K (2005) On-line database of the chromosome numbers of the genus Cardamine (Brassicaceae). Biologia 60(4):473–476
Marhold K, Kempa M, Kučera J et al (2021) Database of names, chromosome numbers, ploidy levels and genome sizes of the tribe Cardamineae. https://cardamine.sav.sk. Accessed 29 Aug 2021
Lyčka M, Peska V, Demko M et al (2021) WALTER: an easy way to online evaluate telomere lengths from terminal restriction fragment analysis. BMC Bioinformatics 22(1):1–14. https://doi.org/10.1186/s12859-021-04064-0
Rivero R, Sessa EB, Zenil-Ferguson R (2019) EyeChrom and CCDB curator: visualizing chromosome count data from plants. Appl Plant Sci 7(1):e01207. https://doi.org/10.1002/aps3.1207
Howe KL, Contreras-Moreira B, De Silva N et al (2020) Ensembl Genomes 2020—enabling non-vertebrate genomic research. Nucleic Acids Res 48(1):689–695. https://doi.org/10.1093/nar/gkz890
Acknowledgments
This work has been supported by the State Research Agency (PID2020-119163GB-I00). Maria Luisa Gutiérrez holds a Personal Técnico de Apoyo contract (PTA2018-015819-I), Roi Rodríguez-González and Inés Fuentes hold Garantía Juvenil contracts (MIN19/CAT/IBB001 and C19/CAT/IBB001, respectively), Joan Pere Pascual-Díaz holds a predoctoral fellowship (PRE2021-097873) and Sònia Garcia a Ramón y Cajal contract (RYC-2014-16608), all from the Government of Spain.
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Gutiérrez, M.L., Rodríguez-González, R., Pascual-Díaz, J.P., Fuentes, I., Garcia, S. (2023). Online Resources Useful for Plant Cytogenetics and Cytogenomics Research. In: Heitkam, T., Garcia, S. (eds) Plant Cytogenetics and Cytogenomics. Methods in Molecular Biology, vol 2672. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3226-0_33
Download citation
DOI: https://doi.org/10.1007/978-1-0716-3226-0_33
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-3225-3
Online ISBN: 978-1-0716-3226-0
eBook Packages: Springer Protocols