UNLABELLED: The Plant rDNA database (www.plantrdnadatabase.com) is an open access online resource providing detailed information on numbers, structures and positions of 5S and 18S-5.8S-26S (35S) ribosomal DNA loci. The data have been obtained from >600 publications on plant molecular cytogenetics, mostly based on fluorescent in situ hybridization (FISH). This edition of the database contains information on 1609 species derived from 2839 records, which means an expansion of 55.76 and 94.45%, respectively. It holds the data for angiosperms, gymnosperms, bryophytes and pteridophytes available as of June 2013. Information from publications reporting data for a single rDNA (either 5S or 35S alone) and annotation regarding transcriptional activity of 35S loci now appears in the database. Preliminary analyses suggest greater variability in the number of rDNA loci in gymnosperms than in angiosperms. New applications provide ideograms of the species showing the positions of rDNA loci as well as a visual representation of their genome sizes. We have also introduced other features to boost the usability of the Web interface, such as an application for convenient data export and a new section with rDNA-FISH-related information (mostly detailing protocols and reagents). In addition, we upgraded and/or proofread tabs and links and modified the website for a more dynamic appearance. This manuscript provides a synopsis of these changes and developments. DATABASE URL: http://www.plantrdnadatabase.com.

Laboratori de Botànica Unitat associada CSIC Facultat de Farmàcia Universitat de Barcelona Barcelona 08028 Catalonia Spain BioScripts Centro de Investigación y Desarrollo de Recursos Científicos Sevilla 41012 Andalusia Spain Institute of Biophysics Academy of Sciences of the Czech Republic Brno CZ 612 65 Czech Republic and Institut Botànic de Barcelona Barcelona 08038 Catalonia Spain

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Lafontaine D.L., Tollervey D. (2001) The function and synthesis of ribosomes. Nat. Rev. Mol. Cell Biol., 2, 514–520 PubMed

Garcia S., Lim K.Y., Chester M., et al. (2009) Linkage of 35S and 5S rRNA genes in Artemisia (family Asteraceae): first evidence from angiosperms. Chromosoma, 118, 85–97 PubMed

Garcia S., Panero J.L., Siroky J., Kovarik A. (2010) Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family. BMC Plant Biol., 10, 176. PubMed PMC

Mazzella C., Rodríguez M., Vaio M., et al. (2010) Karyological Features of Achyrocline (Asteraceae, Gnaphalieae): stable karyotypes, low DNA content variation and linkage of rRNA genes. Cytogenet. Genome Res., 128, 169–176 PubMed

Galián J.A., Rosato M., Rosselló J.A. (2012) Early evolutionary colocalization of the nuclear ribosomal 5S and 45S gene families in seed plants: evidence from the living fossil gymnosperm Ginkgo biloba. Heredity (Edinb)., 108, 640–646 PubMed PMC

Garcia S., Kovařík A. (2013) Dancing together and separate again: gymnosperms exhibit frequent changes of fundamental 5S and 35S rRNA gene (rDNA) organisation. Heredity (Edinb)., 111, 23–33 PubMed PMC

Sone T., Fujisawa M., Takenaka M., et al. (1999) Bryophyte 5S rDNA was inserted into 45S rDNA repeat units after the divergence from higher land plants. Plant Mol. Biol., 41, 679–685 PubMed

Wicke S., Costa A., Muñoz J., Quandt D. (2011) Restless 5S: the re-arrangement(s) and evolution of the nuclear ribosomal DNA in land plants. Mol. Phylogenet. Evol., 61, 321–332 PubMed

Liu Y., Forrest L.L., Bainard J.D., et al. (2013) Organellar genome, nuclear ribosomal DNA repeat unit, and microsatellites isolated from a small-scale of 454 GS FLX sequencing on two mosses. Mol. Phylogenet. Evol., 66, 1089–1094 PubMed

Gall J.G., Pardue M.L. (1969) Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc. Natl Acad. Sci. USA, 63, 378–383 PubMed PMC

John H.A., Birnstiel M.L., Jones K.W. (1969) RNA-DNA hybrids at the cytological level. Nature, 223, 582–587 PubMed

Alvarez I., Wendel J.F. (2003) Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol., 29, 417–434 PubMed

Nieto Feliner G., Rosselló J.A. (2007) Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol. Phylogenet. Evol., 44, 911–919 PubMed

Ribeiro T., Barão A., Viegas W., Morais-Cecíli L. (2008) Molecular cytogenetics of forest trees. Cytogenet. Genome Res., 120, 220–227 PubMed

Malinska H., Tate J.A., Matyasek R., et al. (2010) Similar patterns of rDNA evolution in synthetic and recently formed natural populations of Tragopogon (Asteraceae) allotetraploids. BMC Evol. Biol., 10, 291. PubMed PMC

Heslop-Harrison J.S.P., Schwarzacher T. (2011) Organisation of the plant genome in chromosomes. Plant J., 66, 18–33 PubMed

Garcia S., Garnatje T., Hidalgo O., et al. (2007) Extensive ribosomal DNA (18S-5.8S-26S and 5S) colocalization in the North American endemic sagebrushes (subgenus Tridentatae, Artemisia, Asteraceae) revealed by FISH. Plant Syst. Evol., 267, 79–92

Hamon P., Siljak-Yakovlev S., Srisuwan S., et al. (2009) Physical mapping of rDNA and heterochromatin in chromosomes of 16 Coffea species: a revised view of species differentiation. Chromosome Res., 17, 291–304 PubMed

Garnatje T., Hidalgo O., Vitales D., et al. (2012) Swarm of terminal 35S in Cheirolophus (Asteraceae, Centaureinae). Genome, 55, 529–535 PubMed

Srisuwan S., Sihachakr D., Siljak-Yakovlev S. (2006) The origin and evolution of sweet potato (Ipomoea batatas Lam.) and its wild relatives through the cytogenetic approaches. Plant Sci., 171, 424–433 PubMed

Robledo G., Lavia G.I., Seijo G. (2010) Genome re-assignment of Arachis trinitensis (Sect. Arachis, Leguminosae) and its implications for the genetic origin of cultivated peanut. Genet. Mol. Biol., 33, 714–718 PubMed PMC

Gupta P.K., Kulwal P.L., Rustgi S. (2005) Wheat cytogenetics in the genomics era and its relevance to breeding. Cytogenet. Genome Res., 109, 315–327 PubMed

Gan Y., Liu F., Chen D., et al. (2013) Chromosomal locations of 5S and 45S rDNA in gossypium genus and its phylogenetic implications revealed by FISH. PLoS One, 8, e68207. PubMed PMC

Garcia S., Garnatje T., Kovařík A. (2012) Plant rDNA database: ribosomal DNA loci information goes online. Chromosoma, 121, 389–394 PubMed

Roa F., Guerra M. (2012) Distribution of 45S rDNA sites in chromosomes of plants: structural and evolutionary implications. BMC Evol. Biol., 12, 225. PubMed PMC

Vallès J., Canela M.Á., Garcia S., et al. (2013) Genome size variation and evolution in the family Asteraceae. Caryologia, 66, 221–235

Peruzzi L., Caparelli K.F., Bedini G. (2014) A new index for the quantification of chromosome number variation: an application to selected animal and plant groups. J. Theor. Biol., 353, 55–60 PubMed

Matyášek R., Renny-Byfield S., Fulneček J., et al. (2012) Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids. BMC Genomics, 13, 722. PubMed PMC

Bou Dagher-Kharrat M., Abdel-Samad N., Douaihy B., et al. (2013) Nuclear DNA C-values for biodiversity screening: case of the Lebanese flora. Plant Biosyst., 147, 1228–1237

Garcia S., Hidalgo O., Jakovljević I., et al. (2013) New data on genome size in 128 Asteraceae species and subspecies, with first assessments for 40 genera, 3 tribes and 2 subfamilies. Plant Biosyst., 147, 1219–1227

Sharma S.K., Mehra P., Kumari J., et al. (2012) Physical localization and probable transcriptional activity of 18S-5.8S-26S rRNA gene loci in some Asiatic Cymbidiums (Orchidaceae) from north-east India. Gene, 499, 362–366 PubMed

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