Plant rDNA database: ribosomal DNA loci information goes online
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Number, position and structure of the 5S and 18S-5.8S-26S ribosomal DNA (rDNA) loci are important species characteristics. In recent decades, we have witnessed accumulation of rDNA data, and there is a need to compile, store and analyse this information, and to make it accessible to a broader scientific community. An online resource, accessible at www.plantrdnadatabase.com, has been developed to accomplish these goals. Current knowledge regarding chromosomal rDNA sites is provided for more than 1,000 plant species (including more than 1,400 different accessions). The data comes from fluorescent in situ hybridisation experiments (FISH) from more than 300 publications. Additional information is also displayed, such as ploidy level, mutual arrangement of rRNA genes, genome size and life cycle. The webpage is intuitive and user-friendly, including different search options, and currently holds information published (or in press) up until January 2011; frequent updates are planned. We expect this database to be used for data-mining, analysing rDNAs from different angles, unit organisation, distribution, evolution and linkage of rDNA patterns with phylogenetic relationships.
KeywordsPloidy Level rDNA Locus rDNA Site Query Form Angiosperm Phylogeny
The authors thank researchers that contributed and continue contributing to molecular cytogenetic knowledge in plants. The comments and suggestions on the manuscript of Professor Joan Vallès and Dr. Oriane Hidalgo (Universitat de Barcelona) have also been much appreciated. Similarly, authors thank Francisco Gálvez (@iguannaweb and @bioscripts) for implementing and designing the database within the internet environment. Librarians helping with the literature compilation, Karina Barros and Isidora Manso (Institut Botànic de Barcelona) and Hana Hudcová (Institute of Biophysics) are also thanked. This work has been supported by the Spanish and Catalan governments (projects CGL2010-22234-C02-01 and 02/BOS, and project 2009SGR00439, respectively) and the Czech Science Foundation (P501-10-0208; P501/12/G090). SG benefited from a Beatriu de Pinós postdoctoral contract with the support of the Comissionat per a Universitats i Recerca (CUR) del Departament d’Innovació, Universitats i Empresa de la Generalitat de Catalunya (Catalan government). The authors declare that they have no conflict of interest.
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