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GSAD and Plant rDNA database: two open platforms with plant cytogenetic information

25 July 2014 Universidad de Barcelona

Having cytogenetic information about plants is basic to classify species and promote new studies on agriculture and crop improvement. This is the main objective of two online platforms that collect chromosome information and provide it to the scientific community. The platforms have been developed by the EtnoBioFic Research Group, composed by experts from the Botany Laboratory of the Faculty of Pharmacy of the University of Barcelona (affiliated with CSIC), the Botanical Institute of Barcelona (IBB-CSIC-ICUB), and Paris-Sud University (France).

Plant rDNA Database is the first database that collects information about the position of genes that codify plant ribosomal DNA (DNAr). The website Genome Size in Asteraceae Database (GSAD) is an exhaustive catalogue of genome size data for one of the largest and economically important Angiosperm families: Asteraceae.

Genes that codify ribosomal DNA

Name, position and organization of ribosomal DNA genes (5S and 18S-5.8S-26S) in chromosomes are characteristic of a certain species, genus or group of plants. Therefore, this information is completely useful for basic research, genotype study, evolutionary biology and crop improving programmes. “By consulting this website, researchers can know if there is any published result about any taxonomic group and access to a catalogue that enables to analyse and compare data” explains Sònia Garcia, researcher from the Botany Laboratory of the Faculty of Pharmacy and member of the EtnoBioFic Research Group.

The database about ribosomal DNA was obtained from more than 600 scientific papers about plant molecular cytogenetics. “More than 50% of papers indexed at the database have been published for the last ten years; that proves that there is an increasing interest in this information and a need for compilation”, affirms Sònia Garcia. “To date —adds the researcher—, it was so difficult to find these data as they were scattered in many publications”. The data base includes information about DNAr gene localization of angiosperms, gymnosperms, bryophytes and pteridophytes.

The first database about the genome size of a plant family

The portal GSAD includes data about the genome size of about 1,200 Asteraceae species, one of the largest families of angiosperms, collected from 133 scientific papers. The family Asteraceae is worldwide distributed, except in the Antarctica. It includes around 25,000 species; some of them are economically important, for instance: sunflowers, lettuces, artichokes and chrysanthemums. It is the first database that gathers this type of information about this plant family.

Evolutionary genetics comparative studies with living beings use genome size and the total amount of nuclear DNA to evaluate the cost of sequencing programmes. “GSAD provides researcher with direct information, so they do not have to look for it in numerous publications”, points out Garcia. “Therefore, double efforts are avoided, knowledge gaps are more easily detected and the aspects about Asteraceae genome studies that arouse more interest are identified”, she concludes.

These two tools provided to the international scientific community emerge from the research developed by EtnoBioFic Research Group, led by Professor Joan Vallès, from the Department of Natural Products, Plant Biology and Edaphology of UB and the Botany Laboratory of the Faculty of Pharmacy, and by Teresa Garnatje, researcher at the Botanical Institute of Barcelona (IBB-CSIC-ICUB). The group is mainly interested in understanding the evolutionary history of different plant groups as well as their genome evolution and the processes involved in it. Besides cytogenetic studies, the group also develops studies focused on phylogenetics and phylogeography. Its research lines are also based on the study of the history of botany and ethnobotanical research; in other words, it develops studies about the relationships between people and plants and also on the traditional knowledge about plants —particularly in the Catalan language territories. They are mostly conducting ethnofloristic works, with emphasis in medicinal and food plant uses.

Platforms websites:

Plant rDNA Database

Genome Size in Asteraceae Database (GSAD)

Attached files

  • The online platforms collect chromosome information and provide it to the scientific community.

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