Select output fields

Family Genus Specific epithet Specific authority Infraspecific epithet Infraspecific authority
2C mean1(pg) 2C mean1(mbp) 2C range1 pg Life cycle
Other specifications (cultivar, population, strain, etc.) Original reference Journal Year
Telomere type Telomere type based in genome sequenced hybrid
Number of 5S signals Range of 5S signals Position2 of 5S signals (5S P)
Number of 35S3 signals Range of 35S signals Position2 of 35S signals (35S P) Arrangement
Total number of rDNA signals (5S+35S) (Total) Number of chromosomes with both 5S and 35S signals (SC)
Number of chromosomes with both 5S and 35S in the same arm (SA) Number of chromosomes with co-localized 5S and 35S signals (Coloc.)

Write conditions

Family   Genus   Specific epithet
Chromosome number from: -   Ploidy level from: -

Select filters

Land plants group
Angiosperm group
Sort by
Show
 

For help with searching and querying the database, go to HELP

1 1C genome size and n chromosome number for bryophytes.
2 Position refers to that of most chromosomes in the species and can be either interstitial (i), (peri-)centromeric (c) and (sub-)terminal or satellite (t).
3 35S=45S=18S-5.8S-26S rDNA

New applications and improvements

New information on sequenced plant genomesNEW

Information on plant species whose genome has been fully sequenced. The page allows browsing publications of plant genomes sequenced by family. Every species is linked with the corresponding publication presenting the sequenced genome.

New information on telomere composition NEW

Data on telomere motives has been extracted from the same source publication of rDNA-FISH in the cases where this information was included. Additionally, other general sources on telomere composition have been used. Some assumptions have been made to organize the data. When a given telomere sequence was confirmed for several species in a genus, this has been considered that any other species from the same genus would present the same telomere sequence. We also state that a given species may have “probably” or “possibly” a given telomere type when there is evidence at the family or order level, respectively. Where there is no evidence above the taxonomic level order the status is “unknown”. In few cases (particularly in species of order Asparagales) presence of more than one telomere signal may be due cross-hybridisation between telomere probes.

Visual 2C (Genome size representation tool)

If genome size data is available for a given species it appears represented as a blue bar whose size is directly proportional to 2C value. A red line in the graph will indicate the mean genome size for the genus to which the species belongs. This provides a comparison between genome sizes of related species at a glance. See an example here:

NOR

In this new section we provide information about the transcriptional activity of the 35S loci, checking the presence of secondary constrictions, satellites or NORs (nucleolar organiser regions, the hallmarks of transcription activity of residing rRNA genes) whenever the publication stated this, i.e. if experiments based on silver nitrate staining had been done, or when the satellites or secondary constrictions were evident in the chromosome spreads. Therefore, an “x” mark in the NOR box indicates that the paper contains evidence of transcriptional activity, but it does not state how many rDNA loci are actually active.

K (Karyotype tool)

This application offers a visual representation of the karyotypes from the data provided in the database, without the need of consulting the source application. The karyotype will appear in a pop-up window when clicking the chromosome symbol in the K box. These are the basic chromosome types:

All the other possible chromosome types and signal combinations can be consulted here.

Examples on how the karyotype tool works can be found here.

NOTES

Due to the complexity of translating data into pictures, some premises and assumptions have been considered to simplify the application:

Help with searching

The plantrDNAdatabase has been organized so that you can make either a Simple or an Advanced Search.

Simple Search

The Simple Search is basic and aimed to obtain easily fast results. You only have to type the name of the family, genus, species or even specific epithet of your interest in the Search Box and the results will automatically be displayed.

By default, the information that will appear in this type of search, besides chromosome number and ploidy level, is: number and position of 5S and 35S signals, presence of a linked 5S-35S arrangement and ID number of the source publication (Ref.) whose complete name will appear by moving your cursor over it. You can also obtain, by clicking the options below the search box, the authority of the plant name and the 2C genome size (in pg). The total number of records for your search is shown at the right top of the results. A given Simple Search can be later refined by clicking in the Advanced Search and selecting any of the available options.

NOTE: With some of the type genera of families, those that have left their complete name for the name of the family, when typing their names, information on data of the full family will appear. This will only happen in these cases:

This can be avoided by clicking once the space bar after the name of the genus.

Advanced Search

The Advanced Search allows different options to refine your search. You can access from any tab of the webpage (excepting ‘News’) by clicking the word ‘Advanced’ highlighted in bold. Then a query form will appear.

In the first section of the query form you can select, by clicking in the corresponding box, all the output fields that you want in your search record. There are some options ticked by default (explained at the Simple Search).

Therefore, if you want additional information, like life cycle or number of chromosomes with co-localized 5S and 35S signals, for example, then click in the appropriate boxes and these data will be shown if available:

The second section allows you writing conditions, where it can be chosen that only results for a given family, genus or species are shown. Also, you can choose that your search only presents results for (a) given ploidy level(s) and chromosome number(s).

For example, you can ask the database to give you rDNA data for diploid to tetraploid Brassicaceae by entering ‘Brassicaceae’ in the family box and entering ‘2’ and ‘4’ in the ploidy level boxes:

NOTE: Numbers have to be written in arabic numerals.

Finally, the third section enables to apply filters to your search either by land plant group, division, angiosperm group (of course only applicable to angiosperms) and life cycle (see figure below). There is a last option that permits to sort the results by family, genus, species, genome size, chromosome number or ploidy level; as for the previous filters, the appropriate choice has to be selected from the drop-down box under the option 'Sort by' at the bottom of the query form. The results of searches are automatically sorted by alphabetical order.

Once the different options are chosen, click the ‘Search’ button at the right bottom of the query form. To perform subsequent advanced searches you can refresh the query form by clicking the ‘Delete’ button at the right top of the form.

NOTES:

FAMILY NOMENCLATURE

The standard/APG (Angiosperm Phylogeny Group) family names have been followed in the webpage, even in the cases that the original publications used the traditional, non-standard family names. Also there are some recent phylogenetic changes that have been considered, which merge some families into others. Here you will find a correspondence:

POSITION OF SIGNALS IN CHROMOSOMES

The positions of rDNA signals in chromosomes have been reduced to only three different options for the sake of clarity. These are:

Only the most abundant position has been selected to characterize each kind of rDNA loci, although in some species there may be more than one possible location. The source publication should always be consulted in case of doubt.

Once the Advanced Search is started, you cannot use the Simple Search unless you refresh your query form (by clicking the button ‘Delete’) or your session.
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