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The search field accepts scientific plant names, i. e. names of genera or Brassicaceae tribes.

Examples:

  • Camelineae — will find information about all member genera of tribe Camelineae.
  • Arabidopsis — will find information about the genus Arabidopsis.

After having typed 3 characters, you'll be provided with suggestions from the database.

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Export diagram or data.

Diagram as SVG
Newick

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Scalable Vector Graphics: a graphics format suitable for import into many graphics programs e. g. Adobe, Corel, Inkscape...
"Comma-separated values": a data format suitable for import into most spreadsheet and database programs. The column separator used here is the semicolon. Character coding is UTF-8.
A format commonly used in phylogenetics to represent a tree structure as nested brackets.
"American standard code for information interchange": the name can be used almost synonymously with "plain text", also including a very limited graphics capability.
A format commonly used to store alignments along with meta-information, e. g. analysis parameters. Used e. g. by PAUP* and MrBayes.
Probably due to its simplicity the most frequently used sequence or alignment format ever designed. Used by a vast majority of bioinformatics programs and packages.
Widely used alignment format. Required as input by many bioinformatics programs. The interleaved version is exported here. Unfortunately very limited meta-information capabilities.
The alignment format originally used by the GCG Wisconsin bioinformatics package (e. g. Pileup). Still widely used as an alignment format.
The format used by Clustal (and some other programs) to store alignments.
Manual

A collapsible phylogenetic diagram of Brassicaceae tribes.

Drag with left mouse button to pan, use the mouse-wheel to zoom in and out. Click on grey-filled nodes to collapse or display them.

Click on tribe names to display corresponding search results.

ITS Phylogenetics Tool

As currently delimited, the Brassicaceae comprise 49 tribes, 321 genera, and 3660 species. Of these, 20 genera and 34 species remain to be assigned to tribes. These figures differ substantially from those estimated five years ago, in which 25 tribes, 338 genera, and 3709 species were recognized. This is summarized in the most recent taxonomic family-wide framework (Al-Shehbaz, 2012).

At the moment, all of our phylogenetic visualizations are based on a ”synoptic diagram of phylogenetic relationships“ presented recently (Franzke et al., 2011). The version 1.1.9 stage of BrassiBase provides the opportunity to run your own “barcode sequence” (internal transcribed spacers 1 and 2 of nuclear ribosomal DNA, including the 5.8 S gene) against the database.

The most likely phylogenetic position will be indicated and will refer to most reliable phylogenetic hypotheses.

The presented results cannot replace any detailed phylogenetic analysis. This tool is intended only to provide first hints for subsequent analyses (e.g. ingroup-outgroup comparisons) or the development of comparative experiments including different species. It should be kept in mind that the presented trees are based on ITS only, and they are actually not constraint in their topology by evidence given from phylogenetic studies. For the pros and cons of ITS in phylogenetic studies please refer to the corresponding BrassiBase introduction (Kiefer et al. 2013).

References
  • Al-Shehbaz IA. 2012. A generic and tribal synopsis of the Brassicaceae (Cruciferae). Taxon 65(5): 931–954
  • Berger SA, Krompass D, Stamatakis A. 2011. Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood Syst Biol 60(3): 291-302.
    The code was adapted for BrassiBase by A. Stamatakis and is available as part of the standard RAxML release.
  • Franzke A, Lysak MA, Al-Shehbaz IA, Koch MA, Mummenhoff K. 2011. Cabbage family affairs: the evolutionary history of Brassicaceae. Trends in Plant Sciences 16: 108-116
  • Junier, T, and Zdobnov, EM. 2010. The Newick Utilities: High-throughput Phylogenetic tree Processing in the UNIX Shell. Bioinformatics 26:1669-1670. [Full text]
  • Katoh and Standley. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 2013 30:772-780
  • Stamatakis A. 2006. RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models”, Bioinformatics 22(21):2688–2690.
  • Comprehensive list of references about phylogenetic concepts within the Brassicaceae
Sequences and Alignments

All sequences used in creating the reference alignments for BrassiBase were taken from GenBank. Alignments were initially created using MUSCLE and edited extensively in a subsequent step. All alignments were checked for plausibility using phylogenetic analyses (using Maximum Likelihood methods). Alignments are available for the different Brassicaceae tribes on the corresponding summary pages (use search box to the right, e.g.).

  • Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2013. GenBank. Nucleic Acids Res 41(Database issue):D36-42
  • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5), 1792-97.

 

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Brassicaceae tribe phylogeny and statistics


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