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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.

Manual

To test your own ITS data against our database, click on the "Analyze own sequence"-button and paste a single ITS query sequence in FASTA format into the search field.

Best results are obtained with trimmed sequences (usually starting with TCG) similar to the example provided here.

Orientation of the sequence will be determined and corrected accordingly.

  1 tcgatacctg tccaaaacag aacaacccgc gaacgaacga tcatcactct cggttggccg
 61 gtttcttagt tgatcccgag cctgccgatt ccgtggttcc gcgtacttgt cctcatgggt
121 catttgcgta gctcccggat atcacaaaac cccggcacga aaagtgtcaa ggaacatgca
181 ataaaacagc ctgcttttgc tgccccggag acggcgtgtg cgcttaagct gtgctgcaat
241 ataaagtcta taacgactct cggcaacgga tatcttggct ctcgcatcga tgaagaacgt
301 agcgaaatgc gatacttggt gtgaattgca gaatcccgtg aaccatcgag tctttgaacg
361 caagttgcgc cccaagcctt ctggctgagg gcacgtctgc ctgggtgtca caaatcgtcg
421 tccccatcct ttgcggatac cggacggaag ctggtctccc gtgtgttacc gcacgcggtt
481 ggcctaaatc tgagctgagg acgccttgga gcgtctcgac atgcggtggt gaaacaaagc
541 ctcgtcattt tgtcggtcgc tcctgtccaa atgctctcga tgacccaaag tctttaac
The nuclear encoded "internal transcribed spacer" inbetween rRNA genes. Usually a block consisting of the 3' part of "internal transcribed spacer 1", the 5.8S ribosomal RNA gene and the 5'-part of the "internal transcribed spacer 2" are used as a phylogenetic marker.

The results of the EPA algorithm are summarized here:

Your query sequence is tested against each of the tribe reference trees, using the EPA mode of RAxML. A classification value is obtained for each attempted placement and normaized as a percentage, with the best value set to 100%. The results are evaluated and can be displayed as a bar plot.

The resulting tree can be displayed in the context of the synthetic family-wide tribe tree of the Brassicaceae, with the query sequence placed at the most likely position in the relevant tribe. If more than one position is to be considered, likelihoods are color-coded (Orange is best.).

"Evolutionary placement algorithm"
See Stamatakis (2006) and Berger et al. (2011).

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

Collapsible tree of Brassicaceae tribes

Collapsible tree of Brassicaceae tribes

Number of genera per tribe

Number of genera per tribe

Number of species per tribe

Number of species per tribe

Percentage of synonyms in genera of a tribe

Percentage of synonyms in genera of a tribe

Standard phylogenetic diagram

Standard phylogenetic diagram

Radial graph of Brassicaceae tribes

Radial graph of Brassicaceae tribes

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