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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 52 tribes, 341 genera, and 3977 species. Of these, 11 genera and 19 species remain to be assigned to tribes. These figures differ substantially from those estimated five years ago, in which 49 tribes, 321 genera, and 3660 species were recognized, of which 20 genera and 34 species were lacking tribal assignment (Al-Shehbaz, 2012).

BrassiBase's phylogenetic visualizations are based on a ”synoptic diagram” of phylogenetic relationships“ presented by Franzke et al. (2011) and continuously updated with most recent findings (e.g. Huang et al., 2016).

BrassiBase provides the opportunity to run your own “ITS barcode sequence” (internal transcribed spacers 1 and 2 of nuclear ribosomal DNA, including the 5.8 S gene) as query against the database.

A putative phylogenetic position will be indicated. However, the presented results cannot replace any detailed phylogenetic analysis! This tool is intended only to provide reference points for subsequent own analyses. It should be kept in mind that the presented trees are based on ITS sequences only, and they are also not constraint in their topology by evidence given from other phylogenetic studies. For the pros and cons of ITS sequences as marker in phylogenetic studies please refer to Kiefer et al. (2014).

References
  • Beilstein, MA, Nagalingum, N, Clements, MD, Manchester, SR, Mathews, S. 2010. Dated molecular phylogenies indicate a Miocene origin for Arabidopsis. Proceedings of the National Academy of Sciences, U.S.A. 107(43): 18724 – 18728.
  • Al-Shehbaz, IA. 2012. A generic and tribal synopsis of the Brassicaceae (Cruciferae). Taxon 61(5): 931 – 954.
  • Franzke A, Lysak MA, Al-Shehbaz IA, Koch MA, Mummenhoff K. 2011. Cabbage family affairs: the evolutionary history of Brassicaceae. Trends Plant Sci. 16(2): 108 – 116. doi: 10.1016/j.tplants.2010.11.005
  • Huang CH, Sun R, Zeng YH, Zhang N, Cai L, Zhang Q, Koch MA, Al-Shehbaz IA, Edger PP, Pires JC, Tan DY, Zhong Y, Ma H. 2016. Resolution of Brassicaceae phylogeny using nuclear genes uncovers nested radiations and supports convergent morphological evolution. Molecular Biology and Evolution 33(2): 394 – 412. doi: 10.1093/molbev/msv226.
  • Kiefer M, Schmickl R, German DA, Lysak M, Al-Shehbaz IA, Franzke A, Mummenhoff K, Stamatakis A, Koch MA. 2014. BrassiBase: Introdcution to a novel database on Brassicaceae evolution. Plant Cell Physiol., 55(1): e3, doi:10.1093/pcp/pct158.
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.
  • Löytynoja A, Goldman N (2010) webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics 11:579
  • 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.

 

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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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