BrassiBase is a developing online-accessible knowledge and database system of cross-referenced information and resources on Brassicaceae (Cruciferae) taxonomy, systematics and evolution, including chromosome numbers, traits and characters, germplasm resources, and accurate enumeration of all species, genera and tribes. Biological, molecular and evolutionary knowledge is exponentially increasing in the mustard family. However, because of the complex and overwhelming biological diversity of the family, it is difficult to assess research results within a larger evolutionary framework. Many species have been proven to be remarkable study objects but are rarely available. Biological material and resources, either collected directly in the wild or held in germplasm collections, have often been taxonomically misidentified; and only very rarely has the material been further characterized and documented. There is also no comprehensive survey of character and trait distribution among Brassicaceae lineages, though family-wide phylogenies are meanwhile available. In order to close these gaps, we will make accessible to the scientific community the research data focusing on adaptive characters and their evolution in the Brassicaceae. In this context, we will also provide a comprehensive documentation of the taxonomy and systematics of the entire family. This will include a database with all relevant taxonomic, systematic and phylogenetic literature, a comprehensive data collection of characters and traits, a DNA-based identification tool for genera and species, electronic interactive keys for the identification of genera and species, and a setup of a carefully selected and documented germplasm collection representing main lineages of the family. BrassiBase has been launched within the framework of the DFG (German Research Foundation) priority programme SPP 1529 “Adaptomics − Evolutionary plant solutions to ecological challenges/Molecular mechanisms underlying adaptive traits in the Brassicaceae s.l.”.
The first release of the database (version 1.1, june 2012) has been announced in a Special Issue of Taxon (Vol. 61, 2012), dedicated to Brassicaceae and Brassicales systematics and taxonomy. This earlier version of the database introduced the underlying taxonomic framework.
The second release (versions 1.1.9, August 2013) builds on the taxonomic content of version 1.1, incorporated taxonomic information into a “taxonomy tool” and has implemented now two major new features: A “Phylogenetics Tool” and a “Cytogenetics Tool”. We kindly ask to cite the paper(s) given in the references section below whenever you extract respective information or obtain material.
- Koch MA, Kiefer M, German DA, Al-Shehbaz IA, Franzke A, Mummenhoff K, Schmickl R. 2012. BrassiBase: Tools and biological resources to study characters and traits in the Brassicaceae – version 1.1 TAXON 61(5): 1001-1009.
- 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.
Usually web pages may be freely distributed and copied. However, it is requested that in any subsequent use of this work, BrassiBase be given appropriate acknowledgment and cited as:
Koch MA, Kiefer M, German DA, Al-Shehbaz IA, Franzke A, Mummenhoff K, Schmickl R. 2012. BrassiBase: Tools and biological resources to study characters and traits in the Brassicaceae – version 1.1 TAXON 61(5): 1001-1009.
Kiefer M, Schmickl R, German DA, Lysak M, Al-Shehbaz IA, Franzke A, Mummenhoff K, Stamatakis A, Koch MA. 2014. BrassiBase: Introduction to a novel database on Brassicaceae evolution. Plant Cell Physiol., 55(1): e3, doi:10.1093/pcp/pct158.
NOTE: BrassiBase provides also plant material resources for registered users. Please consider the DESIDERATA document. Requests will be checked carefully and you will get a response via eMAIL about charges and availability of respective material.
Databases of molecular and other data on the BrassiBase Web site include such examples as nucleotide sequences (linked with GenBank), cytogenetic data or morphological characters. They are designed to provide and encourage access within the scientific community to sources of current and comprehensive information. Therefore, BrassiBase itself places no restrictions on the use or distribution of the data contained therein. Nor do we accept data when the submitter has requested restrictions on reuse or redistribution. However, some submitters of the original data (or the country of origin of such data) may claim patent, copyright, or other intellectual property rights in all or a portion of the data (that has been submitted). BrassiBase is not in a position to assess the validity of such claims and since there is no transfer or rights from submitters to BrassiBase, BrassiBase has no rights to transfer to a third party. Therefore, BrassiBase cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in the databases.
Liability: For any information and data BrassiBase does not warrant or assume any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed.
Endorsement: BrassiBase does not endorse or recommend any commercial products, processes, or services.
This site is maintained by Heidelberg University and is protected by various copyrights of Heidelberg University. Violations and misuse are subject to criminal prosecution in a federal court. For site security purposes, as well as to ensure that this service remains available to all users, we may use software programs to monitor traffic and to identify unauthorized attempts to upload or change information or otherwise cause damage. In the event of authorized law enforcement investigations and pursuant to any required legal process, information from these sources may be used to help identify an individual.
Privacy: We will not sell, distribute or lease your personal information (required for registration purposes only) in any way unless we have your permission or are required by law.
Heidelberg, Germany, November 12, 2012.
Agreement on the supply of living plant material1 for non-commercial purposes leaving the International Plant Exchange Network
Against the background of the provisions and decisions of the Convention on Biological Diversity of 1992 (CBD) and in particular those on access to genetic resources and benefit-sharing, the garden is dedicated to promoting the conservation, sustainable use, and research of biological diversity. The University Heidelberg Botanic Garden therefore expects its part- ners in acquiring, maintaining, and transferring plant material to always act in accordance with the CBD and the Convention on the International Trade in Endangered Species (CITES).
The responsibility for legal handling of the plant material passes on to the recipient upon receipt of the material. The re- quested plant material will be supplied to the recipient only on the following conditions:
- Based on this agreement, the plant material is supplied only for non-commercial use such as scientific study and educational purposes as well as environmental protection. Should the recipient at a later date intend a commercial use or a transfer for commercial use, the country of origin‘s prior informed consent (PIC) must be obtained in writing before the material is used or transferred. The recipient is responsible for ensuring an equitable sharing of benefits.
- On receiving the plant material, the recipient endeavours to document the received plant material, its origin (country of origin, first receiving garden, „donor“ of the plant material, year of collection) as well as the acquisition and transfer conditions in a comprehensible manner.
- In the event that scientific publications are produced based on the supplied plant material, the recipient is ob- liged to indicate the origin of the material (the supplying garden and if known the country of origin) and to send these publications to the garden and to the country of origin without request.
- On request, the garden will forward relevant information on the transfer of the plant material to the body char- ged with implementing the CBD2.
- The recipient may transfer the received plant material to third parties only under these terms and conditions and must document the transfer in a suitable manner (e.g. by using the documentation form, such as provided in Annex 1.3).
Our seed packets will be limited within Europe to 100 g, outside Europe to 50 g.
Non IPEN members have to return the agreement on the previous page signed by an entitled repre- sentative of their institution before we can provide seeds to them!
I accept the above conditions.
1 According to the CBD “genetic resources” means genetic material of actual or potential value. This definition covers both living and not living material. The Code of Conduct and the IPEN covers only the exchange of living plant material (living plants or parts of plants, diaspores) thus falling in the definition of genetic resources.
2 ideally, the national focal point in the garden‘s home country
The newest stable versions of the following software were used on this site:
- Rice,P. Longden,I. and Bleasby,A. 2000. EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics 16(6):276-277
- IIP High resolution image viewer
- D3 - JS library for building data-driven documents
- Katoh, Standley. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30:772-780
- MySQL - DBMS
- Junier, T. and Zdobnov, E.M. 2010. The Newick Utilities: High-throughput Phylogenetic tree Processing in the UNIX Shell. Bioinformatics 26:1669-1670.
- PHP - server-side scripting language
- Prettyphoto - lightbox-like image viewer
- Stamatakis, A. 2006. RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models”, Bioinformatics 22(21):2688–2690.
- Berger, S. A., 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.