An introduction to Kew's DNA and tissue collection
The Lab-based Collections team at Kew describe the DNA and Tissue Collection and its relationship to the wider scientific community.
Lab-based Collections team
The Lab-based Collections team, located in the Jodrell Laboratory at Kew, has responsibility for the DNA and Tissue Collection and associated database, the genome size database, and the microscope slide collection, digital collection and associated databases. Molecular and tissue banks are collections in the traditional sense, although often regarded as being different since they have specific technologies associated with preparation, storage and maintenance of the specimens and different data requirements. The DNA and Tissue Collection was established in 1992 at the same time as the Molecular Systematics Laboratory in the Jodrell Laboratory building. In 2010, we began to incorporate silica-dried tissue into the collection to allow for more flexibility of future use and reduce time between receiving and accessioning of material.
DNA and tissue collection
The DNA and tissue collection contains nearly 50,000 specimens as tissue and/or extracted DNA, which represents over 37,000 species (8-14% of the total number), 7,000 genera (~50% of the total number) and nearly all the families of angiosperms. There is an associated collection of population level samples held separately. The Collection has reciprocal agreements with the South African National Biodiversity Institute (SANBI) and the University of Johannesburg.
Best practice
Developing and following improved protocols ensures a longer life expectancy for DNA and tissue collections. To help disseminate best practice, in 2006 Kew published DNA and Tissue Banking for Biodiversity and Conservation: Theory, Practice and Uses (Savolainen et al., 2006). More recently, information on best practice has been provided online within Kew.
Examples of best practice include:
- Storage of DNA at -80°C rather than -20°C to reduce the activity of any nucleases and increase sample longevity (some are over 30 years old, predating the official establishment of the DNA and Tissue Collection at Kew).
- Maintaining quality of the aliquots through a standardised purification technique, though some material is particularly recalcitrant such as Bromeliaceae and Cactaceae, either because of mechanical structure or secondary metabolites.
- 'Preventative conservation' to prevent damage occurring, for example by storing material in a suitable and secure environment or packing it in an appropriate way using archival quality material. 'Archival' or 'conservation' quality refers to materials that are physically durable and chemically stable. Several types of plastics and fabrics fall into this category. Such items are said to be 'inert' and do not release degradation products that can be harmful to collections. Using this type of material ensures the safety and stability of collections for long-term storage.
However, specimens without data are useless. This does not just include taxonomic information such as the family, genus and species, but also the author, the collector including date, number and location, the source of the material and quality of the extract. This information also contains links to the herbarium specimen(s), as well as to other material in Kew’s collections. The collector information allows the specimen to be tracked from its source to our collection, and then to GenBank, for example.
The importance of networks
The creation of the DNA Bank Network in 2009 enabled us to harmonise our database structures with other institutions, thus making the collection more widely available. As part of this harmonisation of data a minimum set of field values is required before accepting new samples for accession. There will be a further blog entry giving more details of the accession process.
The DNA Bank Network was folded into the Global Genome Biodiversity Network (GGBN) in 2013. GGBN, created in 2011, aims to ensure consistent quality and improve best practice, as well as harmonise the exchange of data and material between institutions. There have been eight new members since Kew joined officially in June 2014, when Kew co-hosted the first international conference for GGBN.
The aim of GGBN is to provide 'genome quality samples from across the Tree of Life' through a process in which the data is administered and curated locally but shared with the world through the GGBN Data Portal. Basically, it provides biorepositories with standardised methods for making genomic collections widely available, as well as community standards and best practices for collection and data management.
In the last few decades, biodiversity databases and DNA databases have not been well integrated. Biodiversity databases often lack the increasingly important DNA information and DNA databases do not offer accuracy of taxonomic identification and voucher information or any specimen documentation. GGBN aims to correct this and it is important that Kew plays a role in this organisation. Well-curated molecular collections at Kew form an essential foundation for our 2020 Strategic Output constructing the 'Plant and Fungal Trees of Life', and will be important long beyond this.
Reference
Savolainen, S., Powell, M. P. P., Davis, K., Reeves, G. & Corthals, A. (2006). DNA and Tissue Banking for Biodiversity and Conservation: Theory, Practice and Uses. Kew Publishing, Kew, in association with IUCN. Available to buy