Sequencing genomes with the Museum’s Frozen Collection | Digital Collections Programme

1) museum species

To commemorate the Wellcome Trust Sanger Institute turning 25 in 2018, the Institute and its collaborators are sequencing 25 new genomes of species that reside in the UK and represent the richness of species in this country. 

Sequencing the genomes would be a valuable tool for the scientists who work with these species to help understand how the organism relates to close evolutionary relatives. Information from genomes can also help us understand the world’s current big questions such as crop security, climate change and disease. For example David Notton has nominated the solitary Red Mason bee Osmia bicornis (from the Megachile family) because out of 276 species of bee in the UK, there is only one honey bee and just a few bumblebees, whereas the great majority of native bees are other types of bees, including Mining, Leafcutter and Mason bees. Existing genomes are biased towards social bees. There is currently no genome representing the family Megachilidae, so it is really important to have this family of bees represented by a genome.

In August 2017, there was an open call to scientists around the country to propose and champion the UK species that they wanted to be sequenced as part of this initiative. From this call, twenty species have already been decided, and the remaining five will be voted for by the public and school children on the ‘I’m a Scientist, Get Me Out of Here’ platform between the 6 November – 8 December 2017.

Amongst the twenty decided species, three Museum specimens have already been sourced as materials from which the genomes will definitely be sequenced by Sanger during 2018. It’s possible that the Museum will be asked to provide further specimens for this project. There are two reasons why the Museum could be asked for more material. Firstly, Museum Scientists have seven species in the public vote, from which we are really hoping that at least one of these will make it through to sequencing. To find out more about these species and how to vote for them visit our news item about the vote. The second reason is that we have a fantastic resource in the Molecular Collection at the Museum that is able to preserve some of our newly collected specimens in ultra-cold storage at -80˚C on a long term basis. -80˚C halts cellular degradation, preserves the genetic resources, and keeps the specimens fit for the purpose of further research. It’s possible that due to this resource, we may be asked for more specimen samples throughout this project.

Jacqueline Mackenzie-Dodds, Molecular and Frozen Collections Manager gave us a sneak peek into this collection.

This collection of frozen specimens and tissue samples holds valuable genetic resources for future molecular research into organisms from across the tree of life. Together with similar frozen collections in natural history museums and other institutions worldwide, these collections complement each other to represent global genetic biodiversity. Networking linking data portals across these collections allows researchers to discover and access the material they need without having to start from scratch and re-collect the same species again from the field. Researchers can easily ask the following questions: where is it, what quality is it and how do I get it for my work?

The collection has many links with projects around the world, including Zoos, Aquaria, botanical gardens and herbaria worldwide. This includes the Frozen Ark Project for endangered animals, the Global Genome Biodiversity Network representing as much global biodiversity as possible amongst its members (>65 institutions worldwide), the Millennium Seedbank at Kew, and other environmental-biodiversity biobanking initiatives such as ESBB and ISBER (European, Middle Eastern and African Society for Biobanking and Biopreservation, and the International Society for Biological and Environmental Repositories). These biobanks work together to address big human societal issues including disease (including crop pests), food security, biodiversity crisis (such as species loss and invasive species), and climate change. Repositories like this may be the last places genetic resources can be found for endangered or extinct species, to be used for research or preserved for the future.

The Molecular Collections facility frozen collection has a total capacity of ~2 million samples, but the freezers are not full yet. We have around 750K samples so far, held in a variety of temperatures and formats (fresh tissues, tissues in ethanol, dried with silica gel or on paper cards, frozen DNA extracts) at room temperature, +4 ˚C fridges, -20, -80 and -196 ˚C freezers. eg. These samples range from top quality (fresh flash frozen samples), fully sorted, with metadata records fully accessioned on the Museum’s collections management system, to older unsorted yet to be accessioned ‘legacy’ samples where some degradation has occurred over the specimen’s life time before it was rescued by the Molecular Collections facility. These legacy collections remain extremely valuable (e.g. rare species), as new technologies are enabling us to unlock more information from poorer quality degraded specimens every year e.g. new next generation sequencing methods. Once a specimen has been stored in the molecular facility, no more degradation will occur, so the specimen is protected for future scientific use.

My favourite specimens are the UK Insect Pollinator Initiative specimens – all ~50K of them! These specimens represent the UK’s diversity of all pollinator species not just bees (beetles, flies, moths, butterflies as well), collected over a period of 4 years providing a wealth of accumulated data as well as continued genetic resources to be extracted to build on the work already done. Having been involved from the beginning of this archiving project I feel very proud of it.

To find out more about the IPI archive, visit our previous blog post or access the dataset on the Museum’s Data Portal.

Sending off the specimens

The samples and specimens are retrieved from the freezers. These can then be divided into a smaller ‘subsamples’ if necessary (e.g. piece of tissue/leg of insect.) The sample is then placed in a 2D barcoded vial for tracking purposes and sent to the Sanger Institute inside a Dry Ice Shipper polystyrene box. This keeps the samples at -80 ˚C during transit. Any unused material are returned to NHM for re-accessioning back in the repository for other users in the future.

Minimal destructive sampling is preferred wherever possible, but for some processes the whole specimen has to be destroyed to generate adequate amounts of DNA. If we have large number of specimens for the same species and they are not Types (example specimens on which a species is named,) rare or endangered, then it is usually justifiable to authorise destruction of one whole specimen. Each destructive sampling request is considered carefully case by case and approved, or not, by the collections manager. However, once a specimen has been destroyed in this way, it has not disappeared; it has been transformed into another information format, e.g. tissue to DNA to sequence data, which tells us some completely new and valuable stories.

The results will be made publicly available and will lead to future studies to understand the biodiversity of the UK and aid the conservation and understanding of these species. We’ll be sharing more details of the Museum-championed species during the voting period 6 November – 8 December online and via twitter. If you’d like to decide which final five species go forward to have their genome sequenced, visit the ‘I’m a Scientist, Get Me Out of Here’ website and register to vote: https://25genomes.imascientist.org.uk/

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