DNA and tissue issues – databasing genetic resources at Museum Victoria Dianne Bray & Joanna Sumner Sciences, Museum Victoria 2014 Global EMu User Conference Washington DC

Museum Victoria – four campuses Royal Exhibition Building Melbourne Museum Immigration Museum Scienceworks

Australia, Victoria, Marvellous Melbourne, Carlton MV & KE

Then… the 1900s

Museum Victoria’s Natural Sciences Collections Almost 17 million specimens Individual specimens, lots, bulk items Wet (EtOH, formalin) Dry (skins, skeletal material, pinned insects) Slides, SEM stubs Frozen tissues, DNA, RNA, Clones Models, Scientific Artworks Fossils, minerals, meteorites, rocks… Live Exhibits – in Forest Gallery and exhibitions Now…

Natural History collections date back to the 1850s & beyond DNA and Tissue Collections established late1980s as individually managed research-based samples 1996 – MV’s first DNA lab built offsite 2000 – Melbourne Museum opened with new DNA Laboratory 2007 – Tissue data centralised using KE Emu, and relevant tabs/fields developed More than 40,000 tissue samples Amenable to DNA/(RNA) extraction and genomic research Most samples from MV voucher specimens Samples also from specimens identified and/or photographed in the field, then released Other samples from voucher specimens held elsewhere Available to researchers worldwide Museum Victoria, Melbourne Australia

MV DNA Lab

MV Genetic Resources A c ollection resource supporting current and future research Housed in a variety of media -80°C Freezers – frozen, EtOH, RNALater, DMSO -20°C Freezers – unregistered tissues, DNA/RNA, Clones Whatman FTA Cards – blood Skin swabs – amphibia Most samples from Australia Others – Papua New Guinea, Indonesia, New Zealand, Antarctica/subantarctic and many other regions

MV Genetic Resources Mostly vertebrates Inverts mostly unreg Stored in 2ml barcoded Cryotubes Cryotubes barcoded using MVWise Collections Locations System: barcoded to a position in a box, in a rack, on a shelf in a particular freezer.

Significant Tissue Sub Collections A great diversity of bird tissues from Papua New Guinea collected in the 1980s, plus a large number of tissues from Australian birds Sulawesi mammals, birds and reptiles Dragon lizards (agamids) from Australia and central Asian desert regions of Kazakhstan and Uzbekistan Frog tissues and DNA extractions from current and past PhD research Deep-sea benthic and mesopelagic fishes from the Tasman Sea & off NW Australia Large cephalopod, echinoderm and land snail collections

A fieldwork snapshot

Managing genetic resources with KE Emu Voucher specimen data

Voucher specimen: Relationships Tab

Voucher specimen: Parts Tab Relationship hierarchy – children, grandchildren

Tissue sample: Tissue Tab records tissue type, preservation, other institution voucher #, tissue availability

DNA/RNA: Genetics 1 Tab Extraction data

DNA Extraction: Genetics 2 Tab Records gene regions sequenced, primer data, GenBank #

DNA/RNA: Multimedia Tab

Managing tissue grants with KE Emu MV’s EMu Transactions Module records: The use of MV tissue samples/extractions, including: –Tissue grants to internal & external researchers –Destructive sampling of collection specimens – internal & external research Incoming tissue grants to MV researchers and students Incoming tissue grants: Catalogued on EMu – recorded as ‘not part of the State Collections’ if they remain the property of the granting institution Genetic products catalogued on Emu – again recorded as ‘not part of the State Collections’ if they remain the property of the granting institution Research recorded on Emu Catalogue Tissue and Genetics Tabs

Transaction Record: destructive sampling of MV type specimens All destructive sampling of MV collection specimens is recorded on MV Transactions module. Muscle tissue removed from the hind limb of 3 paratypes Sequenced successfully using ancient DNA techniques Gibber Earless Dragon Tympanocryptis intima

Catalog: Transactions Tab Transactions Module used to record loans, tissue grants and destructive sampling History of specimen use displays on the specimen Catalog record Comments mirrored from Transactions Module

Catalog record: DNA extraction Parent record = Voucher specimen D 1173 DNA successfully extracted using Ancient DNA techniques No tissue record as tissue sample used up

Catalog: Genetics 1 Tab Also need to record whether or not DNA was successfully extracted from the tissue – negative results are informative.

Catalog: Genetics 2 Tab Records: The gene region that was amplified and sequenced, and primers used The GenBank Accession number (hyperlink to GenBank record yet to come) Important and informative to record If researchers were unable to amplify DNA PDF of MPE publication is attached to the MMR

Future changes? Global Genome Biodiversity Network (GGBN ) –Developing standards for sharing DNA and tissues information –Drafting DarwinCore DNA and Tissue extension for GGBN –MV a GGBN Associate Member –The Nagoya Protocol on access to genetic resources and the fair and equitable sharing of benefits arising from their utilisation to the Convention on Biological Diversity Sets out core obligations for contracting Parties to take measures in relation to access to genetic resources, benefit-sharing and compliance. May need to improve the way we record permit information in EMu Currently working on feeding data to Atlas of Living Australia

The Australian Wildlife Biobank : Protect MV’s past and future biological tissue collections: the core of MV’s active DNA and biological research program Liquid nitrogen cryofacility to house tissue samples, DNA, RNA, reproductive tissues & embryos Sufficiently low temperatures (-150°C) to prevent sample degradation and retain reproductive tissue viability (eg - eggs, sperm and embryos) Optimise DNA Laboratory workspaces to support best-practice molecular research processes Concentrated effort to database unregistered tissues, extractions MV Molecular Collections – what’s next?

Australian Wildlife Biobank

Very much looking forward to hearing and discussing how others manage genetic resources, destructive sampling, grants & data sharing. Also like to hear how others deal with the challenges of ensuring that data makes its way into Emu – we can build, but will they use? Thank you Dianne J Bray Senior Collections Manager Sciences, Museum Victoria Dr Joanna Sumner Manager Genetic Resources Sciences, Museum Victoria