Environmental Genomics

The Environment Institute Where ideas grow Professor Alan Cooper Environmental genomics

Environmental genomics: Rapid biodiversity assessment of any sample Australian Centre for Ancient DNA, The University of Adelaide

Environmental genomics: Current Funding ARC LINKAGE project (2009). $0.5M, plus industry contributions (ca. 0.6M) = $1.1M Future Fellowship (2009). $1M

What is ACAD? • Internationally leading centre for study of preserved genetic information • Expertise with multiplex analysis (many genes) of biologically complex, trace-level samples, and 2nd Generation Sequencing • Able to use existing museum and herbaria collections to generate reference database of taxonomically ID’d taxa • AQIS approved facility • Suitable for forensics (standard and environmental), sedimentary, and water analysis

Individual (still-air) working rooms • 3 Laboratories – incl. high- tech ancient facility, museum grade specimens, modern lab • Trambarn - AQIS approved • Positive air-pressure • UV sterilisation • Controlled personnel flow • 16 researchers -20’C • International visitors workrooms • Evolution, archaeology, biodiversity/climate change, Air shower forensics - collaboration with AFP, DEH, NGS, Air flow UV Entry

ancient DNA lab = ultra-low DNA environment

Environmental Genomics • Takes advantage of massive increase in sequencing power of 2nd and now 3rd Generation sequencing to perform vertical genetic bar-coding • Capable of working with diverse taxonomic groups rapidly and simultaneously – using deep (multi-marker) characterisation of genetic diversity within any sample. • Do not need to know what is present a priori, and can map species across a broad scale (eg landscape, soil, water, complex samples), and without need for prior taxonomic knowledge • De novo assessment of biodiversity, eg mining, developing world • Rapid, powerful, high resolution - using flexible, standard platform • Remove constraints (esp. time) of traditional morphological approaches, ideal for mining, primary industries • Needs active involvement of existing taxonomic and ecological expertise to identify accuracy, and potential uses

What is 2nd Generation Sequencing? • It is already out of date. • Parallel analysis of millions of different DNA sequences using chip-based arrays, or microwells • Very cheap per base. 1st human genome = $Bn, currently <$50k • Produces massive amounts of data, only few % of current products analysed • 3rd Generation released next year. Active moves to locate machine at Adelaide for metagenomics. Promises of human genome in 3 minutes, for $5k. • Key constraint in this revolution in biological science – who is going to analyse the data??

3rd Generation Sequencing - Oxford Nanopore Technologies a-hemolysin nanopore (ribbon diagram) with covalently attached cyclodextrin (teal) transiently binds a DNA base (red) traversing the pore. A, G, T, C and CM are separated according to charge and mass. No need for dyes, CCD cameras etc

Current partners • PIRSA: Paul Heithersay – sediment-based survey of biodiversity across South Australia, focusing on plant and animal taxa • Australian Federal Police: Paul Kirkbride – forensic analysis of soils for geographic predictions, evidence analysis • SA Water: Chris Saint – microbial diversity of water systems, including re-use, de-salination plants, and reservoirs. Unknown pathogens • SA Pathology: Hamish Scott, Tuckweng Kok (James Paton) – microbial diversity within hospital/medical systems, unknown pathogens • DEH: Hugh Cross, Andy Lowe – analysis of herbarium specimens, grasses • José Facelli – ecological interpretation of EG data vs field sites • Biomatters Ltd (Geneious): Shane Sturrock – design and implementation of software interface between raw genomics output, and end-users. Training postdocs and PhDs in bioinformatics. • Daniel Huson (MEGAN) – leading metagenomics analytical software

Sample extraction Ancient DNA methods developed to extract trace signals from complex biological samples – eg sediments, old bones (mostly microbes), faeces Bulk processing (eg sediments), and selective hybridisation or primer-based capture techniques to pull out useful sequences from high background levels. Connect to High throughput sequencing Water = bulk processing and filtering, perhaps with semi-permanent sensors (IPAS) R+D on DNA extraction and isolation procedures

Informative loci The environmental genomics approach harnesses to power of genomics technology, by focusing the amplified loci to contain only taxonomically informative genes. Candidate loci, and suitable databases, already exist although generally short and with limited coverage. Examples include COI/12S/cytb (vertebrates, invertebrates), 16S (bacterial), rbcL/trnL, matK (plants). We will use extra domains within these loci, and additional loci (eg nuclear introns, vWF, RAG-1, others) as necessary. The system has large capacity.

Future directions • Genographic project • newly collected material (!), needs rates and demographic analysis

Metagenomic studies of ancient samples confirm that most of the DNA is exogenous/microbial

Voucher specimens The environmental signals must be identified through comparison with voucher specimens – eg taxonomically identified material. The same genetic loci must be sequenced to allow identification Suitable material includes museums, herbaria, microbial cultures and collections – but new samples will need to be gathered and processed throughout the project

Current constraints Need locally sited 2nd or 3rd Generation machine Desperate need for bioinformaticians (students and trained maths/engineers/physicists PhD and postdocs

Acknowledgements Kyle Armstrong Paul Brotherton Wolfgang Haak Jeremy Austin

The Environment Institute Where ideas grow Next Seminar: 16 October Assoc. Prof. Bronwyn Gillanders Giant Australian cuttlefish: a globally unique species under threat?

Environmental Genomics

by University of Adelaide on Oct 08, 2009

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