TrEnD Laboratory Bioinformatics

The trace and environmental DNA (TrEnD) lab is specialised in using degraded and ancient DNA to answer a number of biological questions. The significance of this research spans the areas of health, conservation, forensics, biosecurity, biodiversity, fisheries management and archaeology. We use next-generation sequencing (NGS) technologies and Bioinformatics to study a variety of fields. Various projects in TrEnD lab that utilised Magnus/Zeus CPU time in 2020 are listed below. - Invasive species monitoring in WA and Qld ports by govt depts. and commercial groups - eDNA detection of the rare Pilbara olive python for its conservation management - Investigation of commercial & native oyster species inhabiting coastal sites - Plant origin of pollen found in honey - Investigation of marine areas for dugongs, seagrasses and invasive species around a planned infrastructure build - Stygofauna diversity funded by ARC - Baffin Island Ice Cores Funded by NSF - Study of ticks microbiome funded by an NHMRC grant - Schizomids mitochondrial assembly

Principal investigator

Morten Allentoft
Magnifying glass

Area of science

Ancient DNA (aDNA), Genomics

Systems used

Magnus, Zeus, Managed Storage

Applications used

A wide range of applications were used for bioinformatic analysis including, AdapterRemoval, OBITools, USEARCH, DADA2, BLAST, LULU, fastSTRUCTURE, MitoZ, GTDBTK, eDNAFlow
Partner Institution: Curtin University| Project Code: pawsey0159

The Challenge

Many of the projects in the TrEnD lab address the national strategic priority; living in a changing environment. As a community we are more aware than ever of the impacts we have made, and are having, on our environment.

The Solution

Using DNA preserved in fossil bones, seawater, sediments, ice cores, faecal material (and other substrates) a key outcome of our research is to provide perspective on biodiversity and humanity’s role in shaping it. Best-practice restoration, management and conservation can only be achieved if we understand what it is we are trying to restore and conserve.

The Outcome

In the TrEnD lab we generated a wealth of NGS data related to the above listed projects. We employed Pawsey resources to analyse these data with respect to the following general areas:
(1) ZOTU/ASV generation, blast searching and taxonomy assignment
(2) Mitochondrial de novo assemblies
(3) Phylogeny and population Structure

List of Publications

Saccò, M., Blyth, A.J., Humphreys, Cooper, S.J., White, N.E., Campbell, M., Mousavi-Derazmahalleh, M., Hua, Q., Mazumder, D., Smith, C., Griebler, C., Grice, K. (2021). Rainfall as a trigger of ecological cascade effects in an Australian groundwater ecosystem. Scientific Reports, 11(1), 1-15.

Seersholm, F., Lykke Hansen, K., Heydenrych, M., Hansen, A. J., Bunce, M., Allentoft, M. E. (2021). Ancient DNA preserved in small bone fragments from the P.W. Lund collection. Ecology and Evolution, 11(5), 2064-2071.

Mousavi-Derazmahalleh, M., Stott, A., Lines, R., Peverley, G., Nester, G., Simpson, T., Zawierta, M., De La Pierre, M., Bunce, M., Christophersen, C. T. (2021). eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA (eDNA) sequences exploiting Nextflow and Singularity. Molecular Ecology Resources, in press.

West, K., Travers, M. J., Stat, M., Harvey, E. S., Richards, Z. T., DiBattista, J. D., . . . Bunce, M. (2021). Large‐scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north‐western Australia. Diversity and Distributions, in press.

West, K. M., Adam, A. S., White, N., Robbins, W. D., Barrow, D. Lane, A., Richards, Z. (2021). The applicability of eDNA metabarcoding approaches for sessile benthic surveying in the Kimberley region, north‐western Australia, Environmental DNA, in press.

West, K. M., Heydenrych, M., Lines, R., Tucker, T., Fossette, S., Whiting, S. and Bunce, M. (2021). Development of a 16S metabarcoding assay for the environmental DNA (eDNA) detection of aquatic reptiles across northern Australia. Marine and Freshwater Research, in press.

Bessey, C., Jarman, S. N., Berry, O., Olsen, Y. S., Bunce, M., Simpson, T., Power, M., McLaughlin, J., Edgar, G.J., Keesing, J. (2020). Maximizing fish detection with eDNA metabarcoding. Environmental DNA, 2(4), 493-504.

DiBattista, J. D., Reimer, J. D., Stat, M., Masucci, G. D., Biondi, P., De Brauwer, M., Wilkinson, S. P., Chariton, A. A., Bunce, M. (2020). Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems. Scientific Reports, 10(1), 1-15.

Michael, P. J., Jones, D., White, N., Hane, J. K., Bunce, M., & Gibberd, M. (2020). Crop-zone weed mycobiomes of the south-western Australian grain belt. Frontiers in microbiology, 11(2944).

Nester, G. M., De Brauwer, M., Koziol, A., West, K. M., DiBattista, J. D., White, N. E., Power, M., Heydenrych, M. J., Harvey, E., Bunce, M. (2020). Development and evaluation of fish eDNA metabarcoding assays facilitate the detection of cryptic seahorse taxa (family: Syngnathidae). Environmental DNA, 2(4), 614-626.

Seersholm, F. V., Werndly, D. J., Grealy, A., Johnson, T., Early, E. M. K., Lundelius, E. L., . . . Bunce, M. (2020). Rapid range shifts and megafaunal extinctions associated with late Pleistocene climate change. Nature Communications, 11(1), 1-10.

Van der Heyde, M., Bunce, M., Dixon, K., Wardell-Johnson, G., White, N.E. and Nevill, P., (2020). Changes in soil microbial communities in post mine ecological restoration: Implications for monitoring using high throughput DNA sequencing. Science of The Total Environment, 749, 142262.

West, K. M., Richards, Z. T., Harvey, E. S., Susac, R., Grealy, A., & Bunce, M. (2020). Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia. Scientific Reports, 10(1), 1-15