Next Generation Sequencing and the exploration of biodiversity

Researchers:
Staff: Maurizio Rossetto; Hannah McPherson; Marlien van der Merwe; Peter D Wilson Students: Monica Fahey; Josh Hayes; Susan Rutherford; Juelian Siow; Sam Yap
Project sponsors:
Bioplatforms Australia Ltd Foundation & Friends of the Botanic Gardens
Project partners:
Eric Coissac (University of Grenoble), Robert Henry (UQ), Robert Lanfear (MQU), Andrew Lowe (University of Adelaide), Pierre Taberlet University of Grenoble), Diversity Arrays Technology Pty Ltd
Contact:
Maurizio Rossetto

Project aims

  • The resource efficiency of Next Generation Sequencing (NGS) technologies offers new opportunities for expanding field- and lab-based biodiversity studies.
  • Genomic research provides unique insights into natural systems. 
  • We are testing and applying novel techniques to address ecological and evolutionary questions that could not be explored before.

 

Project Summary

Sequencing technologies are rapidly evolving and improving, and now offer an array of new opportunities for evolutionary ecology studies. 

Our evolutionary ecology team has gained considerable expertise in the application of a range of NGS-based approaches. These include: the bioinformatic assembly of whole cpDNA data derived from whole-genome sequencing (for biogeographic and phylogenetic studies); whole transcriptome (RNA) analyses to identify the distribution of putative adaptive markers along environmental gradients; genome reduction approaches (such as DArTs) for general population genetic studies; and the analysis of environmental DNA (eDNA) to investigate landscape-level distribution of biodiversity (including plants, animals, fungi and bacteria).

Research Update

The majority of our current projects rely on genomic information captured using a range of NGS-based techniques. 

For example, one of our main research projects, Restore & Renew, uses a genotyping by sequencing method (DArTseq) to obtain distribution-wide measures of genomic diversity across over 200 NSW species commonly used in restoration projects. 

We use innovative eDNA approaches to investigate changes in overall diversity across a latitudinal rainforest gradient (from Sydney to Cape York). Our preliminary findings identify the impact of edaphic factors and temperature on the distribution of diversity.