Abstract – Mobilising collections through genomics
The National Research Collections Australia (NRCA) have been the primary repository for Australian biodiversity samples for the past century, archiving 15 million specimens of insects, vertebrates, plants, algae and lichens. The different sample types require a variety of preservation methods, very few of which are amenable to conventional methods of molecular genetics research. This Environomics project aimed at developing collection genomics methods that enable DNA sequencing across the breadth of these vast repositories, thereby unlocking their genomic potential for a broad range of applications and life sciences research. This includes enabling the generation of reference sequences for molecular species identification and for investigation of population genomic changes over time, which benefits biodiversity monitoring with traditional and emerging techniques like environmental DNA (eDNA) sequencing and metabarcoding. These methods are rapidly changing how government agencies and larger companies assess and monitor biodiversity, e.g., for improved biosecurity, better management of fish stocks, more efficient conservation of natural resources and understanding of algal blooms in a changing environment.
This project comprised three subprojects that address different preservation methods used across the NRCA collections. The subproject “High-throughput collection genomics“ aimed to develop a new method that enables the efficient generation of DNA reference sequences from the taxonomically identified specimens in the NRCA, irrespective of organism and specimen age. The subproject delivered novel platform technology that enables the cost-effective sequencing of large numbers of collection specimens with highly degraded DNA, across the kingdoms of life and with 93% cost reduction for reagents through miniaturisation of reactions. It provided the capability and capacity to generate mitochondrial and chloroplast reference sequences from the collections through genome skimming, thereby opening up the largest part of the NRCA and natural history collections around the world to DNA sequencing. About 3,000 insect, plant and lichen specimens were sequenced to test and demonstrate the broad applicability and throughput of the novel platform technology.
The subproject “ANFC formalin preserved specimen” investigated the sequencing of particularly damaged and cross-linked DNA. Collections, such as the Australian National Fish Collection (ANFC), that contain wet or fluid filled specimens have at some stage treated the specimens with formalin, which impacts our ability to obtain fully digitised genetic records for all specimens. The overarching aim of the project was to test our ability to genetically identify (to species level) formalin exposed specimens using Sanger and Illumina sequencing. The subproject succeeded in optimising a formalin fixed paraffin embedded (FFPE) protocol to enable the extraction of usable DNA from specimens fixed in formalin for less than 8 weeks. This DNA was used for DNA barcoding, demonstrating that up to 53% of formalin preserved (< 8 weeks) specimens of the test set were identified to species level with this approach.
The subproject “Genome evolution of long-term algal cultures“ researched the genetic and morphological changes in living algal collections. Micro-algal species are continuously adapting to their environment. Strains maintained long-term in living laboratory cultures also undergo adaptation, resulting in physiological and genetic changes. These changes can result in strains no longer representing the physiology of the species or environment they originated from and therefore losing their usefulness as research cultures. This is an important consideration for collections of living algae, including the Australian National Algae Culture Collection (ANACC), which may maintain cultures indefinitely. But there are few opportunities to quantify culture evolution, because this requires maintaining multiple cultures in parallel. We had a unique opportunity to compare four cultures of the cyanobacterium Raphidiopsis raciborskii strain CS-506, the original progenitor clone was isolated 23 years ago, with three daughter cultures split between 2 and 10 years ago, that have been maintained separately through serial dilution, and undergone demonstrable morphological modifications. This project quantified the genome modifications that have occurred as a result of continuous long-term culture.
If you would like to know more about this work, please contact Dr Andreas Zwick.