Two years into his R.J.L. Hawke Post Doctoral Fellowship for Antarctic Environmental Science, Dr Bruce Deagle has made good progress in research examining the genome (DNA) of Antarctic krill. Prior to receiving the fellowship, Dr Deagle spent more than 10 years applying genetic technologies to research on many aspects of animal ecology, including DNA-based analysis of seal diet and characterization of genetic structuring in fish populations. His inaugural three-year fellowship was named in honour of former Prime Minister Bob Hawke’s contribution to protecting the Antarctic environment (see Reflecting on an Antarctic legacy in this issue).
My fellowship research, which is based within the ecological genetics group of the Australian Antarctic Division, involves two projects focused on characterising genomic variation in Antarctic krill (Euphausia superba).
The original aim of the fellowship was to document the complete genetic code of an individual krill. However, recent estimates of krill genome size indicate that it is huge. At 50 billion base pairs it is about 15 times larger than the human genome, making a comprehensive sequencing and genome assembly project infeasible. Instead, I am part of a team using ‘high-throughput DNA sequencing’ to characterise smaller parts of the genome, and at the same time address ecologically important questions about this keystone Antarctic species.
One aspect of my work involves developing krill genomic markers suitable for studying population structure. Such markers are DNA sequences shared by all krill, which vary enough to be able to detect potential differences amongst different krill swarms occurring locally or separated by great distances. To find useful genetic markers we are using a new technique called ‘restriction associated DNA sequencing’. This method allows many individuals to be examined and genetic variation between them documented.
So far we have analysed about 100 krill and have over 40 billion bases of DNA sequence data — more than ten complete human genomes worth of DNA sequence! The krill were collected from five sites around Antarctica, both during previous Antarctic Division marine research voyages and by collaborators from the Alfred-Wegener Institute in Germany. The characterised genetic variation will be used to estimate levels of connectivity between Antarctic regions and provide information on stock structure for fisheries management. It will also produce a catalogue of genetic variation in krill, providing a valuable reference for a range of future genetic studies.
A second part of my project involves producing a detailed ‘transcriptome’ (a list of functional genes) for krill by sequencing the subset of the genome that is being actively used (transcribed) within krill tissues. The analysis of data produced so far is a major undertaking and we are currently working with colleagues from the University of Padova in Italy to assemble an annotated transcriptome database (a list of krill genes and details of their function).
We are applying this data to investigating findings from experiments carried out in the Antarctic Division krill aquarium, which show that elevated carbon dioxide (CO2) levels can severely impact normal development of krill embryos. In this component of the project we have sequenced the transcriptome of larval krill exposed to various levels of CO2. Once our analysis is complete we will have a list of genes in these krill that are responding to changes in CO2. Analysis of the function of these genes will allow examination of the underlying physiological pathways that are being affected.
With a year left in this fellowship there is still a large amount of data analysis to be done and millions of DNA sequences clogging up my computer’s hard-drive waiting to be analysed. However, we have already come a long way towards the goal of characterising the genome of Antarctic krill and these data promise to revolutionise the study of this important species.
Bruce Deagle
R.J.L. Hawke Post-Doctoral Fellow,
Australian Antarctic Division