AWARD CODE and TITLE
2008/314.27
FRDC People Development Program: 2011 FRDC International Travel
Bursaries
AWARD RECIPIENT: Prof. Abigail Elizur
ADDRESS:
DATE: 23/11/2011
University of the Sunshine Coast
Locked Bag 4
MAROOCHYDORE QLD 4558
Australia
ACTIVITY UNDERTAKEN
Attended a workshop on Analysis of new generation sequencing, hosted by Michigan State
University.
OUTCOMES ACHIEVED TO DATE
In this course I have learned what are the applications of new generation sequencing technologies, as well as technical aspects on what programs are used to analyse large sequence data sets for a variety of applications. We covered how sequences should be prepared, what are the limitations, and what types of samples and sample sizes are to be used. I have applied this knowledge in a number of cases.
1.
We have obtained partial transcriptome sequences and genomic sequences for the crystal bay prawns. We have started analysis of these sequences and have obtained high quality DNA markers for the genetic program, as well as identified a suit of genes associated with response to feed and are currently completing their analysis. In the same species we were able to identify genes effecting color formation in a rnage of tissues. Currently these new generation sequences are contributing to our research on
HPV and its impacts on prawns.
2.
We have applied this knowledge in analysis of yellowtail kingfish transcriptome data.
Here we have also isolated high quality DNA markers and applied those in the genetic program. We are currently examining genes associated with fat metabolism in YTK using transcriptome data.
3.
Have applied the knowledge acquired in this course to advise Clean Seas Tuna RMAG and Paspaley pearls regarding technical requirements for constructive sequencing applications by third parties.
4.
The knowledge obtained enables me to assess the relevance and role new generation sequencing can have in the aquaculture industry and advise on this matter.
Acknowledgments
I would like to acknowledge the support by FRDC who funded the cost of my travel and participation in the New generation sequencing course. University of the Sunshine Coast who

paid my salary while I was in this course, and Prof Titus Brown for delivering such complicated concepts in the clear way that he did.
Need
This application funded attendance in a two week intensive course on next generation sequencing. The course covered all aspects of bioinformatics analysis needed for transcriptomes and genome sequencing, as well as trained in the analysis of sequences I have brought from our own work.
At USC we have moved into the field of transcriptome and genome sequencing, and now have transcriptomes of 8 prawn tissues, pearl oyster, 2 fish tissues, and we are about to embark on edible oyster sequencing, as well as tuna genomics. While we were capable of doing the basic analysis, this course have greatly contributed to our capacity to evaluate what is needed and what can we achieve from this important resource.
There are not many groups in Australia doing wide genome analysis of aquaculture species, and this training and materials provided in the course has put me in a position to not only service my FRDC and CRC grant industry partners, but also to advise interested parties in
Australia who are interested in expanding into this field. USC is investing in building up its aquaculture genetics portfolio, and this training opportunity would add to the strength of the group.
Elizur would extend her knowledge gained in this travel to the aquaculture community through lectures at a CRC or industry forums where there is potential for uptake. She will communicate with the CRC about opportunities to present to the student forum where molecular approaches could be adopted to address some of the research questions.
Objectives
The original objective has been-To take part in a two week intensive course on analysis of next generation sequencing.
This objective has been fully achieved, and the knowledge applied.
Methods
In the course, we have covered the following subjects:
Python and bash shell scripting, cloud computing/Amazon EC2, basic software installation on UNIX, installing and running maq, bowtie, and velvet, querying mappings and evaluating assemblies.
The course was held at the W.K. Kellogg Biological Station on Gull Lake in western
Michigan, where I arrived on Sunday, June 5th through noon on Friday, June 17th.
The instructors were:
C. Titus Brown (http://ged.msu.edu/) holds a Ph.D. in Developmental Biology from Caltech, and has worked on digital evolution, physical meteorology, developmental biology, and genomics. He now works on bacterial metagenomics.

Ian Dworkin (https://www.msu.edu/~idworkin/) holds a Ph.D. in Evolutionary Genetics from the University of Toronto, and has worked on Quantitative and statistical genetics,
Evolutionary biology, genomics and developmental biology. He now works on Drosophila developmental genetics.
Dr. Istvan Albert (http://www.personal.psu.edu/iua1/) holds a Ph.D. in Physics from the
University of Notre Dame and has worked in statistical physics, data mining, bioinformatics and genomics. He was fascinated by our tuna work and offered to help with identification of male and female specific sequences.
In the course I have also formed contacts with other scientists and we have formed a network discussing sequence analysis options.
Results/Discussion
The main thing I have learned is what can and what cannot be expected from new generation sequencing, and what level of coverage is needed for what type of applications. This is critical information, and is shaping the way we are now planning our work, and enabled me to critically evaluate proposals in this area.
Benefits and Adoption
The aquaculture industry will benefit from these skills, as I would be able to advise across the board on the requirements, in terms of tissues, replications, budgets and platforms concerning engagement of nw generation sequencing. I have also realised that a dedicated experienced bioinformatics scientist is needed for serious analysis of large scale data, and am working at securing such position at USC, to compliment our work.
Further Development
With the drop in the costs associated with full genome and transcriptome sequencing, it is easy to carry out experiments which are not well planned, and later realise one does not the right data to address question. I am keen to ensure we are in a position to utilise the best and most cost effective service providers, and to have consortiums form within the small aquaculture R&D community in Australia, to carry out effective use of this significant technology to the overall benefit of the industry. This will be a major challenge in an environment which tends to work as independent groups, however with the support of the funding bodies, should be achieved.