Gus Severin (Honours)

Gus Severin is an Honours student in Genetics who started in Semester 1, 2017. Gus is working with Åsa on the ARC Linkage Grant with Microbiogen Pty Ltd. The focus of Gus’s project is using genomics and selection experiments to identify key genetic differences between a xylose-metabolising yeast strain of interest and “wild-type” lab strains that cannot grow on xylose. Before joining the lab, Gus was Science student in BABS, Majoring in Genetics.

Update: Gus was awarded First Class Honours for his project and has since got a job with Microbiogen.

Lorne Genome 2017: PacBio sequencing, de novo assembly and haplotype phasing of diploid yeast strains

Richard J Edwards, Åsa Pérez-Bercoff, Tonia L Russell, Paul V Attfield & Philip JL Bell.

Abstract

PacBio Single Molecule Real Time (SMRT™) sequencing is rapidly becoming the technology of choice for de novo whole genome sequencing. The long read lengths and random error of PacBio data make genome assembly considerably easier and more accurate than short read data. In polyploid genomes, heterozygosity – particularly in structural variants – generates some additional challenges for de novo genome assembly. For some regions, homologous chromosomes are assembled together into a chimeric sequence. However, long reads from heterozygous regions will often assemble into two distinct contigs, fragmenting the assembly. Despite these challenges, long reads present new opportunities for assembly of polyploid genomes. Where the heterozygosity (i.e. density and number of polymorphisms) is high enough, polymorphisms can be phased into distinct “haplotigs” derived from a single parent.

We have performed genome sequencing of novel diploid Saccharomyces cerevisiae strains using the PacBio RSII at the UNSW Ramaciotti Centre for Genomics. In addition, we have generated an “in silico diploid” strain by combining sequence data from two haploid strains that we previously sequenced and assembled. Here, we report on progress regarding de novo diploid assembly and efforts towards full haplotype phasing of these strains. Our in silico diploid enables us to assess how successfully we can reconstruct known parental chromosomes and haplotypes. The types and levels of heterozygosity required for haplotype phasing will be discussed, along with the challenges presented by heterozygous chromosomal translocations.

EMBL-ABR network: an interview with Richard Edwards

From the EMBL-ABR February newsletter:

On 3 February we released an interview with Richard Edwards, the developer of SLiMSuite, an open source bioinformatics tool for the prediction of short linear motifs (SLiMs) and related sequence analysis. In this interview Richard reflects on bioinformatics in Australia as well as the realities of building a sustainable model for the development and maintenance of useful bioinformatics tools such as his.

You can read the full interview: here.

Peter Santosa (SVRS Student)

Peter is a 3rd year Advance Science student who worked in the lab in January-February 2017 on the Summer Vacation Research Scholarship (SVRS). Peter was working on a bacterial sequencing project in collaboration with Mike Manefield at UNSW. We have successfully used PacBio sequencing to fully and contiguously assemble the genome of a new bacterial strain from a mixed culture. Peter’s project was analysing assembled contigs from other organisms in the culture.

Peter is undertaking a double major of molecular and cell biology and microbiology at UNSW.

Jiehao Wang (SVRS Student)

Jiehao Wang is a third year Bachelor of Advanced Science (Honours) undergraduate, majoring in pathology and pharmacology. He joined the Edwards Lab in 2016 on a second semester School of Biotechnology and Biomolecular Sciences (BABS) research scholarship. After finishing the project, Jiehao continued to work with Dr Richard Edwards in the summer of 2017 under the BABS school Summer Vacation Research Scholarship (SVRS) as an intern. During his time at the laboratory, he worked on the comparative yeast genomics project in 2016, and helped to identify Ty elements (Transposable Yeast elements) in genome assemblies in 2017.

Academic Qualifications

Expected 2018, Bachelor of Advanced Science (Honours) in Pathology and Pharmacology - University of New South Wales, Sydney, Australia.

[LinkedIn]

The cane toad genome project

What are we doing? The Edwards Lab is part of an Australian, Portuguese and Brazilian consortium led by Peter White to sequence and assemble the genome of the cane toad (Rhinella marina). We are leading the bioinformatics component of the assembly effort.

How are we doing it? We are using a combination of Illumina (HiSeq X and NovaSeq) short read sequencing, PacBio (RS II) long read and sequence and 10x Genomics Chromium linked reads.

Details to follow. Please get in touch if you are interested in the project.

Opportunities

Honours and postgraduate* projects are available to work on the assembly and annotation. (*PhD students should have their own scholarship.)

Consortium members

Miguel Carneiro (CIBIO-InBIO), Richard Edwards (UNSW), Nuno Ferrand (CIBIO-InBIO), Eddie Holmes (U Sydney), Craig Moritz (ANU), Lee Ann Rollins (Deakin), Fernando Sequeira (CIBIO-InBIO), Rick Shine (U Sydney), Marcelo Vallinoto de Souza (Federal University of Pará & CIBIO-InBIO), Peter White (UNSW), Marc Wilkins (UNSW).

BABS is recruiting - academic positions available in bioinformatics, systems biology, medical genomics and biotechnology

The School of Biotechnology and Biomolecular Sciences (BABS) at the University of New South Wales, Sydney, Australia, is seeking to recruit world class scholars with outstanding and recognised research records in Biotechnology, Bioinformatics, Systems Biology or Medical Genomics.

Our School, located at the Kensington campus in Sydney, is part of the Faculty of Science. We have an international reputation in biotechnology, molecular and cellular biology, and microbiology. Particular areas of research strength within these fields include proteomics and genomics, gene regulation, metabolism,environmental microbiology and infectious diseases.

We currently have combined track (research and teaching) opportunities to join BABS as part of a strategic initiative in Systems level Biology and Genomics in the School. BABS hosts the Ramaciotti Centre for Genomics, which has world class facilities for sequencing and is arguably Australia’s premier facility for research genomics. BABS is also home to the Systems Biology Initiative, which is supported by high performance computing facilities, including national supercomputers. Our researchers also have access to outstanding proteomics and metabolomics facilities at the UNSW Bioanalytical Mass Spectrometry Facility and the Mark Wainwright Analytical Centre which provide state-of-the-art facilities and services for animal studies; in vivo and ex vivo preclinical imaging; flow cytometry; biochemical, biophysical and chemical analyses; and electron microscopy. We have collaborative links with the Garvan Institute, the Lowy Cancer Research Centre and other biomedical research organisations within and outside Sydney.

For more information about the School, please visit: www.babs.unsw.edu.au/

About UNSW Australia

• UNSW Australia is a research-intensive university ranked in the world’s top 50 (QS 2016)
• Strong regional and global engagement improving and transforming lives through excellence in research, outstanding education and a commitment to advancing a just society
• The top university in the state of New South Wales in the 2015 Excellence in Research for Australia

UNSW is at the cutting edge of academia with a strong and growing international reputation. A global leader in discovery, innovation, impact, education and thought leadership, can make an enormous difference to the lives of people in Australia and around the world. The recently launched UNSW 2025 Strategy is an innovative, ambitious and altruistic agenda, reflecting a conviction across our University to achieve great things for society during the next decade.

Further details

Further details can be found here:

• Bioinformatics, Systems Biology or Medical Genomics.
• Biotechnology.

Any enquiries contact: Associate Professor Mark Tanaka

Applications close: Sunday 13 November 2016 (AEST)