The 2017 BABS Genome Competition is on

BABS researchers are involved in sequencing the genomes of a number of iconic Australian species. These include the koala, the cane toad, and Sandy the Dingo (winner of the PacBio World’s Most Interesting Genome competition). Now, we’re asking: what next?

This year, BABS has launched a new initiative: the BABS Genome Project. We will be using the latest sequencing technologies at the Ramaciotti Centre for Genomics to sequence a brand new genome of an Australian organism. Students and staff of BABS3291 Genes, Genomes and Evolution, will be the first scientists in the world to analyse the data.

Australia has some of the most interesting - and deadly! - animals on earth. If you could sequence one, which would it be? Let us know at the BABS Genome survey. If you are a BABS student and give us the reason for your selection, you could win one of five $50 gift cards.

UNSW Genome Annotation Workshop

NOTE: Regrettably, this event has now been cancelled. We hope to organise something similar in future and will be in touch with registered individuals to gauge interest.

We are pleased to announce that we are hosting Monica Munoz-Torres from the Berkeley Bioinformatics Open-Source Projects group (BBOP) at Lawrence Berkeley National Laboratory as part of her EMBL-ABR Australian tour, sponsored by the School of Biotechnology and Biomolecular Sciences (BABS) and NSW Systems Biology Initiative (SBI).

In addition to a BABS seminar (details to follow), Monica will be giving a one-day Primer on Genome Annotation workshop at UNSW, with a particular emphasis on collaborative genome annotation using WebApollo.

• When: 0900-1700, July 7th, 2017
• Where: Red Centre, UNSW, Sydney, Australia
• Contact: richard.edwards@unsw.edu.au

You can pre-register for the workshop here or fill in the form below. Places are limited to 30 participants. We will be in touch to let you know if you have a place. Formal registration will require a $20 registration fee.

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.

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