Tuesday, 11 July 2017

The SLiMEnrich Shiny App is now live

SLiMEnrich

Sobia’s first Shiny App is now up and running for final pre-publication testing on our new EdwardsLab RShiny server. Please feel free to try it out. Any comments and suggestions can be posted here, by email, or via the GitHub issues page.

The SLiMEnrich App allows users to predict Domain-Motif Interactions (DMIs) from Protein-Protein Interaction data (PPI) and to estimate the background distribution of expected DMI by chance through a randomisation approach. The walkthrough has more details.

SLiMEnrich can be used to:

  • Estimate the enrichment of SLiM-mediated DMI in a given PPI dataset.
  • Generate predictions for DMI-mediated from a PPI dataset. Predictions are based on known SLiM-Domain interactions.
  • Estimate the False Positive Rate of those DMI predictions.
  • With a bit of imagination, SLiMEnrich can be adapted to generate and assess predictions for other kinds of interactions. See docs for details.

    SLiMEnrich is available via the SLiMEnrich RShiny webserver and can be downloaded for local running from the SLiMEnrich GitHub repo.

    Tuesday, 4 July 2017

    GEN2017: Mitochondrial variation and heteroplasmy in Australian and Hawai’ian cane toads

    If you were attending this year’s Annual Conference of the Genetics Society of Australasia with the NZ Society for Biochemistry & Molecular Biology, hopefully you made it to the oral presentation of Lee Ann Rollins. Although we do not yet have enough PacBio data for a pure long read assembly of the nuclear genome, the mitochondrion is another matter!

    Mitochondrial variation and heteroplasmy in Australian and Hawai’ian cane toads.

    Lee A Rollins[1], Mark F Richardson[1], Daniel M Selechnik[2], Andrea J West[1], Timothy G Amos[3], Richard J Edwards[3] & Richard Shine[2]

    1. School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, VIC, Australia
    2. School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
    3. School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia

    Abstract

    Background/Aims. Invasive species can adapt to new environments despite low levels of standing genetic diversity due to small founding numbers or sequential introductions. The iconic Australian cane toad was sourced from an introduced population in Hawai’i and conflicting evidence exists regarding the level of genetic diversity across these invasions.

    Methods. We extracted mitochondrial sequence data from the genome of one individual sequenced using the PacBio RSII and Illumina X10 platforms. From these data, we assembled and annotated the mitochondrial genome. RNAseq data from 18 individuals collected from Hawai’i and 68 individuals from Australia were aligned to the reference sequence. We quantified polymorphism across samples and heteroplasmy (multiple mitochondrial haplotypes within individuals).

    Results. A complete, annotated mitochondrial reference genome was constructed consisting of 18154 base pairs (bp), the largest reported bufonid mitochondrial genome. We aligned RNAseq data to the entire reference sequence, with the exception of a 347bp region containing several 104bp repeats. We identified 16 polymorphisms (17 haplotypes); one haplotype was common to 65 individuals sampled in both introductions. Heteroplasmy was detected at most polymorphic sites and also at multiple sites where the predominant haplotype was common to all individuals.

    Conclusions. Mitochondrial diversity is low in Australian and Hawai’ian cane toads. Our findings add to the growing body of evidence that heteroplasmy may be ubiquitous across taxa. Selection within heteroplasmic individuals (recently demonstrated in expanding populations) may provide an important source of variation in genetically depauperate populations.

    Funding. Australian Research Council DE150101393 (LAR) and FL120100074 (RS)

    Friday, 30 June 2017

    Research Snapshot - June 2017

    Research interests in the Edwards lab stem from a fascination with the molecular basis of evolutionary change and how we can harness the genetic sequence patterns left behind to make useful predictions about contemporary biological systems. We are a bioinformatics lab but like to incorporate bench data through collaboration wherever possible.

    Main Research

    The core research in the lab is broadly divided into three main themes:

    1. Short Linear Motifs (SLiMs)

    SLiMs are short regions of proteins that mediate interactions with other proteins. A major focus of the lab is the computational prediction of SLiMs from protein sequences. This research originated with Rich’s postdoctoral research, during which he developed a sequence analysis methods for the rational design of biologically active short peptides. He subsequently developed SLiMDisc, one of the first algorithms for successfully predicting novel SLiMs from sequence data - and coined the term “SLiM” into the bargain. This subsequently lead to the development of SLiMFinder, the first SLiM prediction algorithm able to estimate the statistical significance of motif predictions. SLiMFinder greatly increased the reliability of predictions. SLiMFinder has since spawned a number of motif discovery tools and webservers and is still arguably the most successful SLiM prediction tool on benchmarking data.

    Current research is looking to develop these SLiM prediction tools further and apply them to important biological questions. Of particular interest is the molecular mimicry employed by viruses to interact with host proteins and the role of SLiMs in other diseases, such as cancer. Other work is concerned with the evolutionary dynamics of SLiMs within protein interaction networks.

    2. The evolution of novel functions.

    Previous work in the lab has focused on the evolution of functional specificity following gene duplication. Since moving to UNSW, activities have shifted more towards the use of PacBio long read sequencing and other cutting-edge sequencing technologies, working closely with the Ramaciotti Centre for Genomics. We are collaborating with industrial and academic partners to de novo sequence, assemble, annotate and interrogate the genomes of a selection of microbes with interesting metabolic abilities. Most notably, we have an ARC Linkage Grant with Microbiogen Pty Ltd. to understand how a strain of Saccharomyces cerevisiae has evolved to efficiently use xylose as a sole carbon source: something vital for second generation biofuel production that wild yeast cannot do. This project combines detailed molecular characterisation of highly adapted yeast strains with “molecular palaeontology” to trace the evolutionary process and identify functionally significant loci under selection.

    3. Whole genome sequencing and assembly.

    Following our experiences with de novo whole genome assembly in yeast, the lab is getting involved in an increasing number of genome sequencing projects. The biggest of these is leading the bioinformatics and assembly effort in a consortium to sequence the cane toad genome. The lab is also leading the BABS Genome project to sequence iconic Australian species for use in teaching and public engagement.

    Previous Research

    The lab has been involved in a number of interdisciplinary collaborative projects applying bioinformatics tools and molecular evolution theory to experimental biology, often using large genomic, transcriptomic and/or proteomic datasets. These projects often involved the development of bespoke bioinformatics pipelines and a number of open source bioinformatics tools have been generated as a result. Please see the Publications and Lab software pages for more detail, or get in touch if something catches your eye and you want to find out more.

    Tuesday, 20 June 2017

    UNSW Genome Annotation Workshop cancelled

    Regrettably, due to unforeseen circumstances, EMBL-ABR’s Monica Munoz-Torres Australian tour has been cancelled. As a result, the planned UNSW Genome Annotation Workshop will no longer be going ahead. We hope to organise something similar in future, so will leave the registration page up for a bit longer to get a list of interested parties.

    Sunday, 21 May 2017

    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.

    Wednesday, 10 May 2017

    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.

    Monday, 27 February 2017

    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.

    Sunday, 12 February 2017

    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.

    Friday, 3 February 2017

    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.

    Monday, 9 January 2017

    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]