genome annotation image

29/05/2020

Australian BioCommons and QCIF are collaborating to establish and operate systems to enable sharing and improvement of draft genome annotations for Australian researchers.

A genome annotation platform will enable researchers nationally and internationally to work together on analysing the structure and function of genetic transcripts, speeding up the process far beyond the current traditional means of collaboration and publication.

Last year, the Australian BioCommons consulted researchers undertaking genome annotation (dubbed the ‘Genome Annotation Special Interest Group’), and produced a high-level, community-agreed overview of infrastructure that would support these activities.

Genome annotation is the process of identifying and labelling features on a genome assembly. The higher the quality of the annotation, the higher the utility of the genome in comparative, functional, evolutionary and ecological genomics.

One key part of the infrastructure identified in the interest group’s roadmap is a system to enable collaborative improvement of draft genome annotations, required after automated genome annotation has occurred. Essential components of this infrastructure include:

  • resources and tools for collaborative curation and improvement of the annotation quality of draft genome annotations
  • a system to enable sharing of draft genome annotations, involving visualisation through a genome browser.

QCIF will operate an Apollo* service for use by Australian-based genome projects. This will enable collaborative, real-time, genome annotation editing through a JBrowse-based Web-browser. 

Following curation of the annotations using Apollo, draft genome assemblies and the accompanying curated annotations will have the possibility to be openly accessible. This will enable data sharing outside the project and provide resources to underpin comparative genome analyses.

Director of QCIF’s Facility for Advanced Bioinformatics, Dr Dominique Gorse, who leads the platform’s deployment, said the availability of the service will be critical to many genome projects harnessing the power of sequencing technologies to characterise the genomes of species of Australian interest. 

“The study of these genomes will revolutionise the understanding of biology, biodiversity and evolution,” he said. 

Dr Jeff Christiansen, Associate Director (Engagements and Operations), Australian BioCommons, said: “We’re looking forward to having this service established as one of the items outlined in the Genome Annotation Roadmapping exercise.”

The service developed by QCIF will provide:

  • connectivity to other relevant components of the Australian BioCommons infrastructure (e.g. Galaxy Australia)
  • appropriate user authorisation and sharing mechanisms to allow for data sharing, solely at the discretion of a data custodian
  • documentation on how to use the system (including a knowledge base with community-contributed content)
  • a ticketed support system for users. 

The platform is part of the “Optimising Queensland Infrastructure In ‘Omics’ Sciences” project funded by Bioplatforms Australia and the Queensland Government Research Infrastructure Co-Investment Fund (RICF) as a new service of the Australian BioCommons.

See our separate story about QCIF hiring JCU bioinformatician Dr Justin Lee to work as Platform Developer and System Administrator on this project.

*Apollo was developed by the Environmental Genomics and Systems Biology group at the Lawrence Berkeley National Laboratory in Berkeley, California, USA. It is used by many groups internationally and in Australia to support the manual curation of genome annotations. 

Training on how to use Apollo has previously been conducted in Australia in collaboration with the group at Lawrence Berkeley National Laboratory (see a recording of the event here). Australian BioCommons and QCIF will likely hold similar training again at some point.