Wheat Genome Annotation Platform
New genomes are being sequenced at an increasing rate, including genomes of unique and valuable Australian species. However, much of the value of a genome assembly comes from identifying where the important features are: the genes, splice variants, repetitive regions, and small RNAs. This process, called ‘annotation’, can be very time-consuming, requiring careful attention. Automated annotation approaches need manual curation and annotation to reach a high standard. The most successful genome annotation projects have typically involved numerous researchers and multiple lines of evidence, including RNA and protein data obtained from the target species, data from related species, and computational gene model predictions based on the DNA sequence.
Thus there is a need for collaborative bioinformatics infrastructure to incorporate multiple sources of information, and support multiple users with the ability to check others’ annotations. The current best-practice approach to this problem is the Apollo software, which fulfils these criteria. However, Apollo still requires hosting with sufficient memory and compute resources, which may be inaccessible locally to some Australian researchers. It may also be challenging to set up, especially for biologists without a computing background. This infrastructure-level problem is solved by providing a ‘pre-packaged’ Apollo setup in the Genome Annotation Platform, accessible to everyone with an Australian research affiliation via the national NeCTAR Research Cloud.
Genome Annotation Platform for the wheat chromosome 7A
Currently EMBL-ABR is working on a Genome Annotation Platform setup for the Australian research community. This is a collaborative cloud-based platform for Australian researchers (and international collaborators) to annotate a reference genome using one or more lines of evidence. It is set up as an Apollo server running in a custom Genomics Virtual Lab instance on the NeCTAR cloud.
Our first step in this direction is a Genome Annotation Platform for the wheat chromosome 7A. This activity follows the EMBL-ABR Activity EoI, and will serve as a pilot project towards other domain and species specific genome annotation platforms.
The Wheat Genome Annotation Platform is being set up to enable collaborative manual genome annotation of wheat chromosome 7A. The wheat genome is extremely large and complex, and has been the target of a major international collaborative sequencing effort led by the International Wheat Genome Sequencing Consortium including numerous Australian research groups.
Chromosome 7A is now well assembled, but automated annotation is limited in its ability to identify true gene boundaries, splice variants and other important functional genomic features. This activity follows the EMBL-ABR Activity EoI, and will serve as a pilot project towards other domain- and species-specific Genome Annotation Platforms.
Current project outline and scope can be found here.
Are you interested in joining this Activity? Please contact us!
EMBL-ABR Activity Lead: Wheat Annotation
Rudi Appels is the EMBL-ABR Activity Lead for Wheat Annotation. Rudi is part of Murdoch University and AgriBio. Rudi is specialised in wheat research including being among the founders of the International Wheat Genome Sequencing Consortium (IWGSC). Get in touch with Rudi here.
EMBL-ABR Activity Lead: Wheat Bioinformatics
Gabriel Keeble-Gagnere is the EMBL-ABR Activity Lead for Wheat Bioinformatics. Gabriel works for AgriBio and is heavily involved in wheat genome assembly activities as part of IWGSC. Get in touch with Gabriel here.