Wheat Tan Spot Pan-Genomics High Through Put Analysis (2018)Pyrenophora tritici-repentis (Ptr) is a necrotrophic fungal pathogen that causes the major wheat disease, tan spot. This project sets out to provide essential genomics-based resource support to better understand the pathogenicity mechanisms of this important pathogen. This project has acquired a world-wide catalogue of Ptr isolates for comparative and pan genomics analysis. These isolates represent a number of new and existing races to identify key effector elements in pathogenicity. This expansion of available Ptr genomics resources directly facilitates research aimed at controlling tan spot disease.
Principal investigatorPaula Moolhuijzen email@example.com
Area of scienceBioinformatics
Systems usedMagnus, Zeus and Nimbus
Applications usedBLAST, EvidenceModeller, KAKS Calculator
To ensure quality genome production we conduct comprehensive gene searches against a number of large non-redundant databases to annotate all genomes, cluster identified elements and conduct further alignments to identify variations and determine if specific genes or regions are under selective pressure. To process this data a high through put environment is required. For instance currently a typical pan-genomics analysis has over 322K individual computational tasks.
Our approach for a typical pan-genomics analysis is to batch the hundreds of thousands individual computational tasks and run these in parallel on Pawsey’s HPC Magnus. This has been highly successful with all analysis results returning within 24 hours.
Through Pawsey’s HPC project (FL3) and Nimbus we have increased the genomic resources for Pyrenophora tritici-repentis, a major wheat pathogen and causal agent of tan spot disease, by seven-fold. In 2018 a collection of Pyrenophora tritici-repentis isolates were sourced from Australia, Europe, North Africa and the USA for genome assembly, annotation and comparative analyses to identify key pathogenic factors and advance public knowledge on wheat tan spot disease.
In 2018 eight annotated genomes of Pyrenophora tritici-repentis were published in DDBJ/EMBL/GenBank under accessions NQIK00000000, MVBF00000000, MVBG00000000, MVBH00000000, MVBI00000000, MUXC00000000, NRDI00000000 and NQWZ00000000.
In 2018 an extra twelve annotated genomes were also submitted to DDBJ/EMBL/GenBank.
List of Publications
In 2018 project FL3 published four manuscripts based directly on the high-through-put analyses conducted on Pawsey resources.
1: Moolhuijzen P, See PT, Hane JK, Shi G, Liu Z, Oliver RP, Moffat CS.
Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis
reveals chromosomal variations and genome plasticity. BMC Genomics. 2018 Apr
23;19(1):279. doi: 10.1186/s12864-018-4680-3.
2: Moolhuijzen PM, See PT, Oliver RP, Moffat CS. Genomic distribution of a novel
Pyrenophora tritici-repentis ToxA insertion element. PLoS One. 2018 Oct
31;13(10):e0206586. doi: 10.1371/journal.pone.0206586.
3: Moffat CS, Stoll T, Moolhuijzen P. Proteomics of the wheat tan spot pathogen
Pyrenophora tritici-repentis. BMC Res Notes. 2018 Nov 29;11(1):846. doi:
4: Moolhuijzen P, See PT, Moffat CS. Exploration of wheat and pathogen
transcriptomes during tan spot infection. BMC Res Notes. 2018 Dec 19;11(1):907.
Published Pyrenophora tritici-repentis annotated genomes released under DDBJ/EMBL/GenBank accessions NQIK00000000, MVBF00000000, MVBG00000000, MVBH00000000, MVBI00000000, MUXC00000000, NRDI00000000 and NQWZ00000000.
Figure 1. Bionanno optical mapping of an Australian wheat pathogen Pyrenophora tritici-repentis M4