Genome analysis of barley leaf rust pathogen, Puccinia hordei

J Chen, P Zhang, C Dong and R Park

Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, NSW, 2567

Puccinia hordei is an obligate biotrophic parasite that causes rust disease on barley. Up to 62% yield loss of barley caused by the pathogen has been recorded. To better study its pathogenesis, we sequenced its genome with the aim to search for effector and other pathogenicity related genes. 500bp and 3000bp DNA insert size libraries were constructed and sequenced on Illumina platform. The sequencing data was assembled with SOAPdenovo into 15,913 scaffolds (127Mbp) of high continuity (N50 22Kbp). The genome assembly is shown to be highly complete by CEGMA, a pipeline that measures presence of eukaryotic core genes. About 55% of the genome is reported as repeat, resembling the repeat contents of other rust pathogen species. We predicted gene models by using RNA-Seq of plant leaf tissues infected by the pathogen. 36% of the RNA-Seq reads could be mapped to the assembled genome and about 29k gene models were predicted based on the mapping. Functional annotation of the gene models shows hundreds of interesting candidates for effector proteins. The high quality genome assembly and gene annotation provides a good reference genome for comparative genomics and will facilitate identification of virulence related genes.