Genome sequencing of four Pyricularia species provides insights into the evolution of Blast-Disease Fungi

Luis B. Gomez Luciano 1,2,3 Isheng Jason Tsai 1 Yukio Tosa 4 Izumi Chuma 4 Hitoshi Nakayashiki 4 Mei-yeh Jade Lu 1 Wen-Hsiung Li 1,2,3,5
1Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
2Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 40227, Taiwan
3Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
4Department of Agrobioscience, Kobe University, Kobe 657-8501, Japan
5Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA

Pyricuaria oryzae is the well-known fungal pathogen of blast disease that destroys rice, millet, wheat, oat, and other crops. Several related species of the fungus also cause blast disease in different hosts. To study the evolution of blast disease pathogens, we sequenced and obtained high-quality de novo genome assemblies of four species from the Pyricularia genus. In particular, we obtained a chromosome-level assembly, using SMRT and Illumina sequencing, of a P. oryzae strain isolated from finger millet. This genome showed overall synteny with the P. oryzae 70-15 reference genome, but we found major intra- and interchromosomal rearrangements and significant differences in gene content. The rearrangements include a partial fusion of two chromosomes, large inversions and insertions. Furthermore, the 500 kb unassigned region of the reference genome is located within a chromosome of the finger millet isolate. Genomes of the four Pyricularia species have undergone notable changes. Their sizes differ by more than 8 Mb, mainly because the proportion of repeats goes from 7.8 to 25.10 %. We predicted effector genes and found a surprising high proportion of effectors comprising gene families. Here we report the genome structure evolution and the repertoire of predicted effector genes and other putative genes involved in adaptation of four Pyricularia species to their hosts, and discuss the implications for blast-disease pathogen evolution.