Abstract
Rice blast caused by Magnaporthe oryzae (M. oryzae) is one of the most destructive diseases, which causes significant rice yield losses and affects global food security. To better understand genetic variations among different isolates of M. oryzae in the nature field, we re-sequenced and analyzed the genomes of three field isolates, QJ08-2006, QJ10-10, and QJ10-3001, which showed distinct pathogenicity on Xin-Yin-Zhan, an elite variety in South China. Genome annotation indicated that these three isolates assemblies have similar genome sizes with 38.4 Mb, 38.3 Mb, and 38.4 Mb, respectively. The QJ08-2006 assembly has 2082 contigs with an N50 of 127.4 kb, the QJ10-10 assembly has 2239 contigs with an N50 of 105.13 kb, the QJ10-3001 assembly has 2025 contigs with an N50 of 133.16 kb. A total of 10,432 genes including 1408 putative secreted protein genes were identified from the annotated isolate QJ08-2006 genome, 10,418 genes including 1410 putative secreted protein genes were identified in QJ10-10, and 10,401 genes including 1420 putative secreted protein genes were identified in QJ10-3001. There are as many as 11,076 identical genes in these three isolates and contained only a few unique genes among three isolates, of which 277 unique genes in QJ08-2006 and 264 unique genes in QJ10-10, and 213 unique genes in QJ10-3001. Most of the predicted secreted protein genes had been identified, and the three re-sequenced strains contained 371, 369, and 387 small Indel, respectively. Avr genes were analyzed in several sequenced Magnaporthe strains, the results revealed that Avr-Pi9 and Avr-Piz-t were present in all the sequenced isolates. The isolates QJ08-2006 contained AvrPib, QJ10-10, and QJ10-3001 had an insertion of a Pot3 element in the promoter of the AvrPib gene. Our results showed that, the rapid dominancy of virulence mutant isolates via clonal propagation displayed in the field after the release of the elite variety Xin-Yin-Zhan.
Highlights
Rice (Oryza sativa) is one of the major staple food crops for more than half of the human population worldwide [1]
A total of 10,432 genes including 1408 putative secreted protein genes were identified from the annotated isolate QJ08-2006 genome, 10,418 genes including 1410 putative secreted protein genes were identified in QJ10-10, and 10,401 genes including 1420 putative secreted protein genes were identified in QJ10-3001
Genomic DNA of isolates QJ08-2006, QJ10-10, and QJ10-3001 were prepared as paired-end libraries and sequenced by using the Illumina HiSeq2000 system at BGI Tech (Shenzhen, China)
Summary
Rice (Oryza sativa) is one of the major staple food crops for more than half of the human population worldwide [1]. Rice blast, caused by the filamentous ascomycete fungus Magnaporthe oryzae Pyricularia oryzae), occurs in every rice-growing regions in worldwide [3] [4], and poses a major threat to global food security [5] [6]. This pathogen can infect leaves, stems, panicles, nodes, and even roots of rice at the whole stage of development and infects wheat and other small grains [7] [8] [9]. As genomes of M. oryzae have been sequenced and the data of the genomes is available to the public [10], rice and M. oryzae have been developed as the classical model system for studying the plant-microbe interactions [11]
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