title: Comparative analysis of the genomes of two field isolates of the rice blast fungus Magnaporthe oryzae.
abstract: Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice worldwide. The fungal pathogen is notorious for its ability to overcome host resistance. To better understand its genetic variation in nature, we sequenced the genomes of two field isolates, Y34 and P131. In comparison with the previously sequenced laboratory strain 70-15, both field isolates had a similar genome size but slightly more genes. Sequences from the field isolates were used to improve genome assembly and gene prediction of 70-15. Although the overall genome structure is similar, a number of gene families that are likely involved in plant-fungal interactions are expanded in the field isolates. Genome-wide analysis on asynonymous to synonymous nucleotide substitution rates revealed that many infection-related genes underwent diversifying selection. The field isolates also have hundreds of isolate-specific genes and a number of isolate-specific gene duplication events. Functional characterization of randomly selected isolate-specific genes revealed that they play diverse roles, some of which affect virulence. Furthermore, each genome contains thousands of loci of transposon-like elements, but less than 30% of them are conserved among different isolates, suggesting active transposition events in M. oryzae. A total of approximately 200 genes were disrupted in these three strains by transposable elements. Interestingly, transposon-like elements tend to be associated with isolate-specific or duplicated sequences. Overall, our results indicate that gain or loss of unique genes, DNA duplication, gene family expansion, and frequent translocation of transposon-like elements are important factors in genome variation of the rice blast fungus.
authors.affiliation: State Key Laboratory of Agrobiotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, China Agricultural University, Beijing, China.
authors.forename: Minfeng
authors.initials: M
authors.lastname: Xue
authors.forename: Jun
authors.initials: J
authors.lastname: Yang
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Li
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
authors.forename: Nan
authors.initials: N
authors.lastname: Yao
authors.forename: Ralph A
authors.initials: RA
authors.lastname: Dean
authors.forename: Wensheng
authors.initials: W
authors.lastname: Zhao
authors.forename: Mi
authors.initials: M
authors.lastname: Shen
authors.forename: Haiwang
authors.initials: H
authors.lastname: Zhang
authors.forename: Chao
authors.initials: C
authors.lastname: Li
authors.forename: Liyuan
authors.initials: L
authors.lastname: Liu
authors.forename: Lei
authors.initials: L
authors.lastname: Cao
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Xu
authors.forename: Yunfei
authors.initials: Y
authors.lastname: Xing
authors.forename: Tom
authors.initials: T
authors.lastname: Hsiang
authors.forename: Ziding
authors.initials: Z
authors.lastname: Zhang
authors.forename: Jin-Rong
authors.initials: JR
authors.lastname: Xu
authors.forename: You-Liang
authors.initials: YL
authors.lastname: Peng
mesh_terms: D004251:DNA Transposable Elements; D005656:Fungal Proteins; D020440:Gene Duplication; D016681:Genome, Fungal; D020082:Magnaporthe / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity*; D008969:Molecular Sequence Data; D005810:Multigene Family; D012275:Oryza / Q000382:microbiology*; D010935:Plant Diseases / Q000382:microbiology*; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D014774:Virulence
chemical_list: D004251:DNA Transposable Elements; D005656:Fungal Proteins