title: Genome comparison of two Magnaporthe oryzae field isolates reveals genome variations and potential virulence effectors.
abstract: BACKGROUND
  Rice blast caused by the fungus Magnaporthe oryzae is an important disease in virtually every rice growing region of the world, which leads to significant annual decreases of grain quality and yield. To prevent disease, resistance genes in rice have been cloned and introduced into susceptible cultivars. However, introduced resistance can often be broken within few years of release, often due to mutation of cognate avirulence genes in fungal field populations.
  
  
  RESULTS
  To better understand the pattern of mutation of M. oryzae field isolates under natural selection forces, we used a next generation sequencing approach to analyze the genomes of two field isolates FJ81278 and HN19311, as well as the transcriptome of FJ81278. By comparing the de novo genome assemblies of the two isolates against the finished reference strain 70-15, we identified extensive polymorphisms including unique genes, SNPs (single nucleotide polymorphism) and indels, structural variations, copy number variations, and loci under strong positive selection. The 1.75 MB of isolate-specific genome content carrying 118 novel genes from FJ81278, and 0.83 MB from HN19311 were also identified. By analyzing secreted proteins carrying polymorphisms, in total 256 candidate virulence effectors were found and 6 were chosen for functional characterization.
  
  
  CONCLUSIONS
  We provide results from genome comparison analysis showing extensive genome variation, and generated a list of M. oryzae candidate virulence effectors for functional characterization.
authors.forename: Chenxi
authors.initials: C
authors.lastname: Chen
authors.forename: Bi
authors.initials: B
authors.lastname: Lian
authors.forename: Jinnan
authors.initials: J
authors.lastname: Hu
authors.forename: Huanchen
authors.initials: H
authors.lastname: Zhai
authors.forename: Xingxing
authors.initials: X
authors.lastname: Wang
authors.forename: R C
authors.initials: RC
authors.lastname: Venu
authors.forename: Erming
authors.initials: E
authors.lastname: Liu
authors.forename: Zhilong
authors.initials: Z
authors.lastname: Wang
authors.forename: Meilian
authors.initials: M
authors.lastname: Chen
authors.forename: Baohua
authors.initials: B
authors.lastname: Wang
authors.forename: Guo-Liang
authors.initials: GL
authors.lastname: Wang
authors.affiliation: Department of Plant Pathology, The Ohio State University, 2021 Coffey Road, Columbus, OH 43210, USA. zonghuaw@163.com.
authors.forename: Zonghua
authors.initials: Z
authors.lastname: Wang
authors.forename: Thomas K
authors.initials: TK
authors.lastname: Mitchell
mesh_terms: D019295:Computational Biology / Q000379:methods; D056915:DNA Copy Number Variations; D020869:Gene Expression Profiling; D014644:Genetic Variation; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing; D054643:INDEL Mutation; D020082:Magnaporthe / Q000235:genetics* / Q000472:pathogenicity; D012275:Oryza / Q000382:microbiology; D010935:Plant Diseases / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D059467:Transcriptome; D014774:Virulence / Q000235:genetics