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Open Access Research article

Genome comparison of two Magnaporthe oryzae field isolates reveals genome variations and potential virulence effectors

Chenxi Chen1, Bi Lian12, Jinnan Hu1, Huanchen Zhai24, Xingxing Wang2, RC Venu1, Erming Liu3, Zhilong Wang3, Meilian Chen2, Baohua Wang2, Guo-Liang Wang13, Zonghua Wang2* and Thomas K Mitchell1*

Author Affiliations

1 Department of Plant Pathology, The Ohio State University, 2021 Coffey Road, Columbus, OH 43210, USA

2 Key Laboratory of Bio-pesticide and Chemistry Biology, Ministry of Education, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou, Fujian 350002, China

3 Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, College of Agronomy, Hunan Agricultural University, 1 Nongda Road, Changsha, Hunan 410128, China

4 College of Bioengineering, Henan University of Technology, 100 Lianhua Ave., Zhengzhou, Henan 450001, China

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BMC Genomics 2013, 14:887  doi:10.1186/1471-2164-14-887

Published: 16 December 2013

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.

Keywords:
Magnaporthe oryzae; Next generation sequencing; Genome comparison; Candidate effectors identification; Isolate-specific genome content