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

BMC Genomics
Chenxi ChenThomas Mitchell

Abstract

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. 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 virul...Continue Reading

References

Nov 1, 1995·Molecular Plant-microbe Interactions : MPMI·S KangB Valent
Jan 1, 1996·Methods in Enzymology·W R Pearson
Oct 1, 1996·Proceedings of the National Academy of Sciences of the United States of America·H W van VeenW N Konings
Mar 23, 2000·Letters in Applied Microbiology·T H Al-Samarrai, J Schmid
Sep 7, 2000·Microbiology and Molecular Biology Reviews : MMBR·S J Saupe
Nov 10, 2001·Annual Review of Phytopathology·J E LeachH Leung
Feb 15, 2002·Molecular Plant-microbe Interactions : MPMI·Mark L FarmanSally A Leong
Sep 23, 2003·Nucleic Acids Research·Brian J HaasOwen White
Oct 7, 2003·Annual Review of Microbiology·Nicholas J Talbot
Apr 23, 2005·Nature·Ralph A DeanBruce W Birren
Jun 28, 2005·Nucleic Acids Research·Mario Stanke, Burkhard Morgenstern
Dec 13, 2005·BMC Genomics·Natalie D FedorovaWilliam C Nierman
Feb 1, 1993·Applied and Environmental Microbiology·N J TalbotJ E Hamer
Dec 13, 2006·Molecular Plant-microbe Interactions : MPMI·Thomas K BaldwinKim E Hammond-Kosack
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
May 11, 2007·Annual Review of Phytopathology·Daniel J Ebbole
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Apr 23, 2008·Current Protocols in Bioinformatics·Nansheng Chen
Jan 1, 1991·Annual Review of Phytopathology·B Valent, F G Chumley
Feb 17, 2009·Nature Reviews. Microbiology·Richard A Wilson, Nicholas J Talbot
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
May 8, 2009·Genome Research·Ruiqiang LiJun Wang
Jun 6, 2009·Bioinformatics·Ruiqiang LiJun Wang
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jun 23, 2009·Genome Research·Martin KrzywinskiMarco A Marra
Dec 15, 2010·Science·Jan SchirawskiRegine Kahmann
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev

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Citations

Aug 16, 2016·Environmental Science and Pollution Research International·Amanda Abdallah ChaibubLeila Garcês de Araújo
Apr 18, 2018·Molecular Plant-microbe Interactions : MPMI·Stefania BertazzoniJames K Hane
May 17, 2018·Annual Review of Phytopathology·Andrea Sánchez-ValletDaniel Croll
Jul 22, 2020·Phytopathology·He YangLi-Jun Ma
Feb 4, 2016·G3 : Genes - Genomes - Genetics·Megan C McDonaldPeter S Solomon
Nov 18, 2015·Molecular Plant Pathology·Haifeng ZhangZhengguang Zhang
Mar 6, 2019·Molecular Biology and Evolution·Luis B Gómez LucianoWen-Hsiung Li
Dec 24, 2020·FEMS Microbiology Letters·Pallabi SahaSubhankar Roy-Barman

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Datasets Mentioned

BETA
FJ81278
ATNU00000000
ATNT00000000
HN19311
SRS453988
SRX316682

Methods Mentioned

BETA
electrophoresis
RNA-Seq
gene knockout
PCR

Software Mentioned

Illumina Genome Analyzer II
SOAPaligner2
PASA
Velvet
SAMtools
Inchworms
snpEff
FASTA
Seqclean
Velvet Columbus

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