title: Global genome and transcriptome analyses of Magnaporthe oryzae epidemic isolate 98-06 uncover novel effectors and pathogenicity-related genes, revealing gene gain and lose dynamics in genome evolution.
abstract: Genome dynamics of pathogenic organisms are driven by pathogen and host co-evolution, in which pathogen genomes are shaped to overcome stresses imposed by hosts with various genetic backgrounds through generation of a variety of isolates. This same principle applies to the rice blast pathogen Magnaporthe oryzae and the rice host; however, genetic variations among different isolates of M. oryzae remain largely unknown, particularly at genome and transcriptome levels. Here, we applied genomic and transcriptomic analytical tools to investigate M. oryzae isolate 98-06 that is the most aggressive in infection of susceptible rice cultivars. A unique 1.4 Mb of genomic sequences was found in isolate 98-06 in comparison to reference strain 70-15. Genome-wide expression profiling revealed the presence of two critical expression patterns of M. oryzae based on 64 known pathogenicity-related (PaR) genes. In addition, 134 candidate effectors with various segregation patterns were identified. Five tested proteins could suppress BAX-mediated programmed cell death in Nicotiana benthamiana leaves. Characterization of isolate-specific effector candidates Iug6 and Iug9 and PaR candidate Iug18 revealed that they have a role in fungal propagation and pathogenicity. Moreover, Iug6 and Iug9 are located exclusively in the biotrophic interfacial complex (BIC) and their overexpression leads to suppression of defense-related gene expression in rice, suggesting that they might participate in biotrophy by inhibiting the SA and ET pathways within the host. Thus, our studies identify novel effector and PaR proteins involved in pathogenicity of the highly aggressive M. oryzae field isolate 98-06, and reveal molecular and genomic dynamics in the evolution of M. oryzae and rice host interactions.
authors.affiliation: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.
authors.forename: Yanhan
authors.initials: Y
authors.lastname: Dong
authors.affiliation: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Li
authors.affiliation: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.
authors.forename: Miaomiao
authors.initials: M
authors.lastname: Zhao
authors.affiliation: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.
authors.forename: Maofeng
authors.initials: M
authors.lastname: Jing
authors.affiliation: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.
authors.forename: Xinyu
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.
authors.forename: Muxing
authors.initials: M
authors.lastname: Liu
authors.affiliation: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.
authors.forename: Xianxian
authors.initials: X
authors.lastname: Guo
authors.affiliation: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.
authors.forename: Xing
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China.
authors.forename: Yongfeng
authors.initials: Y
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China.
authors.forename: Yanhong
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.
authors.forename: Wenwu
authors.initials: W
authors.lastname: Ye
authors.affiliation: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.
authors.forename: Haifeng
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.
authors.forename: Yuanchao
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.
authors.forename: Xiaobo
authors.initials: X
authors.lastname: Zheng
authors.affiliation: Department of Pediatrics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America.
authors.forename: Ping
authors.initials: P
authors.lastname: Wang
authors.affiliation: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.
authors.forename: Zhengguang
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D001483:Base Sequence; D005075:Biological Evolution; D005656:Fungal Proteins / Q000235:genetics; D020869:Gene Expression Profiling; D005800:Genes, Fungal / Q000235:genetics; D016681:Genome, Fungal; D055106:Genome-Wide Association Study; D020082:Magnaporthe / Q000235:genetics* / Q000472:pathogenicity*; D008969:Molecular Sequence Data; D012275:Oryza / Q000382:microbiology*; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology*; D016133:Polymerase Chain Reaction; D014774:Virulence / Q000235:genetics*
chemical_list: D005656:Fungal Proteins
references.citation: Mol Gen Genet. 1992 Mar;232(2):183-90
references.pmid: 1557024
references.citation: BMC Evol Biol. 2008;8:156
references.pmid: 18495022
references.citation: Plant Cell. 2009 Sep;21(9):2928-47
references.pmid: 19794118
references.citation: Mol Plant Microbe Interact. 2009 Apr;22(4):411-20
references.pmid: 19271956
references.citation: PLoS Pathog. 2011 Feb;7(2):e1001302
references.pmid: 21383978
references.citation: Annu Rev Phytopathol. 1991;29:443-67
references.pmid: 18479196
references.citation: Curr Opin Plant Biol. 2007 Aug;10(4):358-65
references.pmid: 17611143
references.citation: Bioinformatics. 2009 Aug 1;25(15):1966-7
references.pmid: 19497933
references.citation: Database (Oxford). 2011;2011:bar009
references.pmid: 21447597
references.citation: Nature. 2005 Apr 21;434(7036):980-6
references.pmid: 15846337
references.citation: Annu Rev Phytopathol. 2009;47:177-206
references.pmid: 19400653
references.citation: Annu Rev Phytopathol. 2004;42:185-209
references.pmid: 15283665
references.citation: Gene. 1997 Oct 1;198(1-2):289-96
references.pmid: 9370294
references.citation: Mol Cells. 2004 Feb 29;17(1):166-73
references.pmid: 15055545
references.citation: Plant Cell. 2009 May;21(5):1573-91
references.pmid: 19454732
references.citation: PLoS Genet. 2009 Dec;5(12):e1000757
references.pmid: 19997500
references.citation: Proc Int Conf Intell Syst Mol Biol. 1998;6:175-82
references.pmid: 9783223
references.citation: Evolution. 2000 Apr;54(2):337-51
references.pmid: 10937212
references.citation: PLoS Pathog. 2012;8(5):e1002711
references.pmid: 22589729
references.citation: Mol Plant Microbe Interact. 2010 Jun;23(6):791-8
references.pmid: 20459318
references.citation: EMBO J. 2003 Nov 3;22(21):5690-9
references.pmid: 14592968
references.citation: Mol Plant Microbe Interact. 2009 Apr;22(4):402-10
references.pmid: 19271955
references.citation: PLoS Pathog. 2011 Jul;7(7):e1002147
references.pmid: 21829350
references.citation: Yeast. 1995 Apr 15;11(4):355-60
references.pmid: 7785336
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: New Phytol. 2012 Oct;196(1):247-60
references.pmid: 22816601
references.citation: BMC Genomics. 2010;11:104
references.pmid: 20146797
references.citation: Nat Commun. 2013;4:1996
references.pmid: 23774898
references.citation: Plant Cell Physiol. 2012 Dec;53(12):2060-72
references.pmid: 23104764
references.citation: Genome Res. 2003 Sep;13(9):2178-89
references.pmid: 12952885
references.citation: Nat Methods. 2011;8(10):785-6
references.pmid: 21959131
references.citation: Mol Plant Microbe Interact. 2007 Oct;20(10):1175-82
references.pmid: 17918619
references.citation: BMC Bioinformatics. 2003 Sep 11;4:41
references.pmid: 12969510
references.citation: Environ Microbiol. 2014 Mar;16(3):788-801
references.pmid: 23895552
references.citation: Nucleic Acids Res. 1999 Jan 15;27(2):573-80
references.pmid: 9862982
references.citation: New Phytol. 2015 Jun;206(4):1463-75
references.pmid: 25659573
references.citation: Annu Rev Phytopathol. 2007;45:437-56
references.pmid: 17489691
references.citation: Mol Plant Microbe Interact. 1995 Nov-Dec;8(6):939-48
references.pmid: 8664503
references.citation: Mol Plant Microbe Interact. 2010 Jan;23(1):112-23
references.pmid: 19958144
references.citation: BMC Genomics. 2013;14:887
references.pmid: 24341723
references.citation: Cell Microbiol. 2010 Jun;12(6):705-15
references.pmid: 20374248
references.citation: Annu Rev Phytopathol. 2009;47:233-63
references.pmid: 19400631
references.citation: Fungal Genet Biol. 2014 Jun;67:51-7
references.pmid: 24731804
references.citation: BMC Bioinformatics. 2004 May 14;5:59
references.pmid: 15144565
references.citation: Mol Plant. 2013 May;6(3):605-20
references.pmid: 23340743
references.citation: Plant Cell. 2010 Apr;22(4):1388-403
references.pmid: 20435900
references.citation: BMC Bioinformatics. 2009;10:202
references.pmid: 19563654
references.citation: FEMS Microbiol Lett. 2007 Aug;273(2):157-65
references.pmid: 17590228
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D277-80
references.pmid: 14681412
references.citation: Plant Cell. 2009 Apr;21(4):1273-90
references.pmid: 19357089
references.citation: Mol Plant Microbe Interact. 2010 Aug;23(8):1053-68
references.pmid: 20615116
references.citation: Plant Cell. 1995 Aug;7(8):1221-33
references.pmid: 7549480
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4
references.pmid: 18077471
references.citation: Med Mycol. 2011 Jul;49(5):449-57
references.pmid: 21254965
references.citation: Biotechniques. 2003 Feb;34(2):374-8
references.pmid: 12613259
references.citation: Bioinformatics. 2012 Nov 1;28(21):2782-8
references.pmid: 22923299
references.citation: Nat Rev Microbiol. 2012 Jun;10(6):417-30
references.pmid: 22565130
references.citation: Genome Res. 2004 May;14(5):988-95
references.pmid: 15123596
references.citation: Nat Genet. 2006 Aug;38(8):953-6
references.pmid: 16832356
references.citation: Plant Cell. 2012 Jan;24(1):322-35
references.pmid: 22267486
references.citation: Plant Physiol. 2005 May;138(1):105-15
references.pmid: 15888683
references.citation: Mol Plant Microbe Interact. 2008 Dec;21(12):1635-42
references.pmid: 18986259
references.citation: Trends Plant Sci. 2013 Oct;18(10):555-65
references.pmid: 23910453
references.citation: Curr Opin Plant Biol. 2009 Aug;12(4):399-405
references.pmid: 19540152
references.citation: BMC Genet. 2014;15:45
references.pmid: 24725999
references.citation: Curr Opin Plant Biol. 2010 Aug;13(4):434-41
references.pmid: 20627803
references.citation: Genome Biol. 2004;5(2):R12
references.pmid: 14759262
references.citation: Mol Plant Microbe Interact. 2009 Feb;22(2):115-22
references.pmid: 19132864
references.citation: Genetics. 1999 Jul;152(3):971-84
references.pmid: 10388817
references.citation: Eukaryot Cell. 2011 Aug;10(8):1062-70
references.pmid: 21642506
references.citation: Mol Microbiol. 2005 Sep;57(5):1224-37
references.pmid: 16101997
references.citation: PLoS One. 2013;8(8):e72686
references.pmid: 24023632
references.citation: Mol Microbiol. 2006 Apr;60(1):67-80
references.pmid: 16556221
references.citation: PLoS One. 2011;6(1):e16439
references.pmid: 21283626
references.citation: FEMS Microbiol Lett. 2009 Apr;293(2):160-9
references.pmid: 19260966
references.citation: Plant Cell. 2012 Nov;24(11):4748-62
references.pmid: 23204406
references.citation: Annu Rev Phytopathol. 2002;40:349-79
references.pmid: 12147764
references.citation: Nucleic Acids Res. 2008 Apr;36(7):2284-94
references.pmid: 18287116
references.citation: Plant Cell. 2008 Apr;20(4):1118-33
references.pmid: 18390593
references.citation: Biosci Biotechnol Biochem. 2009 Aug;73(8):1779-86
references.pmid: 19661696
references.citation: Genome Res. 2013 Aug;23(8):1271-82
references.pmid: 23685541
references.citation: Plant Cell. 2011 Jun;23(6):2064-86
references.pmid: 21653195
references.citation: Bioinformatics. 2008 Mar 1;24(5):713-4
references.pmid: 18227114
references.citation: Plant Mol Biol. 2000 Apr;42(6):819-32
references.pmid: 10890530
references.citation: Plant Cell. 2000 Nov;12(11):2019-32
references.pmid: 11090206
references.citation: Annu Rev Microbiol. 2003;57:177-202
references.pmid: 14527276
references.citation: Plant Cell. 1993 Nov;5(11):1575-90
references.pmid: 8312740
references.citation: PLoS Genet. 2012;8(8):e1002869
references.pmid: 22876203
references.citation: Science. 2010 Aug 20;329(5994):953-5
references.pmid: 20724636
references.citation: Nat Genet. 2000 May;25(1):25-9
references.pmid: 10802651
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W451-4
references.pmid: 15980510
references.citation: Plant Cell. 2005 Jun;17(6):1839-50
references.pmid: 15894715
references.citation: Curr Opin Plant Biol. 2012 Aug;15(4):483-92
references.pmid: 22483402
references.citation: Curr Opin Plant Biol. 2008 Aug;11(4):396-403
references.pmid: 18657470
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Genome Res. 2010 Feb;20(2):265-72
references.pmid: 20019144
references.citation: Plant J. 2004 Dec;40(6):909-19
references.pmid: 15584956