ADDIN EN.REFLIST Castanera R, Lopez-Varas L, Borgognone A, LaButti K,
Lapidus A, Schmutz J, Grimwood J, Perez G, Pisabarro A G,Grigoriev I V. 2016.
Transposable elements versus the fungal genome: impact on whole-genome
architecture and transcriptional profiles. PLoS
Genetics, 12, e1006108.
Chen S B, Songkumarn P, Venu R, Gowda M, Bellizzi M, Hu J
N, Liu W D, Ebbole D, Meyers B,Mitchell T. 2013. Identification and
characterization of in planta–expressed secreted effector proteins from Magnaporthe
oryzae that induce cell death in rice. Molecular
Plant-Microbe
Interactions, 26, 191-202.
Cho Y, Ohm R A, Grigoriev I V,Srivastava A. 2013.
Fungal‐specific transcription factor AbPf2 activates pathogenicity in Alternaria
brassicicola. The Plant Journal, 75, 498-514.
Chujo T,Scott B. 2014. Histone H3K9 and H3K27 methylation
regulates fungal alkaloid biosynthesis in a fungal endophyte–plant symbiosis. Molecular Microbiology, 92, 413-434.
Connolly L R, Smith K M,Freitag M. 2013. The Fusarium
graminearum histone H3K27 methyltransferase KMT6 regulates development and
expression of secondary metabolite gene clusters. PLoS Genetics, 9,
e1003916.
Croll D,McDonald B A. 2012. The accessory genome as a
cradle for adaptive evolution in pathogens. PLoS
Pathogens, 8, e1002608.
Dallery J-F, Lapalu N, Zampounis A, Pigné S, Luyten I,
Amselem J, Wittenberg A H, Zhou S, de Queiroz M V,Robin G P. 2017. Gapless
genome assembly of Colletotrichum higginsianum reveals chromosome
structure and association of transposable elements with secondary metabolite
gene clusters. BMC Genomics, 18, 1-22.
Dean R, Van Kan J A, Pretorius Z A, Hammond‐Kosack K E,
Di Pietro A, Spanu P D, Rudd J J, Dickman M, Kahmann R,Ellis J. 2012. The Top
10 fungal pathogens in molecular plant pathology. Molecular Plant Pathology, 13,
414-430.
Dean R A, Talbot N J, Ebbole D J, Farman M L, Mitchell T
K, Orbach M J, Thon M, Kulkarni R, Xu J-R,Pan H. 2005. The genome sequence of
the rice blast fungus Magnaporthe grisea. Nature, 434, 980-986.
Déléris A, Berger F,Duharcourt S. 2021. Role of Polycomb
in the control of transposable elements. Trends
in Genetics, 37, 882-889.
Djamei A, Schipper K, Rabe F, Ghosh A, Vincon V, Kahnt J,
Osorio S, Tohge T, Fernie A R,Feussner I. 2011. Metabolic priming by a secreted
fungal effector. Nature, 478, 395-398.
Dong S M, Raffaele S,Kamoun S. 2015. The two-speed
genomes of filamentous pathogens: waltz with plants. Current Opinion in Genetics Development, 35, 57-65.
Fouché S, Badet T, Oggenfuss U, Plissonneau C, Francisco
C S,Croll D. 2020. Stress-driven transposable element de-repression dynamics
and virulence evolution in a fungal pathogen. Molecular Biology Evolution, 37,
221-239.
Freitag M. 2017. Histone methylation by SET domain
proteins in fungi. Annual Review of Microbiology, 71, 413-439.
Gacek A,Strauss J. 2012. The chromatin code of fungal
secondary metabolite gene clusters. Applied
Microbiology Biotechnology, 95,
1389-1404.
Giraldo M C, Dagdas Y F, Gupta Y K, Mentlak T A, Yi M,
Martinez-Rocha A L, Saitoh H, Terauchi R, Talbot N J,Valent B. 2013. Two
distinct secretion systems facilitate tissue invasion by the rice blast fungus Magnaporthe
oryzae. Nature Communications, 4, 1-12.
Giraldo M C,Valent B. 2013. Filamentous plant pathogen
effectors in action. 11, 800-814.
Gómez-Rubio V. 2017. ggplot2-elegant graphics for data
analysis. Journal of Statistical Software, 77, 1-3.
Guo X R, Zhong D B, Xie W, He Y H, Zheng Y Q, Lin Y, Chen
Z J, Han Y J, Tian D G,Liu W D. 2019. Functional identification of novel cell
death-inducing effector proteins from Magnaporthe oryzae. Rice, 12, 1-12.
Honda S,Selker E U. 2008. Direct interaction between DNA
methyltransferase DIM-2 and HP1 is required for DNA methylation in Neurospora crassa. Molecular Cellular
Biology, 28, 6044-6055.
Hosaka A,Kakutani T. 2018. Transposable elements, genome
evolution and transgenerational epigenetic variation. Current Opinion in Genetics Development, 49, 43-48.
Islam M T, Croll D, Gladieux P, Soanes D M, Persoons A,
Bhattacharjee P, Hossain M, Gupta D R, Rahman M,Mahboob M G. 2016. Emergence of
wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe
oryzae. BMC Biology, 14, 1-11.
Jamieson K, Rountree M R, Lewis Z A, Stajich J E,Selker E
U. 2013. Regional control of histone H3 lysine 27 methylation in Neurospora. Proceedings of the National Academy of
Sciences, 110, 6027-6032.
Kasuga T,Gijzen M. 2013. Epigenetics and the evolution of
virulence. Trends in Microbiology, 21, 575-582.
Kershaw M J,Talbot N J. 2009. Genome-wide functional
analysis reveals that infection-associated fungal autophagy is necessary for
rice blast disease. Proceedings of the
National Academy of Sciences, 106,
15967-15972.
Latorre S M, Reyes-Avila C S, Malmgren A, Win J, Kamoun
S,Burbano H A. 2020. Differential loss of effector genes in three recently
expanded pandemic clonal lineages of the rice blast fungus. BMC Biology, 18, 1-15.
Li B,Dewey C N. 2011. RSEM: accurate transcript
quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 1-16.
Li Y, Han Y J, Qu M Y, Chen J, Chen X F, Geng X Q, Wang Z
H,Chen S B. 2020. Apoplastic cell death-inducing proteins of filamentous plant
pathogens: roles in plant-pathogen interactions. Frontiers in Genetics, 11,
661.
Lin C Y, Wu Z L, Shi H B, Yu J W, Xu M T, Lin F C, Kou Y
J,Tao Z. 2022. The additional PRC2 subunit and Sin3 histone deacetylase complex
are required for the normal distribution of H3K27me3 occupancy and
transcriptional silencing in Magnaporthe oryzae. New Phytologist, 236, 576-589
Meile L, Peter J, Puccetti G, Alassimone J, McDonald B
A,Sánchez-Vallet A. 2020. Chromatin dynamics contribute to the spatiotemporal
expression pattern of virulence genes in a fungal plant pathogen. MBio, 11, e02343-02320.
Meng S, Liu Z Q, Shi H B, Wu Z L, Qiu J H, Wen H, Lin F
C, Tao Z, Luo C X,Kou Y J. 2021. UvKmt6-mediated H3K27 trimethylation is
required for development, pathogenicity, and stress response in Ustilaginoidea
virens. Virulence, 12, 2972-2988.
Mirzadi Gohari A, Mehrabi R, Robert O, Ince I A, Boeren
S, Schuster M, Steinberg G, De Wit P J,Kema G H. 2014. Molecular
characterization and functional analyses of ZtWor1, a transcriptional regulator
of the fungal wheat pathogen Zymoseptoria tritici. Molecular Plant Pathology, 15,
394-405.
Mosquera G, Giraldo M C, Khang C H, Coughlan S,Valent B.
2009. Interaction transcriptome analysis identifies Magnaporthe oryzae BAS1-4 as biotrophy-associated secreted proteins in rice blast disease. The Plant Cell, 21, 1273-1290.
Nishimura T, Mochizuki S, Ishii-Minami N, Fujisawa Y,
Kawahara Y, Yoshida Y, Okada K, Ando S, Matsumura H,Terauchi R. 2016. Magnaporthe
oryzae glycine-rich secretion protein, Rbf1 critically participates in
pathogenicity through the focal formation of the biotrophic interfacial
complex. PLoS Pathogens, 12, e1005921.
Ökmen B, Collemare J, Griffiths S, van der Burgt A, Cox
R,de Wit P J. 2014. Functional analysis of the conserved transcriptional
regulator CfWor1 in Cladosporium fulvum reveals diverse roles in the
virulence of plant pathogenic fungi. Molecular
Microbiology, 92, 10-27.
Pham K T M, Inoue Y, Vu B V, Nguyen H H, Nakayashiki T,
Ikeda K-i,Nakayashiki H. 2015. MoSET1 (histone H3K4 methyltransferase in Magnaporthe
oryzae) regulates global gene expression during infection-related morphogenesis. PLoS Genetics, 11, e1005385.
Rebollo R, Romanish M T,Mager D L. 2012. Transposable
elements: an abundant and natural source of regulatory sequences for host
genes. Annual Review of Genetics, 46, 21-42.
Robinson M D, McCarthy D J,Smyth G K. 2010. edgeR: a
Bioconductor package for differential expression analysis of digital gene
expression data. Bioinformatics, 26, 139-140.
Rodriguez‐Moreno L, Ebert M K, Bolton M D,Thomma B P.
2018. Tools of the crook‐infection strategies of fungal plant pathogens. The Plant Journal, 93, 664-674.
Rovenich H, Boshoven J C,Thomma B P. 2014. Filamentous
pathogen effector functions: of pathogens, hosts and microbiomes. Current Opinion in Plant Biology, 20, 96-103.
Rybak K, See P T, Phan H T, Syme R A, Moffat C S, Oliver
R P,Tan K C. 2017. A functionally conserved Zn2Cys6 binuclear cluster
transcription factor class regulates necrotrophic effector gene expression and
host‐specific virulence of two major Pleosporales fungal pathogens of wheat. Molecular Plant Pathology, 18, 420-434.
Saitoh H, Fujisawa S, Mitsuoka C, Ito A, Hirabuchi A,
Ikeda K, Irieda H, Yoshino K, Yoshida K,Matsumura H. 2012. Large-scale gene
disruption in Magnaporthe oryzae identifies MC69, a secreted protein
required for infection by monocot and dicot fungal pathogens. PloS Pathogens, 8, e1002711.
Sánchez-Vallet A, Fouché S, Fudal I, Hartmann F E, Soyer
J L, Tellier A,Croll D. 2018. The genome biology of effector gene evolution in
filamentous plant pathogens. Annual Review
of Phytopathology, 56, 21-40.
Santhanam P,Thomma B P. 2013. Verticillium dahliae Sge1 differentially regulates expression of candidate effector genes. Molecular Plant-Microbe Interactions, 26, 249-256.
Schmidt S M,Panstruga R. 2011. Pathogenomics of fungal
plant parasites: what have we learnt about pathogenesis? Current Opinion in Plant Biology, 14, 392-399.
Seidl M F,Thomma B P. 2017. Transposable elements direct
the coevolution between plants and microbes. Trends in Genetics, 33, 842-851.
Slotkin R K,Martienssen R. 2007. Transposable elements
and the epigenetic regulation of the genome. Nature Reviews Genetics, 8,
272-285.
Soyer J L, El Ghalid M, Glaser N, Ollivier B, Linglin J,
Grandaubert J, Balesdent M-H, Connolly L R, Freitag M,Rouxel T. 2014.
Epigenetic control of effector gene expression in the plant pathogenic fungus Leptosphaeria
maculans. PLoS Genetics, 10, e1004227.
Studt L, Janevska S, Arndt B, Boedi S, Sulyok M, Humpf
H-U, Tudzynski B,Strauss J. 2017. Lack of the COMPASS component Ccl1 reduces
H3K4 trimethylation levels and affects transcription of secondary metabolite
genes in two plant–pathogenic Fusarium species. Frontiers in Microbiology, 7,
2144.
Studt L, Rösler S M, Burkhardt I, Arndt B, Freitag M,
Humpf H U, Dickschat J S,Tudzynski B. 2016. Knock‐down of the methyltransferase
Kmt6 relieves H3K27me3 and results in induction of cryptic and otherwise silent
secondary metabolite gene clusters in Fusarium fujikuroi. Environmental Microbiology, 18, 4037-4054.
Wang L Y, Chen H, Li J J, Shu H D, Zhang X X, Wang Y C,
Tyler B M,Dong S M. 2020. Effector gene silencing mediated by histone
methylation underpins host adaptation in an oomycete plant pathogen. Nucleic Acids Research, 48, 1790-1799.
Wu C X, Lin Y H, Zheng H W, Abubakar Y S, Peng M H, Li J
J, Yu Z, Wang Z H, Naqvi N I,Li G P. 2021. The retromer CSC subcomplex is
recruited by MoYpt7 and sequentially sorted by MoVps17 for
effective conidiation and pathogenicity of the rice blast fungus. Molecular Plant Pathology, 22, 284-298.
Wu Z L, Qiu J H, Shi H B, Lin C Y, Yue J-N, Liu Z Q, Xie
W, Kou Y J,Tao Z. 2021. Polycomb repressive complex 2 coordinates with Sin3
histone deacetylase complex to epigenetically reprogram genome-wide expression
of effectors and regulate pathogenicity in Magnaporthe oryzae. bioRxiv.
Yoshida K, Saitoh H, Fujisawa S, Kanzaki H, Matsumura H,
Yoshida K, Tosa Y, Chuma I, Takano Y,Win J. 2009. Association genetics reveals
three novel avirulence genes from the rice blast fungal pathogen Magnaporthe
oryzae. The Plant Cell, 21(5), 1573-1591.
Zhang W, Huang J,Cook D E. 2021. Histone modification
dynamics at H3K27 are associated with altered transcription of in planta
induced genes in Magnaporthe oryzae. PLoS
Genetics, 17, e1009376.
Zhong Z H, Chen M L, Lin L Y, Chen R Q, Liu D,
Norvienyeku J, Zheng H K,Wang Z H. 2020. Genetic Variation Bias toward
Noncoding Regions and Secreted Proteins in the Rice Blast Fungus Magnaporthe
oryzae. Msystems, 5, e00346-00320.
Zhong Z H, Lin L Y, Chen M L, Lin L L, Chen X F, Lin Y H,
Chen X, Wang Z H, Norvienyeku J,Zheng H K. 2019. Expression divergence as an
evolutionary alternative mechanism adopted by two rice subspecies against rice
blast infection. Rice, 12, 1-10.
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