Comparative analysis of the genome of the field isolate V86010 of the rice blast fungus Magnaporthe oryzae from Philippines

doi:10.1016/S2095-3119(16)61607-6

Journal of Integrative Agriculture ›› 2017, Vol. 16 ›› Issue (10): 2222-2230.DOI: 10.1016/S2095-3119(16)61607-6

收稿日期:2016-12-28 出版日期:2017-10-20 发布日期:2017-09-30

Comparative analysis of the genome of the field isolate V86010 of the rice blast fungus Magnaporthe oryzae from Philippines

ZHU Kun-peng^{1, 2}, BAO Jian-dong^{1, 2}, ZHANG Lian-hu1^{, 2}, YANG Xue^{1, 2}, LI Yuan^{1, 2}, Zhu Ming-hui^{1, 2}, LIN Qing-yun^{1, 2}, ZHAO Ao^{1, 2}, ZHAO Zhen^{1, 2}, ZHOU Bo³, LU Guo-dong^{1, 2}

¹ State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, P.R.China
² Key Laboratory of Biopesticide and Chemistry Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, P.R.China
³ International Rice Research Institute, Metro Manila, DAPO Box 7777, Philippines

Received:2016-12-28 Online:2017-10-20 Published:2017-09-30
Contact: Correspondence LU Guo-dong, Tel: +86-591-83789478, E-mail: gdlufafu@163.com; ZHOU Bo, E-mail: b.zhou@irri.org
About author:Zhu Kun-peng, E-mail: kunpengzhu2014@126.com;
Supported by:
This work was supported by the grants from the National Natural Science Foundation of China (31528017 and 31461143019).

摘要/Abstract

Abstract: Genome dynamics of pathogenic organisms are driven by plant host and pathogenic organism co-evolution, in which pathogen genomes are used to overcome stresses imposed by hosts with various genetic backgrounds through generation of a range of field isolates. This model also applies to the rice host and its fungal pathogen Magnaporthe oryzae. To better understand genetic variation of M. oryzae in nature, the field isolate V86010 from the Philippines was sequenced and analyzed. Genome annotation found that the assembled V86010 genome was composed of 1 931 scaffolds with a combined length of 38.9 Mb. The average GC ratio is 51.3% and repetitive elements constitute 5.1% of the genome. A total of 11 857 genes including 616 effector protein genes were predicted using a combined analysis pipeline. All predicted genes and effector protein genes of isolate V86010 distribute on the eight chromosomes when aligned with the assembled genome of isolate 70-15. Effector protein genes are located disproportionately at several chromosomal ends. The Pot2 elements are abundant in V86010. Seven V86010-specific effector proteins were found to suppress programmed cell death induced by BAX in tobacco leaves using an Agrobacterium-mediated transient assay. Our results may provide useful information for further study of the molecular and genomic dynamics in the evolution of M. oryzae and rice host interactions, and for characterizing novel effectors and AVR genes in the rice blast pathogen.

Key words: Magnaporthe oryzae , genetic variation , comparative genomics , effectors , avirulence genes

. [J]. Journal of Integrative Agriculture, 2017, 16(10): 2222-2230.

ZHU Kun-peng, BAO Jian-dong, ZHANG Lian-hu, YANG Xue, LI Yuan, Zhu Ming-hui, LIN Qing-yun, ZHAO Ao, ZHAO Zhen, ZHOU Bo, LU Guo-dong. Comparative analysis of the genome of the field isolate V86010 of the rice blast fungus Magnaporthe oryzae from Philippines[J]. Journal of Integrative Agriculture, 2017, 16(10): 2222-2230.

参考文献

Block A, Li G, Zheng Q F, Alfano J R. 2008. Phytopathogen type III effector weaponry and their plant targets. Current Opinion in Plant Biology, 11, 396–403.

Böhnert H U, Fudal I, Dioh W, Tharreau D, Notteghem J L, Lebrun M H. 2004. A putative polyketide synthase/peptide synthetase from Magnaporthe grisea signals pathogen attack to resistant rice. The Plant Cell, 16, 2499–2513.

Chen C, Lian B, Hu J, Zhai H, Wang X, Venu R C, Liu E, Wang Z, Chen M, Wang B, Wang G L, Wang Z, Mitchell T K. 2013. Genome comparison of two Magnaporthe oryzae field isolates reveals genome variations and potential virulence effectors. BMC Genomics, 14, 1–12.

Chen S, Songkumarn P, Liu J, Wang G L. 2009. A versatile zero background T-vector system for gene cloning and functional genomics. Plant Physiology, 150, 1111–1121.

Collmer A, Alfano J R. 2000. Pseudomonas syringae Hrp type III secretion system and effector proteins. Proceedings of the National Academy of Sciences of the United States of America, 97, 8770–8777.

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, Read N D, Lee Y H, Carbone I, Brown D, Oh Y Y, Donofrio N, Jeong J S, Soanes D M, Djonovic S, Kolomiets E, et al. 2005. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature International Weekly Journal of Science, 434, 980–986.

Dong Y, Li Y, Zhao M, Jing M, Liu X, Liu M, Guo X, Zhang X, Chen Y, Liu Y, Liu Y, Ye W, Zhang H, Wang Y, Zheng X, Wang P, Zhang Z. 2015. 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. PLoS Pathogens, 11, e1004801.

Dou D, Kale S D, Wang X, Chen Y, Wang Q, Wang X, Jiang R H, Arredondo F D, Anderson R G, Thakur P B, McDowell J M, Wang Y, Tyler B M. 2008. Conserved C-terminal motifs required for avirulence and suppression of cell death by Phytophthora sojae effector Avr1b. The Plant Cell, 20, 1118–1133.

Ebbole D J. 2007. Magnaporthe as a model for understanding host-pathogen interactions. Phytopathology, 45, 437–456.

Hogenhout S A, Van der Hoorn R A, Terauchi R, Kamoun S. 2009. Emerging concepts in effector biology of plant-associated organisms. Molecular Plant-Microbe Interactions, 22, 115–122.

Hu J, Chen C, Peever T, Dang H, Lawrence C, Mitchell T. 2012. Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer. BMC Genomics, 13, 171–196.

Jantasuriyarat C, Gowda M, Haller K, Hatfield J, Lu G, Stahlberg E, Zhou B, Li H, Kim H, Yu Y, Dean R A, Wing R A, Soderlund C, Wang G L. 2010. Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction. Plant Physiology, 138, 105–115.

Jones, Jonathan D G, Jeffery L D. 2006. The plant immune system. Nature, 444, 323–329.

Kang S, Lebrum M H, Farrall L, Valent B. 2001. Gain of virulence caused by insertion of a Pot3 transposon in a Magnaporthe grisea avirulence gene. Molecular Plant-Microbe Interactions, 14, 671–674.

Kang S, Sweigard J A, Valent B. 1995. The PWL host specificity gene family in the blast fungus Magnaporthe grisea. Molecular Plant-Microbe Interactions, 8, 939–948.

Kim S, Park J, Park S Y, Mitchell T K, Lee Y H. 2010. Identification and analysis of in planta expressed genes of Magnaporthe oryzae. BMC Genomics, 11, 635–643.

Kumar J, Nelson R J, Zeigler R S. 1999. Population structure and dynamics of Magnaporthe grisea in the Indian Himalayas. Genetics, 152, 971–984.

Kurtz S, Phillippy A, Delcher A L, Smoot M, Shumway M, Antonescu C, Salzberg S L. 2004. Versatile and open software for comparing large genomes. Genome Biology, 5, 1–9.

Leung H, Borromeo E S, Bernardo M A, Notteghem J L. 1988. Genetic analysis of virulence in the rice blast fungus Magnaporthe grisea. Phytopathology, 78, 1227–1233.

Li W, Wang B, Wu J, Lu G, Hu Y, Zhang X, Zhang Z, Zhao Q, Feng Q, Zhang H, Wang Z, Wang G, Han B, Wang Z, Zhou B. 2009. The Magnaporthe oryzae avirulence gene AVRPiz-t encodes a predicted secreted protein that triggers the immunity in rice mediated by the blast resistance gene Piz-t. Molecular Plant-microbe Interactions, 22, 411–420.

Liu W, Liu J, Ning Y, Ding B, Wang X, Wang Z, Wang G L. 2013. Recent progress in understanding PAMP- and effector-triggered immunity against the rice blast fungus Magnaporthe oryzae. Molecular Plant, 6, 605–620.

Ma L J, Does H C, Borkovich K A, Coleman J J, Daboussi M J, Di Pietro A. 2010. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature, 464, 367–373.

Ma L, Lukasik E, Gawehns F, Takken F L. 2012. The use of agroinfiltration for transient expression of plant resistance and fungal effector proteins in Nicotiana benthamiana Leaves. Methods in Molecular Biology, 835, 61–74.

Miki S, Matsui K, Kito H, Otsuka K, Ashizawa T, Yasuda N, Fukiya S, Sato J, Hirayae K, Fujita Y, Nakajima T, Tomita F, Sone T. 2009. Molecular cloning and characterization of the AVR-Pia locus from a Japanese field isolate of Magnaporthe oryzae. Molecular Plant Pathology, 10, 361–374.

Orbach M J, Farrall L, Sweigard J A, Chumley F G, Valent B. 2000. A telomeric avirulence gene determines efficacy for the rice blast resistance gene Pi-ta. The Plant Cell, 12, 2019–2032.

Ray S, Singh P K, Gupta D K, Mahato A K, Sarkar C, Rathour R, Singh N K, Sharma T R. 2016. Analysis of Magnaporthe oryzae genome reveals a fungal effector, which is able to induce resistance response in transgenic rice line containing resistance gene, pi54. Frontiers in Plant Science, 7, 1140.

Rehmeyer C, Li W, Kusaba M, Kim Y S, Brown D, Staben C, Dean R, Farman M. 2006. Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae. Nucleic Acids Research, 34, 4685–4701.

Ribot C, Césari S, Abidi I, Chalvon V, Bournaud C, Vallet J, Lebrun M H, Morel J B, Kroj T. 2013. The Magnaporthe oryzae effector AVR1-CO39 is translocated into rice cells independently of a fungal-derived machinery. The Plant Journal, 74, 1–12.

Smith D R, Lee R W. 2008. Nucleotide diversity in the mitochondrial and nuclear compartments of Chlamydomonas reinhardtii: Investigating the origins of genome architecture. BMC Evolutionary Biology, 8, 156.

Sonnhammer E L, von Heijne G, Krogh A. 1998. A hidden Markov model for predicting transmembrane helices in protein sequences. International Conference on Intelligent Systems for Molecular Biology, 6, 175–182.

Talbot N J. 2003. On the trail of a cereal killer: Exploring the biology of Magnaporthe grisea. Microbiology, 57, 177–202.

Wessler S R. 2006. Transposable elements and the evolution of eukaryotic genomes. Proceedings of the National Academy of Sciences of the United States of America, 103, 17600–17601.

Wu J, Kou Y, Bao J, Li Y, Tang M, Zhu X, Ponaya A, Xiao G, Li J, Li C, Song M Y, Cumagun C J, Deng Q, Lu G, Jeon J S, Naqvi N I, Zhou B. 2015. Comparative genomics identifies the Magnaporthe oryzae avirulence effector AVRPi9 that triggers Pi9-mediated blast resistance in rice. New Phytologist, 206, 1463–1475.

Xue M, Yang J, Li Z, Hu S, Yao N, Dean R A, Zhao W, Shen M, Zhang H, Li C, Liu L, Cao L, Xu X, Xing Y, Hsiang T, Zhang Z, Xu J R, Peng Y L. 2012. Comparative analysis of the genomes of two field isolates of the rice blast fungus Magnaporthe oryzae. PLoS Genetics, 8, e1002869.

Yoshida K, Saitoh H, Fujisawa S, Kanzaki H, Matsumura H, Yoshida K, Tosa Y, Chuma I, Takano Y, Win J, Kamoun S, Terauchi R. 2009. Association genetics reveals three novel avirulence genes from the rice blast fungal pathogen Magnaporthe oryzae. The Plant Cell, 21, 1573–1591.

Zhang S, Wang L, Wu W, He L, Yang X, Pan Q. 2015. Function and evolution of Magnaporthe oryzae avirulence gene AVRPib responding to the rice blast resistance gene Pib. Scientific Reports, 5, 11642.

Comparative analysis of the genome of the field isolate V86010 of the rice blast fungus Magnaporthe oryzae from Philippines

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 0

编辑推荐

Metrics