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中国生物工程杂志

CHINA BIOTECHNOLOGY
中国生物工程杂志  2017, Vol. 37 Issue (6): 114-123    DOI: 10.13523/j.cb.20170617
综述     
基因组时代林木抗病分子机理研究的新进展
徐媛媛, 俞翰炳, 吴飞华, 吴晓梅
杭州师范大学生命与环境科学学院 杭州 310036
Molecular Mechanisms of Antimicrobial Defenses and Resistance in Forest Trees in a Genomic Era
XU Yuan-yuan, YU Han-bing, WU Fei-hua, WU Xiao-mei
College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
 全文: PDF(720 KB)   HTML
摘要: 林木的分子病理学研究长期以来落后于农业作物病理学。随着高通量测序技术的问世,林木的分子病理学研究迎来了一个崭新的时代。从2006年至今,杨树、云杉等重要森林树种的全基因组测序相继完成,这为全面解析林木的抗病过程提供了遗传背景。同时,转录组学和全基因组关联分析的应用使得人们能快速地积累大量的数据,从而为揭示林木和病原菌之间的分子互作机制奠定了基础。近两年来CRISPR/Cas9基因编辑等分子生物学技术创新不断。高效的分子生物学技术结合基因组学研究有利于林木育种的研究。以下阐述了林木对抗病原菌入侵的生理机制,综合论述了近十年来基因组学和转录组学研究在木本植物分子病理学方面所取得的成果,总结了分子生物学技术在林木抗病领域的研究成果,分析了存在的问题和未来发展的趋势,以期为林木抗病育种提供参考。
关键词: 分子病理学转录组学林木全基因组关联分析高通量测序    
Abstract: Molecular pathology of forest trees lagged behind the studies on agricultural crop pathology for a long time. The advances of high-throughput sequencing technologies have significantly contributed to the study on molecular pathology of forest trees. Since 2006, the completion of genome sequences of the black cottonwood, the Norway spruce and other important tree species has provided genetic background for the comprehensive understanding of antimicrobial process. Meanwhile, application of transcriptomics and genome-wide association studies has resulted in the rapid accumulation of massive data on molecular interactions between trees and their pathogens. Recently, molecular biology technologies such as CRISPR/Cas9 have emerged or grown rapidly. Effective molecular biology technology combined with genomic research is helpful for tree breeding. An overview of molecular mechanisms about responses of forest trees to their pathogens was provided, it highlights the achievements of the application of genomics and transcriptomics as well as molecular biology technologies on the research of molecular pathology of tree species, and discusses the challenges and prospects for the near future. It is hoped to provide reference for further tree breeding for disease resistance.
Key words: Genome-wide association study    Forest tree    Tanscriptomics    Molecular pathology    Hgh-throughput sequencing
收稿日期: 2016-12-08 出版日期: 2017-06-25
ZTFLH:  Q819  
基金资助: 浙江省自然科学基金资助项目(LZ16C020001,LQ14C020003)
通讯作者: 吴晓梅     E-mail: wuxm@hznu.edu.cn
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引用本文:

徐媛媛, 俞翰炳, 吴飞华, 吴晓梅. 基因组时代林木抗病分子机理研究的新进展[J]. 中国生物工程杂志, 2017, 37(6): 114-123.

XU Yuan-yuan, YU Han-bing, WU Fei-hua, WU Xiao-mei. Molecular Mechanisms of Antimicrobial Defenses and Resistance in Forest Trees in a Genomic Era. China Biotechnology, 2017, 37(6): 114-123.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.20170617        https://manu60.magtech.com.cn/biotech/CN/Y2017/V37/I6/114

[1] Neale D B, Kremer A. Forest tree genomics:growing resources and applications. Nat Rev Genet, 2011, 12(2):111-122.
[2] Kovalchuk A, Kerio S, Oghenekaro A O, et al. Antimicrobial defenses and resistance in forest trees:challenges and perspectives in a genomic era. Annu Rev Phytopathol, 2013, 51:221-244.
[3] Jones J D, Dangl J L. The plant immune system. Nature, 2006, 444(7117):323-329.
[4] Robert-Seilaniantz A, Grant M, Jones J D. Hormone crosstalk in plant disease and defense:more than just jasmonate-salicylate antagonism. Annu Rev Phytopathol, 2011, 49:317-343.
[5] Eyles A, Bonello P, Ganley R, et al. Induced resistance to pests and pathogens in trees. New Phytol, 2010, 185(4):893-908.
[6] Duplessis S, Major I, Martin F, et al. Poplar and pathogen interactions:insights from populus genome-wide analyses of resistance and defense gene families and gene expression profiling. Crit Rev Plant Sci, 2009, 28(5):309-334.
[7] Reeksting B J, Coetzer N, Mahomed W, et al. De novo sequencing, assembly, and analysis of the root transcriptome of Persea americana (Mill.) in response to Phytophthora cinnamomi and flooding. PLoS One, 2014, 9(2):e86399.
[8] Arnerup J, Lind M, Olson A, et al. The pathogenic white-rot fungus Heterobasidion parviporum triggers non-specific defence responses in the bark of Norway spruce. Tree Physiol, 2011, 31(11):1262-1272.
[9] Arnerup J, Nemesio-Gorriz M, Lunden K, et al. The primary module in Norway spruce defence signalling against H. annosum s.l. seems to be jasmonate-mediated signalling without antagonism of salicylate-mediated signalling. Planta, 2013, 237(4):1037-1045.
[10] Tuskan G A, DiFazio S, Jansson S, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, 2006, 313(5793):1596-1604.
[11] Xue L J, Guo W, Yuan Y, et al. Constitutively elevated salicylic acid levels alter photosynthesis and oxidative state but not growth in transgenic populus. Plant Cell, 2013, 25(7):2714-2730.
[12] Yuan Y, Chung J D, Fu X, et al. Alternative splicing and gene duplication differentially shaped the regulation of isochorismate synthase in Populus and Arabidopsis. Proc Natl Acad Sci USA, 2009, 106(51):22020-22025.
[13] Nystedt B, Street N R, Wetterbom A, et al. The Norway spruce genome sequence and conifer genome evolution. Nature, 2013, 497(7451):579-584.
[14] Zimin A, Stevens K A, Crepeau M, et al. Sequencing and assembly of the 22-Gb loblolly pine genome. Genetics, 2014, 196(3):875-890.
[15] Wegrzyn J L, Liechty J D, Stevens K A, et al. Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics, 2014, 196(3):891-909.
[16] Birol I, Raymond A, Jackman S D, et al. Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics, 2013, 29(12):1492-1497.
[17] Al-Dous E K, George B, Al-Mahmoud M E, et al. De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat Biotechnol, 2011, 29(6):521-527.
[18] He N, Zhang C, Qi X, et al. Draft genome sequence of the mulberry tree Morus notabilis. Nat Commun, 2013, 4:2445.
[19] Ming R, Hou S, Feng Y, et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature, 2008, 452(7190):991-996.
[20] Sato S, Hirakawa H, Isobe S, et al. Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. DNA Res, 2011, 18(1):65-76.
[21] Rahman A Y, Usharraj A O, Misra B B, et al. Draft genome sequence of the rubber tree Hevea brasiliensis. BMC Genomics, 2013, 14:75.
[22] Velasco R, Zharkikh A, Troggio M, et al. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One, 2007, 2(12):e1326.
[23] Verde I, Abbott A G, Scalabrin S, et al. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet, 2013, 45(5):487-494.
[24] Wu J, Wang Z, Shi Z, et al. The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res, 2013, 23(2):396-408.
[25] Velasco R, Zharkikh A, Affourtit J, et al. The genome of the domesticated apple (Malus×domestica Borkh.). Nat Genet, 2010, 42(10):833-839.
[26] Zhang Q, Chen W, Sun L, et al. The genome of Prunus mume. Nat Commun, 2012, 3:1318.
[27] Wang N, Thomson M, Bodles W J, et al. Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers. Mol Ecol, 2013, 22(11):3098-3111.
[28] Argout X, Salse J, Aury J M, et al. The genome of Theobroma cacao. Nat Genet, 2011, 43(2):101-108.
[29] Xu Q, Chen L L, Ruan X A, et al. The draft genome of sweet orange (Citrus sinensis). Nat Genet, 2013, 45(1):59-66.
[30] Myburg A A, Grattapaglia D, Tuskan G A, et al. The genome of Eucalyptus grandis. Nature, 2014, 510(7505):356-362.
[31] Sollars E S, Harper A L, Kelly L J, et al. Genome sequence and genetic diversity of European ash trees. Nature, 2017, 541(7636):212-216.
[32] Olson A, Aerts A, Asiegbu F, et al. Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen. New Phytol, 2012, 194(4):1001-1013.
[33] Nordberg H, Cantor M, Dusheyko S, et al. The genome portal of the Department of Energy Joint Genome Institute:2014 updates. Nucleic Acids Res, 2014, 42(Database issue):D26-31.
[34] DiGuistini S, Wang Y, Liao N Y, et al. Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. Proc Natl Acad Sci USA, 2011, 108(6):2504-2509.
[35] Duplessis S, Cuomo C A, Lin Y C, et al. Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc Natl Acad Sci USA, 2011, 108(22):9166-9171.
[36] Van Sluys M A, de Oliveira M C, Monteiro-Vitorello C B, et al. Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa. J Bacteriol, 2003, 185(3):1018-1026.
[37] Ghasemkhani M. Resistance against fruit tree canker in apple-evaluation of disease symptoms, histopathological and RNA-Seq analyses in different cultivars, genetic variation of Neonectria ditissima. Alnarp:Swedish University of Agricultural Sciences, 2015,77:1-64.
[38] Duan Y P, Zhou L J, Hall D G, et al. Complete genome sequence of citrus huanglongbing bacterium, 'Candidatus Liberibacter asiaticus' obtained through metagenomics. Mol Plant Microbe Interact, 2009, 22(8):1011-1020.
[39] Simpson A J, Reinach F C, Arruda P, et al. The genome sequence of the plant pathogen Xylella fastidiosa. Nature, 2000, 406(6792):151-159.
[40] da Silva A C, Ferro J A, Reinach F C, et al. Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature, 2002, 417(6887):459-463.
[41] Yue J X, Meyers B C, Chen J Q, et al. Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes. New Phytol, 2012, 193(4):1049-1063.
[42] Li J, Ding J, Zhang W, et al. Unique evolutionary pattern of numbers of gramineous NBS-LRR genes. Mol Genet Genomics, 2010, 283(5):427-438.
[43] Yang S, Zhang X, Yue J X, et al. Recent duplications dominate NBS-encoding gene expansion in two woody species. Mol Genet Genomics, 2008, 280(3):187-198.
[44] Lozano R, Ponce O, Ramirez M, et al. Genome-wide identification and mapping of NBS-encoding resistance genes in Solanum tuberosum group phureja. PLoS One, 2012, 7(4):e34775.
[45] Arya P, Kumar G, Acharya V, et al. Genome-wide identification and expression analysis of NBS-encoding genes in Malus×domestica and expansion of NBS genes family in Rosaceae. PLoS One, 2014, 9(9):e107987.
[46] Bai J, Pennill L A, Ning J, et al. Diversity in nucleotide binding site-leucine-rich repeat genes in cereals. Genome Res, 2002, 12(12):1871-1884.
[47] 罗莎. 植物NBS类抗病基因的进化. 遗传, 2014, 36(12):1219-1225. Luo S. Evolution of plant NBS encoding disease resistance genes. Hereditas, 2014, 36(12):1219-1225.
[48] Gongora-Castillo E, Buell C R. Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence. Nat Prod Rep, 2013, 30(4):490-500.
[49] Miranda M, Ralph S G, Mellway R, et al. The transcriptional response of hybrid poplar (Populus trichocarpa x P. deltoides) to infection koby Melampsora medusae leaf rust involves induction of flavonoid pathway genes leading to the accumulation of proanthocyanidins. Mol Plant Microbe Interact, 2007, 20(7):816-831.
[50] Azaiez A, Boyle B, Levee V, et al. Transcriptome profiling in hybrid poplar following interactions with melampsora rust fungi. Mol Plant Microbe Interact, 2009, 22(2):190-200.
[51] Rinaldi C, Kohler A, Frey P, et al. Transcript profiling of poplar leaves upon infection with compatible and incompatible strains of the foliar rust Melampsora larici-populina. Plant Physiol, 2007, 144(1):347-366.
[52] Liu J J, Sturrock R N, Benton R. Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola. BMC Genomics, 2013, 14:884.
[53] Kamber T, Buchmann J P, Pothier J F, et al. Fire blight disease reactome:RNA-seq transcriptional profile of apple host plant defense responses to Erwinia amylovora pathogen infection. Sci Rep, 2016, 6:21600.
[54] Martinelli F, Reagan R L, Uratsu S L, et al. Gene regulatory networks elucidating huanglongbing disease mechanisms. PLoS One, 2013, 8(9):e74256.
[55] Martinelli F, Uratsu S L, Albrecht U, et al. Transcriptome profiling of citrus fruit response to huanglongbing disease. PLoS One, 2012, 7(5):e38039.
[56] Harper A L, McKinney L V, Nielsen L R, et al. Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics. Sci Rep, 2016, 6:19335.
[57] Hayden K J, Garbelotto M, Knaus B J, et al. Dual RNA-seq of the plant pathogen Phytophthora ramorum and its tanoak host. Tree Genet Genom, 2014, 10(3):489-502.
[58] Teixeira P J, Thomazella D P, Reis O, et al. High-resolution transcript profiling of the atypical biotrophic interaction between Theobroma cacao and the fungal pathogen Moniliophthora perniciosa. Plant Cell, 2014, 26(11):4245-4269.
[59] Wang X, Shi W, Rinehart T. Transcriptomes that confer to plant defense against powdery mildew disease in Lagerstroemia indica. Int J Genomics, 2015, 2015:528395.
[60] Kanchiswamy C N, Mohanta T K, Capuzzo A, et al. Differential expression of CPKs and cytosolic Ca2+ variation in resistant and susceptible apple cultivars (Malus x domestica) in response to the pathogen Erwinia amylovora and mechanical wounding. BMC Genomics, 2013, 14:760.
[61] Chen L, Ren Y Y, Zhang Y Y, et al. Genome-wide profiling of novel and conserved Populus microRNAs involved in pathogen stress response by deep sequencing. Planta, 2012, 235(5):873-883.
[62] Petre B, Morin E, Tisserant E, et al. RNA-seq of early-infected poplar leaves by the rust pathogen Melampsora larici-populina uncovers PtSultr3;5, a fungal-induced host sulfate transporter. PLoS One, 2012, 7(8):e44408.
[63] La Mantia J, Klapste J, El-Kassaby Y A, et al. Association analysis identifies Melampsora xcolumbiana poplar leaf rust resistance SNPs. PLoS One, 2013, 8(11):e78423.
[64] Zhou M, Wang W, Karapetyan S, et al. Redox rhythm reinforces the circadian clock to gate immune response. Nature, 2015, 523(7561):472-476.
[65] Iwata H, Hayashi T, Terakami S, et al. Potential assessment of genome-wide association study and genomic selection in Japanese pear Pyrus pyrifolia. Breed Sci, 2013, 63(1):125-140.
[66] Mariette S, Wong Jun Tai F, Roch G, et al. Genome-wide association links candidate genes to resistance to Plum Pox Virus in apricot (Prunus armeniaca). New Phytol, 2016, 209(2):773-784.
[67] Iwata H, Minamikawa M F, Kajiya-Kanegae H, et al. Genomics-assisted breeding in fruit trees. Breed Sci, 2016, 66(1):100-115.
[68] Evans L M, Slavov G T, Rodgers-Melnick E, et al. Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations. Nat Genet, 2014, 46(10):1089-1096.
[69] Kumar S, Garrick D J, Bink M C, et al. Novel genomic approaches unravel genetic architecture of complex traits in apple. BMC Genomics, 2013, 14:393.
[70] Rai M K, Shekhawat N S. Recent advances in genetic engineering for improvement of fruit crops. Plant Cell Tiss Org Cult, 2014, 116(1):1-15.
[71] Gambino G, Gribaudo I. Genetic transformation of fruit trees:current status and remaining challenges. Transgenic Res, 2012, 21(6):1163-1181.
[72] Powell W A, Maynard C A, Boyle B, et al. Fungal and Bacterial Resistance in Transgenic Trees. In:Tree Transgenesis. Fladung M, Ewald D, ed. Tree Transgenesis. Berlin/Heidelberg:Springer, 2006. 235-252.
[73] Wang Y, Cheng X, Shan Q, et al. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Biotechnol, 2014, 32(9):947-951.
[74] Nishitani C, Hirai N, Komori S, et al. Efficient genome editing in apple using a CRISPR/Cas9 system. Sci Rep, 2016, 6:31481.
[75] Zhang Y, Liang Z, Zong Y, et al. Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA. Nature Communications, 2016, 7:12617.
[76] Kelliher T, Starr D, Richbourg L, et al. Matrilineal, a sperm-specific phospholipase, triggers maize haploid induction. Nature, 2017, 542(7639):105-109.
[77] Heredia U L, Vazquez-Poletti J L. RNA-seq analysis in forest tree species:bioinformatic problems and solutions. Tree Genet Genom, 2016, 12(2):30.
[78] Lemgo G N, Sabbadini S, Pandolfini T, et al. Biosafety considerations of RNAi-mediated virus resistance in fruit-tree cultivars and in rootstock. Transgenic Res, 2013, 22(6):1073-1088.
[79] 黄三文, 杜永臣, 屈冬玉, et al. 同源转基因将成为利用野生资源进行作物育种的一种有效手段. 园艺学报, 2006, 33(6):1397-1400. Huang S W, Du Y C, Qu D Y, et al. Cisgenesis will become an effective tool of crop improvement in use of wild germplasm. Acta Hortic Sin, 2006, 33(6):1397-1400.
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