Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection

Background1471-2229-9-51American chestnut (Castanea dentata) was devastated by an exotic pathogen in the beginning of the twentieth century. This chestnut blight is caused by Cryphonectria parasitica, a fungus that infects stem tissues and kills the trees by girdling them. Because of the great economic and ecological value of this species, significant efforts have been made over the century to combat this disease, but it wasn't until recently that a focused genomics approach was initiated. Prior to the Genomic Tool Development for the Fagaceae project, genomic resources available in public databases for this species were limited to a few hundred ESTs. To identify genes involved in resistance to C. parasitica, we have sequenced the transcriptome from fungal infected and healthy stem tissues collected from blight-sensitive American chestnut and blight-resistant Chinese chestnut (Castanea mollissima) trees using ultra high throughput pyrosequencing.ResultsWe produced over a million 454 reads, totaling over 250 million bp, from which we generated 40,039 and 28,890 unigenes in total from C. mollissima and C. dentata respectively.The functions of the unigenes, from GO annotation, cover a diverse set of molecular functions and biological processes, among which we identified a large number of genes associated with resistance to stresses and response to biotic stimuli. In silico expression analyses showed that many of the stress response unigenes were expressed more in canker tissues versus healthy stem tissues in both American and Chinese chestnut. Comparative analysis also identified genes belonging to different pathways of plant defense against biotic stresses that are differentially expressed in either American or Chinese chestnut canker tissues.ConclusionOur study resulted in the identification of a large set of cDNA unigenes from American chestnut and Chinese chestnut. The ESTs and unigenes from this study constitute an important resource to the scientific community interested in the discovery of genes involved in various biological processes in Chestnut and other species. The identification of many defense-related genes differentially expressed in canker vs. healthy stem in chestnuts provides many new candidate genes for developing resistance to the chestnut blight and for studying pathways involved in responses of trees to necrotrophic pathogens. We also identified several candidate genes that may underline the difference in resistance to Cryphonectria parasitica between American chestnut and Chinese chestnut.

[1]  Hongyu Zhao,et al.  Study of Arabidopsis thalianaresistome in response to cucumber mosaic virus infection using whole genome microarray , 2004, Plant Molecular Biology.

[2]  P. A. Rea,et al.  The Arabidopsis thaliana ABC Protein Superfamily, a Complete Inventory* , 2001, The Journal of Biological Chemistry.

[3]  G. J. Griffin,et al.  Developmental histopathology of cankers incited by hypovirulent and virulent isolates of Endothia parasitica on susceptible and resistant chestnut trees , 1984 .

[4]  B. Henrissat,et al.  Structures and mechanisms of glycosyl hydrolases. , 1995, Structure.

[5]  Dan Nettleton,et al.  Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.) , 2007, The Plant journal : for cell and molecular biology.

[6]  C. Keever.  Present Composition of Some Stands of the Former Oak-Chestnut Forest in the Southern Blue Ridge Mountains , 1953 .

[7]  J. Ohlrogge,et al.  Sampling the Arabidopsis Transcriptome with Massively Parallel Pyrosequencing1[W][OA] , 2007, Plant Physiology.

[8]  R. Welti,et al.  Plastid omega3-fatty acid desaturase-dependent accumulation of a systemic acquired resistance inducing activity in petiole exudates of Arabidopsis thaliana is independent of jasmonic acid. , 2007, The Plant journal : for cell and molecular biology.

[9]  M. Marra,et al.  Applications of next-generation sequencing technologies in functional genomics. , 2008, Genomics.

[10]  Ncbi.  National Center for Biotechnology Information , 2008 .

[11]  NpPDR1, a Pleiotropic Drug Resistance-Type ATP-Binding Cassette Transporter from Nicotiana plumbaginifolia, Plays a Major Role in Plant Pathogen Defense1 , 2005, Plant Physiology.

[12]  P. Thonart,et al.  Cloning and expression analysis of cDNAs corresponding to genes activated in cucumber showing systemic acquired resistance after BTH treatment , 2004, BMC Plant Biology.

[13]  T. Speed,et al.  GOstat: find statistically overrepresented Gene Ontologies within a group of genes. , 2004, Bioinformatics.

[14]  L. G. Brewer.  Ecology of survival and recovery from blight in American chestnut trees (Castanea dentata (Marsh.) Borkh.) in Michigan , 1995 .

[15]  Cai-guo Xu,et al.  Dual Function of Rice OsDR8 Gene in Disease Resistance and Thiamine Accumulation , 2006, Plant Molecular Biology.

[16]  G. J. Griffin.  Blight Control and Restoration of the American Chestnut , 2000, Journal of Forestry.

[17]  M. Boutry,et al.  NpPDR1, a Pleiotropic Drug Resistance-Type ATP-Binding Cassette Transporter from Nicotiana plumbaginifolia, Plays a Major Role in Plant Pathogen Defense1 , 2005, Plant Physiology.

[18]  J. Kikkert,et al.  In vitro germination and transient GFP expression of American chestnut (Castanea dentata) pollen , 2006, Plant Cell Reports.

[19]  J. Dangl,et al.  Pathogen-induced, NADPH oxidase–derived reactive oxygen intermediates suppress spread of cell death in Arabidopsis thaliana , 2005, Nature Genetics.

[20]  S. Merkle,et al.  Plantlet regeneration from somatic embryos of American chestnut , 1997 .

[21]  S. Merkle,et al.  Somatic embryogenesis in American chestnut , 1991 .

[22]  D. Leibman,et al.  Characterization of a Mitogen-Activated Protein Kinase Gene from Cucumber Required for Trichoderma-Conferred Plant Resistance1 , 2006, Plant Physiology.

[23]  Armand Séguin,et al.  CINNAMYL ALCOHOL DEHYDROGENASE-C and -D Are the Primary Genes Involved in Lignin Biosynthesis in the Floral Stem of Arabidopsisw⃞ , 2005, The Plant Cell Online.

[24]  I. Somssich,et al.  Induction by fungal elicitor of S-adenosyl-L-methionine synthetase and S-adenosyl-L-homocysteine hydrolase mRNAs in cultured cells and leaves of Petroselinum crispum. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[25]  H. Hirochika,et al.  MYB-Related Transcription Factor NtMYB2 Induced by Wounding and Elicitors is a Regulator of the Tobacco Retrotransposon Tto1 and Defense-Related Genes , 2000, Plant Cell.

[26]  M. W. Lee,et al.  A novel jasmonic acid-inducible rice myb gene associates with fungal infection and host cell death. , 2001, Molecular plant-microbe interactions : MPMI.

[27]  C. Nelson,et al.  Molecular mapping of resistance to blight in an interspecific cross in the genus castanea. , 1997, Phytopathology.

[28]  W Brad Barbazuk,et al.  Gene discovery and annotation using LCM-454 transcriptome sequencing. , 2006, Genome research.

[29]  P. Cortesi,et al.  Biological control of chestnut blight with hypovirulence: a critical analysis. , 2004, Annual review of phytopathology.

[30]  H. Yoshioka,et al.  Loss of AtPDR8, a plasma membrane ABC transporter of Arabidopsis thaliana, causes hypersensitive cell death upon pathogen infection. , 2006, Plant & cell physiology.

[31]  S. Tanksley,et al.  EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6000 genes from a basal eudicot , 2006, Plant Molecular Biology.

[32]  A. Osbourn,et al.  A different function for a member of an ancient and highly conserved cytochrome P450 family: From essential sterols to plant defense , 2006, Proceedings of the National Academy of Sciences.

[33]  D. Choi,et al.  Molecular characterization of a pepper C2 domain-containing SRC2 protein implicated in resistance against host and non-host pathogens and abiotic stresses , 2008, Planta.

[34]  J. Chory,et al.  The Arabidopsis DESPERADO/AtWBC11 Transporter Is Required for Cutin and Wax Secretion1[C][W] , 2007, Plant Physiology.

[35]  G. J. Griffin,et al.  Chestnut blight, other Endothia diseases, and the genus Endothia. , 1986 .

[36]  S. Merkle,et al.  Enhancement of American chestnut somatic seedling production , 2005, Plant Cell Reports.

[37]  Giorgio Valle,et al.  The Gene Ontology project in 2008 , 2007, Nucleic Acids Res..

[38]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[39]  D. Roby,et al.  A R2R3-MYB gene, AtMYB30, acts as a positive regulator of the hypersensitive cell death program in plants in response to pathogen attack , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[40]  J. Cairney,et al.  A simple and efficient method for isolating RNA from pine trees , 1993, Plant Molecular Biology Reporter.

[41]  C. Thompson,et al.  Elongation factor-1 alpha is a selective regulator of growth factor withdrawal and ER stress-induced apoptosis , 2002, Cell Death and Differentiation.

[42]  Hongwen Huang,et al.  Molecular evidence for an Asian origin and a unique westward migration of species in the genus Castanea via Europe to North America. , 2007, Molecular phylogenetics and evolution.

[43]  D. Klessig,et al.  Isolation and characterization of a tobacco mosaic virus-inducible myb oncogene homolog from tobacco. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[44]  J. Claverie,et al.  The significance of digital gene expression profiles. , 1997, Genome research.

[45]  May R Berenbaum,et al.  Molecular mechanisms of metabolic resistance to synthetic and natural xenobiotics. , 2007, Annual review of entomology.

[46]  I. Somssich,et al.  The Transcription Factors WRKY11 and WRKY17 Act as Negative Regulators of Basal Resistance in Arabidopsis thaliana[W][OA] , 2006, The Plant Cell Online.

[47]  W. Powell,et al.  Development and germination of American chestnut somatic embryos , 1999, Plant Cell, Tissue and Organ Culture.

[48]  T. Umezawa,et al.  Cinnamoyl-CoA reductase, a key enzyme in lignin biosynthesis, is an effector of small GTPase Rac in defense signaling in rice. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[49]  Armin Djamei,et al.  The MAP kinase kinase MKK2 affects disease resistance in Arabidopsis. , 2007, Molecular plant-microbe interactions : MPMI.

[50]  Joachim Selbig,et al.  Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana , 2007, BMC Bioinformatics.

[51]  Haiying Liang,et al.  Agrobacterium-mediated transformation of American chestnut (Castanea dentata (Marsh.) Borkh.) somatic embryos , 2005, Plant Cell, Tissue and Organ Culture.

[52]  M. Delseny,et al.  A unigene catalogue of 5700 expressed genes in cassava , 2004, Plant Molecular Biology.

[53]  Hur-Song Chang,et al.  Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses , 2002, The Plant Cell Online.

[54]  Alexander F. Auch,et al.  Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA , 2006, Science.

[55]  Y. Lindqvist,et al.  Crystallographic snapshots of oxalyl-CoA decarboxylase give insights into catalysis by nonoxidative ThDP-dependent decarboxylases. , 2007, Structure.