The chestnuts (Castanea), members of the family Fagaceae, naturally occur throughout deciduous forests of eastern North America, Europe, and Asia . The genus includes ecologically and economically important nut and timber producing trees including the Chinese chestnut (Castanea mollissima), Japanese chestnut (Castanea crenata), European Chestnut (Castanea sativa) and American chestnut (Castanea dentata).
American chestnut was once a dominant tree species in forest ecosystems of eastern North America, its range extending from Maine south along the Appalachian Mountains to Alabama and westward to the Mississippi river . In some areas up to 45% of the forest canopy was comprised of American chestnut . This large, fast-growing tree played a central role in forest ecosystems, providing food and habitat for a variety of wildlife. It was also of considerable economic importance, producing strong, rot-resistant timber, a source of tannins, fuel, wood, and nuts [4–6]. Because of its utility, rapid growth, ability to quickly colonize burned or clearcut areas, and edible nuts it has been referred to as the "perfect tree" .
The reign of the American chestnut came to an abrupt end in the early 1900's when a blight, caused by the fungus, Cryphonectria parasitica, was introduced to North America from Asia via infected chestnut nursery stock . The blight was first observed in the Bronx Zoological Park in New York in 1904  and within 50 years the American chestnut was nearly eliminated from the forest . The pathogen infects stem tissues and kills the above ground portions of trees by girdling them. Below ground the trees can survive for many years however, continuously sending up sprouts which are themselves eventually infected. Cryphonectria, which shows a necrotrophic life style is lesser studied than their biotrophic counterparts. Today, except for occasional trees near the edge of its range which have escaped the blight, American chestnut exists primarily as shrubs, sprouting from the stumps of blight-topped trees [2, 9].
Although to a lesser extent, European chestnut (C. sativa) was also devastated by introduction of C. parasitica . Despite their close relationship, sister species of Castanea exhibit very different susceptibilities to Cryphonectria infection. Asian chestnuts, the vector for the spread of Cryphonectria westward, range from somewhat susceptible to nearly immune to infection . Most likely, these species co-evolved with Cryphonectria. Slow growing cankers are often visible on Chinese and Japanese chestnut trees although growth and yield of the trees are not substantially reduced. European chestnut is able to tolerate infection slightly more than American chestnut, which has little or no natural resistance to Cryphonectria infection .
Multiple attempts are being made to develop blight-resistant American chestnut genotypes. The search for natural resistance within American chestnut has been mostly fruitless whereas crosses between American parents exhibiting limited resistance have produced progeny without appreciable resistance . The American Chestnut Foundation  has been breeding for resistance for over three decades by introgression of genes from Chinese chestnut into American chestnut. However, this approach, although successful in developing blight resistant American chestnut varieties, has been slowed by the lack of genetic tools. Another approach to restoration of chestnut is by introduction of hypovirulent genotypes of the pathogen, Cryphonectria parasitica . Hypovirulence is a process in which the virulence of C. parasitica to chestnut trees is reduced by its infection by fungal viruses. For instance, virus-infected individuals of C. parasitica have been shown to produce superficial non-lethal cankers on European chestnut, and regular treatments with the virus are employed to protect chestnut farms in Europe. However, attempts to inoculate existing American Chestnut cankers with hypovirulent strains have met with limited success and may be impractical for reducing blight symptoms in the forest due to the large scale of the land mass affected .
Development of genomic tools will certainly facilitate the isolation of resistance genes, improve the efficiency of backcross breeding, and provide genetic reagents for developing resistant varieties by genetic engineering. American Chestnut is transformable using Agrobacterium tumefaciens [12, 13] and methods for plant regeneration from somatic embryos have been developed [14–16], permitting the production of many individuals from single transformation events. C.A. Maynard's and W.A. Powell's labs have produced transgenic American chestnut trees that are in their second year of field trials (USDA APHIS BRS permit 08-011-105r) demonstrating that all the steps have been developed to genetically engineer this species.
Genomic tools are now being developed to accelerate the identification of resistance genes and the development of blight resistant American chestnut. In this context, a central objective of The Fagaceae Genomic Tools Project  is the sequencing of the transcriptomes of chestnut, oak and beech species with the long-term goal of isolating genes underlying resistance to the chestnut blight. In this study we used an ultra-high throughput pyrosequencing approach  to quickly generate millions of bases of cDNA sequence for plant transcriptome analysis [19–22]. A comparison of capillary sequencing and next generation sequencing methods  showed that pyrosequencing is well adapted for analyzing the transcriptome of both model and non-model species, with lower cost than conventional methods such as microarrays, SAGE, or EST analysis generated using capillary sequencing.
In total, for all tissues, we have generated and analyzed 317,842 and 856,618 sequence reads from American and Chinese chestnut, respectively, for which the Fasta files can be accessed at the Fagaceae project website  and the raw data files in the Short Read Archive at the National Center for Biotechnology Information , accession numbers SRX001799 to SRX001808. Here we focused on comparing the transcriptomes generated from healthy stems and infected canker tissues from American and Chinese chestnut. The comparison between the American and Chinese chestnut canker transcriptomes enabled us to identify a large number of candidate pathogen response genes for use in studying pathways involved in resistance to the chestnut blight.