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

Abdelali Barakat,Kathleen Baier,Nicholas Wheeler,Denis S Diloreto,Yi Zhang,Ron Sederoff,Chris Smith,John E Carlson,William A Powell

doi:10.1186/1471-2229-9-51

Abstract

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.

Highlights

The chestnuts (Castanea), members of the family Fagaceae, naturally occur throughout deciduous forests of eastern North America, Europe, and Asia [1]
Our study resulted in the identification of a large set of complementary DNA (cDNA) unigenes from American chestnut and Chinese chestnut
The expressed sequence tag (EST) 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

Summary

Introduction

The chestnuts (Castanea), members of the family Fagaceae, naturally occur throughout deciduous forests of eastern North America, Europe, and Asia [1]. 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 [2]. In some areas up to 45% of the forest canopy was comprised of American chestnut [3] This large, fast-growing tree played a central role in forest ecosystems, providing food and habitat for a variety of wildlife. It was of considerable economic importance, producing strong, rot-resistant timber, a source of tannins, fuel, wood, and nuts [4,5,6]. Rapid growth, ability to quickly colonize burned or clearcut areas, and edible nuts it has been referred to as the "perfect tree" [5]

Methods

Results

Discussion

Conclusion