Abstract
BackgroundA century ago, Chestnut Blight Disease (CBD) devastated the American chestnut. Backcross breeding has been underway to introgress resistance from Chinese chestnut into surviving American chestnut genotypes. Development of genomic resources for the family Fagaceae, has focused in this project on Castanea mollissima Blume (Chinese chestnut) and Castanea dentata (Marsh.) Borkh (American chestnut) to aid in the backcross breeding effort and in the eventual identification of blight resistance genes through genomic sequencing and map based cloning. A previous study reported partial characterization of the transcriptomes from these two species. Here, further analyses of a larger dataset and assemblies including both 454 and capillary sequences were performed and defense related genes with differential transcript abundance (GDTA) in canker versus healthy stem tissues were identified.ResultsOver one and a half million cDNA reads were assembled into 34,800 transcript contigs from American chestnut and 48,335 transcript contigs from Chinese chestnut. Chestnut cDNA showed higher coding sequence similarity to genes in other woody plants than in herbaceous species. The number of genes tagged, the length of coding sequences, and the numbers of tagged members within gene families showed that the cDNA dataset provides a good resource for studying the American and Chinese chestnut transcriptomes. In silico analysis of transcript abundance identified hundreds of GDTA in canker versus healthy stem tissues. A significant number of additional DTA genes involved in the defense-response not reported in a previous study were identified here. These DTA genes belong to various pathways involving cell wall biosynthesis, reactive oxygen species (ROS), salicylic acid (SA), ethylene, jasmonic acid (JA), abscissic acid (ABA), and hormone signalling. DTA genes were also identified in the hypersensitive response and programmed cell death (PCD) pathways. These DTA genes are candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica.ConclusionsOur data allowed the identification of many genes and gene network candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica. The similar set of GDTAs in American chestnut and Chinese chestnut suggests that the variation in sensitivity to this pathogen between these species may be the result of different timing and amplitude of the response of the two to the pathogen infection. Resources developed in this study are useful for functional genomics, comparative genomics, resistance breeding and phylogenetics in the Fagaceae.
Highlights
A century ago, Chestnut Blight Disease (CBD) devastated the American chestnut
Using a tool developed recently [19], that estimates the amount of sequencing needed to cover the transcriptome of a given species, that takes into consideration the sequencing platform and the number of contigs generated from each species, we determined that as few as two or three additional plates of 454 sequence from different developmental stages and physiological conditions should allow for 100% coverage of the transcriptomes of Chinese and American chestnut
More information from transcript profiling during the time course of infection in these two species is required to address this question. This project has generated over 83,000 transcript contigs from American and Chinese chestnuts and identified hundreds of genes and regulation pathways which may be involved in chestnut resistance to the pathogen C. parasitica
Summary
A century ago, Chestnut Blight Disease (CBD) devastated the American chestnut. Development of genomic resources for the family Fagaceae, has focused in this project on Castanea mollissima Blume (Chinese chestnut) and Castanea dentata (Marsh.) Borkh (American chestnut) to aid in the backcross breeding effort and in the eventual identification of blight resistance genes through genomic sequencing and map based cloning. American chestnut played an especially important economic and ecological role by providing food to various insects, birds, and mammals, and food, fiber, and wood for rural communities, prior to the introduction of the Chestnut Blight Disease (CBD) early in the 20th century [4]. Fagaceae species hold a key position in the phylogeny of angiosperms (Figure 1); they cluster closely to Cucurbitales in the Eurosid I group, which includes several model plant species, such as Medicago truncatula, Glycine max, Populus trichocarpa, and Eucalyptus grandis for which complete or nearly complete whole-genome sequences exist. The close phylogenetic relationships of several model plants should make members of the Fagaceae good models for comparative genomics between woody and herbaceous species
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