The Chestnut Genome Project

The devastation of American chestnut (Castanea dentata) populations in Eastern North America by the chestnut blight fungus (Cryphonectria parasitica) is a well-chronicled environmental disaster. Unlike the American chestnut, the closely related Chinese chestnut (Castanea mollissima) evolved resistance to the sympatric chestnut blight fungus, and is being used as donor for breeding of resistance in C. dentata. We report results for the sequencing of the genome of Chinese chestnut, with analysis of synteny to other genomes, and gene content of the three major blight resistance QTL. A genome assembly covering 724.4 Mbp of the estimated 800 Mb chestnut genome was obtained in 41,270 scaffolds. A consensus of 38,146 genes was predicted and annotated, and confirmed with expression data.  BAC clones tiling the three major blight resistance QTL were sequenced to great depth. Across all three QTL regions, 782 genes were annotated with a diversity of molecular functions and biological processes, including app. 200 genes in the GO stress-response classification, and 15 defense response genes.  The genome scaffolds were integrated with the Chinese chestnut genetic and physical maps, and blocks of syntenies were found between the genomes of Chinese chestnut and ten model plant species, as well as micro-synteny among disease-resistance QTL.  We hope that the Chinese chestnut genome will lead to further understanding of genome organization and of canker disease-resistance and –susceptibility in hardwood trees. The chestnut genome project was supported by The Forest Health Initiative (http://www.foresthealthinitiative.org).