The Chinese Chestnut (Castanea mollissima) Genome

The Chinese chestnut (Castanea mollissima) is important internationally in the nut industry and in the study of resistance to the sympatric chestnut blight fungus (Cryphonectria parasitica). The chestnut blight devastated American chestnut (C. dentata) populations in Eastern North America and is a major pathogen on European chestnut (C. sativa) as well.  Chinese chestnut is serving as donor for breeding of resistance in C. dentata. We have sequenced and assembled a first draft of the Chinese chestnut genome, covering 724.4 Mbp of the estimated 800 Mb chestnut genome in 41,270 scaffolds. A total of 38,146 genes were predicted, annotated, and confirmed with expression data.  BAC clones tiling the three major blight resistance QTL were sequenced to great depth, revealing 782 genes with a diversity of molecular functions and biological processes, including app. 200 genes in the GO stress-response classification, and 15 known defense response genes.  The genome scaffolds were integrated with the Chinese chestnut genetic and physical maps, including telomeric and centromeric chromosomal assignment by FISH of mapped BAC clones.  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 advance breeding and research with chestnuts, and lead to a better understanding of canker disease-resistance and –susceptibility in trees. The chestnut genome project was supported by The Forest Health Initiative (www.foresthealthinitiative.org).