The Chinese Chestnut Genome

Genome-wide marker-assisted selection can further the aims of the TACF back-cross breeding program by using Chinese chestnut (Castanea mollissima) as a reference to identify blight resistance genes introgressed into resistant American x Chinese hybrids. The Forest Health Initiative (http://www.foresthealthinitiative.org) provided support for the construction of a reference genome to meet this aim. Beginning in 2010 several years of sequencing obtained ~60x coverage of the genome yielding an assembly covering over 98% (784 Mbases) of the estimated size of Chinese chestnut genome. This draft assembly, released in 2014 (NCBI accession GCA_000763605.1) is represented by 42,000 scaffolds. These scaffolds were integrated with ~40,000 Sanger-end sequences from BAC clones which comprise a 1.8x physical map of the genome. BAC-ends are partially integrated with an additional ~1200 genetic markers which together served to order scaffolds into pseudochromosomes corresponding to 12 predicted linkage groups. Contigs from previously sequenced and assembled QTL regions have been incorporated into the pseudochromosome assembly. Additional sequencing has been under way since the release of the draft assembly in an effort to characterize sequence variation genome-wide, between and among Chinese and American chestnuts, and across the genus. Whole-genome sequence has been obtained for four additional Chinese genotypes, five American chestnut genotypes, and representative individuals from 6 additional species within the genus, all at approximately 7-10x depth. The draft assembly, pseudochromosomes, and QTL assemblies are available at the Hardwood Genomics website (http://hardwoodgenomics.org/chinese-chestnut-genome).  Data tracks include supplementary data such as SNP calls and gene models, and are also available for download.