The Physical and Genetic Structure of the Chinese Chestnut (Castanea mollissima) Genome

To help further efforts to restore the American chestnut, as well as aid in research among the species within the genus Castanea, we present a high quality reference assembly of the twelve chromosomes of Chinese chestnut (Castanea mollissima). Assembly for the Chinese chestnut was carried out using a variety of insert fragment sizes yielding a draft assembly of over 300,000 contigs. Genome finishing methods reduced heterozygous duplicates, and merged neighboring contigs, reducing this number to 20,150, with an average size of 37kb, and a range of 5kb to 380kb, for a total assembled size of 750.4 Mbp. Existing physical and genetic maps were used as a framework to arrange 5,745 scaffolds (725 Mb) into 12 pseudochromosomes corresponding to linkage groups A through L. Physical contigs from the minimum tiling path were reconstructed by aligning BAC-end sequences to validate the structure of the assembled pseudochromosomes. Alignment of markers from the genetic map identifies the unique recombination signature of each chromosome, further validating the placement, order and orientation of contigs within linkage groups. Blocks of synteny were found between the genomes of Chinese chestnut and model plant species, as well as micro-syntenies in the disease-resistance QTL. Transcripts from various tissues of infected and uninfected Chinese and American trees were mapped to the genome and served as primary evidence for ab initio gene discovery. Consensus calling of gene models supports the presence of 36,478 genes and 38,146 peptide products genome-wide. These were subsequently annotated using functional data from plant transcriptome databases. Public release of completed pseudochromosome sequences is anticipated in 2017, and will be made available through the Hardwood Genomics website (http://hardwoodgenomics.org/chinese-chestnut-genome).