title: Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes.
abstract: BACKGROUND
  Chinese chestnut (Castanea mollissima) has emerged as a model species for the Fagaceae family with extensive genomic resources including a physical map, a dense genetic map and quantitative trait loci (QTLs) for chestnut blight resistance. These resources enable comparative genomics analyses relative to model plants. We assessed the degree of conservation between the chestnut genome and other well annotated and assembled plant genomic sequences, focusing on the QTL regions of most interest to the chestnut breeding community.
  
  
  RESULTS
  The integrated physical and genetic map of Chinese chestnut has been improved to now include 858 shared sequence-based markers. The utility of the integrated map has also been improved through the addition of 42,970 BAC (bacterial artificial chromosome) end sequences spanning over 26 million bases of the estimated 800 Mb chestnut genome. Synteny between chestnut and ten model plant species was conducted on a macro-syntenic scale using sequences from both individual probes and BAC end sequences across the chestnut physical map. Blocks of synteny with chestnut were found in all ten reference species, with the percent of the chestnut physical map that could be aligned ranging from 10 to 39 %. The integrated genetic and physical map was utilized to identify BACs that spanned the three previously identified QTL regions conferring blight resistance. The clones were pooled and sequenced, yielding 396 sequence scaffolds covering 13.9 Mbp. Comparative genomic analysis on a microsytenic scale, using the QTL-associated genomic sequence, identified synteny from chestnut to other plant genomes ranging from 5.4 to 12.9 % of the genome sequences aligning.
  
  
  CONCLUSIONS
  On both the macro- and micro-synteny levels, the peach, grape and poplar genomes were found to be the most structurally conserved with chestnut. Interestingly, these results did not strictly follow the expectation that decreased phylogenetic distance would correspond to increased levels of genome preservation, but rather suggest the additional influence of life-history traits on preservation of synteny. The regions of synteny that were detected provide an important tool for defining and cataloging genes in the QTL regions for advancing chestnut blight resistance research.
authors.affiliation: Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA. mstaton1@utk.edu.
authors.forename: Margaret
authors.initials: M
authors.lastname: Staton
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA. tzhebe@clemson.edu.
authors.forename: Tetyana
authors.initials: T
authors.lastname: Zhebentyayeva
authors.affiliation: Department of Plant Pathology, North Carolina State University, Raleigh, NC, USA. baolukol@ncsu.edu.
authors.forename: Bode
authors.initials: B
authors.lastname: Olukolu
authors.affiliation: USDA/APHIS/BRS, Raleigh, NC, USA. Guang-Chen.Fang@aphis.usda.gov.
authors.forename: Guang Chen
authors.initials: GC
authors.lastname: Fang
authors.affiliation: Southern Institute of Forest Genetics, Southern Research Station, U.S. Forest Service, Saucier, MS, USA. dananelson@fs.fed.us.
authors.forename: Dana
authors.initials: D
authors.lastname: Nelson
authors.affiliation: The School of Forest Resources and The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA. jec16@psu.edu.
authors.forename: John E
authors.initials: JE
authors.lastname: Carlson
authors.affiliation: Department of Forestry, Forest Health Research and Education Center, Lexington, KY, USA. albert.abbott@uky.edu.
authors.forename: Albert G
authors.initials: AG
authors.lastname: Abbott
mesh_terms: D019295:Computational Biology; D019143:Evolution, Molecular; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D019684:Magnoliopsida / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D020161:Physical Chromosome Mapping; D040641:Quantitative Trait Loci; D026801:Synteny / Q000235:genetics*