The Chinese Chestnut (
Castanea mollissima) physical map was developed from two BAC libraries:
The physical map was created at the
Clemson University Genomics Institute.
BAC fingerprinting was performed by high information content fingerprinting protocols (HICF) and standard capillary-based automated electrophoresis. Contig analysis was completed using
FPC software.
The physical map has been anchored to the genetic map through hybridizations of SSR and SNP sequences. Additional hybridizations with EST sequences have also been completed. These both are being used to anchor and orient the
draft Chestnut genome sequence scaffolds.
Physical map publication:
Fang GC, Blackmon BP, Staton ME, Nelson CD, Kubisiak TL, Olukolu BA, Henry D, Zhebentyayeva T, Saski CA, Cheng CH, Monsanto M, Ficklin S, Atkins M, Georgi LL, Barakat A, Wheeler N, Carlson JE, Sederoff R, Abbott AG.
A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map. Tree Genetics & Genomes 2013, 9(2):525-537.
Genetic map publication:
Kubisiak TL, Nelson CD, Staton ME, Zhebentyayeva T, Smith C, Olukolu BA, Fang GC, Hebard FV, Anagnostakis S, Wheeler N, Sisco PH, Abbott AG, Sederoff RR.
A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica). Tree Genetics & Genomes 2013, 9(2):557-571.
Statistics for Version 4 (current version, updated since publication)
| Total Fingerprinted BACs |
126,449 |
| Contigs |
1,300 |
| Singlets |
12,941 |
| E value |
1e-30 |
| Overgos |
1390 |
| BAC-end sequences |
42,970 [GenBank:HN270092-HN275251, JY172573-187037] |
Download the fpc file for analysis (fpc format, see more at
FPC software website):
Statistics for Version 3 (published in Fang et al., 2013)
| Total Fingerprinted BACs |
126,449 |
| Contigs |
1,377 |
| Singlets |
12,919 |
| E value |
1e-30 |
| Overgos |
1048 |
With an estimated average band size of 1740 bp, then total coverage of contigs is 1,311 Mb with the longest contig (#3362) covering 7000 kb. Assuming a genome of 794 kb and an average insert size of 119 kb, the physical map coverage is expected to be 18X.
Funded by the NSF Plant Genome Research Program grant "Genomic tool development for the Fagaceae" (#0605135) and the Forest Health Initiative.
