Resource Type
P. serotina
Common Name
Black Cherry
Organism Image

Other Common Names: wild black cherry, rum cherry, or mountain black cherry
Order: Rosales
Family: Rosaceae
Chromosome Number: 2n = 16

Cross Reference
NameProgramDate Constructed
de novo Black Cherry (Prunus serotina) Unigene v1.0 (Penn State)NewblerSep 30th, 2012
Analysis Details
Provides detailed information on the programs used to assemble and annotate the data.
NameProgramDate Constructed
Black Cherry (blastx against sprot)blastxFeb 8th, 2017
Interpro Analysis of Black Cherry (Prunus serotina)InterProScanFeb 8th, 2017
GO for P. serotina InterproScan 5InterProScan GOFeb 21st, 2017
Black Cherry (blastx against trembl)blastx tremblFeb 8th, 2017
de novo Black Cherry (Prunus serotina) Unigene v1.0 (Penn State)NewblerSep 30th, 2012
Confirmed Polymorphic SSRs

John Carlson at Pennsylvania State University screened a subset of the above predicted SSRs.


DNA from twelve black cherry trees was collected for microsatellite screening from unrelated trees in a seed orchard at Penn Nursery (Pennsylvania Department of Conservation and Natural Resources, Bureau of Forestry, Spring Mills, PA), including parent trees R-14 and 11 of a genetic mapping population. DNA was extracted using a modified CTAB method, and DNA quality was assessed on 1% agarose gels. Species primer sets were tested against all collected genotypes within a species with a PCR reaction mixture containing between 4-6 ng DNA per reaction volume, and PCR cycles as follows: 95°C-5 min, 35 cycles of 95°C- 30s, 60°C-45s, 72°C-1 min, and a final 72°C-10 min. Both amplification and polymorphism were detected on 2% agarose gels stained with 0.05% (w/v) ethidium bromide. Polymorphism was estimated based on band width.


Of the 96 tested SSRs, 48 successfully amplified and 26 were found to be polymorphic.

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Predicted SSRS (genomic)

Publication: Staton M, Best T, Khodwekar S, Owusu S, Xu T, Xu Y, Jennings T, Cronn R, Arumuganathan AK, Coggeshall M, Gailing O. Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing. PloS one. 2015 Dec 23;10(12):e0145031.

In order to develop SSR resources for ten important North American hardwood tree species, we individually barcoded and multiplex sequenced DNA from ten hardwood forest tree species using short reads produced from an Illumina HiSeq. Raw reads can be downloaded from the NCBI short read archive, project SRP021923. Bioinformatic processing included trimming, assembly, SSR identification and primer design, processing details including scripts are available.


Untrimmed Pairs 11,929,916
Untrimmed Bases 2,409,843,032
Reconstructed Fragments 7,834,224
Reconstructed Fragments - Bases 1,285,895,782
Dinucleotide repeats with primers 8,046
Trinucleotide repeats with primers 750
Tetranucleotide repeats with primers 136

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