gSSRs
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.
Details from low coverage whole genome sequencing of ten hardwood trees:
- Black cherry (Prunus serotina)
- Black walnut (Juglans nigra)
- Blackgum (Nyssa sylvatica)
- Green ash (Fraxinus pennsylvanica)
- Honeylocust (Gleditsia triacanthos)
- Redbay (Persea borbonia)
- Sugar maple (Acer saccharinum)
- Sweetgum (Liquidambar styraciflua)
- White ash (Fraxinus americana)
- White oak (Quercus alba)
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. SSR design was sucessful for all ten species, with a marked prevalence of dinucleotide repeats in all species:
Download Excel files with SSRs and primers:
