Summary
Resource Type
Organism
Abbreviation
N. sylvatica
Genus
Nyssa
Species
sylvatica
Common Name
Blackgum
Organism Image
Description

Other Common Names: black tupelo, tupelo
Order: Cornales
Family: Cornaceae

Cross Reference
Transcriptome
NameProgramDate Constructed
de novo Blackgum (Nyssa sylvatica)Trinity, built under bowtie-1.0.1 and samtools-1.1; CD-HIT-ESTOct 13th, 2014
[Archived] de novo Blackgum (Nyssa sylvatica) - 120313Trinity; CD-HIT-ESTDec 3rd, 2013
Analysis Details
Provides detailed information on the programs used to assemble and annotate the data.
NameProgramDate Constructed
Blackgum Ozone TreatmentsHTSeq; RPKMFeb 12th, 2016
Blackgum (blastx against TrEMBL)blastxApr 16th, 2016
[Archived] de novo Blackgum (Nyssa sylvatica) - 120313Trinity; CD-HIT-ESTDec 3rd, 2013
Blackgum (blastx against sprot)blastxFeb 12th, 2016
Interpro Analysis of Blackgum (Nyssa sylvatica)InterProScanFeb 12th, 2016
de novo Blackgum (Nyssa sylvatica)Trinity, built under bowtie-1.0.1 and samtools-1.1; CD-HIT-ESTOct 13th, 2014
Biological Samples
The following browser provides a list of biosamples associated with this organism.
Biosample NameBiosample Provider
BG-7HR-CoMark Coggeshall
BG-7HR-80ppbMark Coggeshall
BG-7HR-225ppbMark Coggeshall
BG-29Day-225Mark Coggeshall
BG-28Day-COMark Coggeshall
BG-28Day-80Mark Coggeshall
BG-28Day-225Mark Coggeshall
BG-28Day-125Mark Coggeshall
BG-14DAy-CoMark Coggeshall
BG-14DAy-80ppbMark Coggeshall

Pages

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.

Statistics:

Untrimmed Pairs 8,395,992
Untrimmed Bases 1,695,990,384
Reconstructed Fragments 317,872
Reconstructed Fragments - Bases 53,005,119
Dinucleotide repeats with primers 1,062
Trinucleotide repeats with primers 40
Tetranucleotide repeats with primers 1

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