Summary
Resource Type
Organism
Abbreviation
L. styraciflua
Genus
Liquidambar
Species
styraciflua
Common Name
American Sweetgum
Organism Image
Description

Other Common Names: redgum, sapgum, starleaf-gum, bilsted
Order: Saxifragales
Family: Altingiaceae
Chromosome Number: 2n=30, 32 1

Cross Reference
Transcriptome
NameProgramDate Constructed
de novo American sweetgum (Liquidambar styraciflua)Trinity, built under bowtie-1.0.1 and samtools-1.1; CD-HIT-ESTJan 5th, 2015
Analysis Details
Provides detailed information on the programs used to assemble and annotate the data.
NameProgramDate Constructed
American Sweetgum (blastx against TrEMBL)blastxApr 22nd, 2016
Interpro Analysis of Sweetgum (Liquidambar styraciflua)InterProScanJan 5th, 2015
American Sweetgum (blastx against sprot)blastxApr 22nd, 2016
American Sweetgum Ozone TreatmentsHTSeq; RPKMApr 21st, 2016
de novo American sweetgum (Liquidambar styraciflua)Trinity, built under bowtie-1.0.1 and samtools-1.1; CD-HIT-ESTJan 5th, 2015
Biological Samples
The following browser provides a list of biosamples associated with this organism.
Biosample NameBiosample Provider
SG-80-28Mark Coggeshall
SGHEAT4LMark Coggeshall
SG-CO-14Mark Coggeshall
SGDRHT7DPMark Coggeshall
SGDRHT7DLMark Coggeshall
SGDRHT7DRMark Coggeshall
SGCOLD24RMark Coggeshall
SG-CO-7Mark Coggeshall
SGHEAT4RMark Coggeshall
SG-225-28Mark Coggeshall

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Confirmed Polymorphic SSRs

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

Methods

Twenty four American sweetgum trees were sampled from a Pennsylvania State University provenance trial (University Park, PA). 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.

Results

Of the 96 tested SSRs, 44 successfully amplified and 28 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.

Statistics (combination of two sequenced libraries):

Untrimmed Pairs 4,440,505
Untrimmed Bases 896,982,010
Reconstructed Fragments 702,100
Reconstructed Fragments - Bases 115,182,987
Dinucleotide repeats with primers 1,632
Trinucleotide repeats with primers 201
Tetranucleotide repeats with primers 56

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