Liquidambar styraciflua

Summary

Reference Genome

JBrowse

Feature Search

Transcriptome

Analysis Details

Biological Samples

Mapping Population

Confirmed Polymorphic SSRs

Predicted SSRS (genomic)

Polymorphic SSRS

Libraries

Physical and Genetic Map

Ontology Browser

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	NCBITaxon:4400

Feature Search

You can search this organism’s features in the database by entering search terms in the box. You can search by feature name or annotation.

Transcriptome

Name	Program	Date Constructed
de novo American sweetgum (Liquidambar styraciflua)	Trinity, built under bowtie-1.0.1 and samtools-1.1; CD-HIT-EST	Jan 5th, 2015

Analysis Details

Provides detailed information on the programs used to assemble and annotate the data.

Name	Program	Date Constructed
American Sweetgum (blastx against TrEMBL)	blastx	Apr 22nd, 2016
Interpro Analysis of Sweetgum (Liquidambar styraciflua)	InterProScan	Jan 5th, 2015
American Sweetgum (blastx against sprot)	blastx	Apr 22nd, 2016
American Sweetgum Ozone Treatments	HTSeq; RPKM	Apr 21st, 2016
de novo American sweetgum (Liquidambar styraciflua)	Trinity, built under bowtie-1.0.1 and samtools-1.1; CD-HIT-EST	Jan 5th, 2015

Biological Samples

Name	Tissue	Treatment	Description
SG-80-28	leaf	ozone (80ppb) 28 days	seedlings exposed to ozone (80ppb) for 28 days (6 pooled)
SGHEAT4L	leaf	heat (40C) 4 hours	seedlings exposed to heat (40C) for 4 hours - leaf sample
SG-CO-14	leaf	ozone (10ppb) 14 days	seedlings exposed to ozone (10ppb) for 14 days (6 pooled)
SGDRHT7DP	petiole	drought (<1.0mpa) 7 days	seedlings exposed to drought for 7 days - petiole sample
SGDRHT7DL	leaf	drought (<1.0mpa) 7 days	seedlings exposed to drought for 7 days - leaf sample
SGDRHT7DR	root	drought (<1.0mpa) 7 days	seedlings exposed to drought for 7 days - root sample
SGCOLD24R	root	24 hours cold (4C)	seedlings exposed 24 hours cold (4C) - root sample
SG-CO-7	leaf	ozone (10ppb) 7 hours	seedlings exposed to ozone (10ppb) for 7 hours (6 pooled)
SGHEAT4R	root	heat (40C) 4 hours	seedlings exposed to heat (40C) for 4 hours - root sample
SG-225-28	leaf	ozone (225ppb) 28 days	seedlings exposed to ozone (225ppb) for 28 days (6 pooled)

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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.

Download Data

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

Download Files:

Excel file with statistics, SSR motifs and primers
Reconstructed Fragments - Fastq File WARNING: large file 261Mb
Sequences with SSRs and designed primers - Fasta File