Gleditsia triacanthos

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	G. triacanthos
Genus	Gleditsia
Species	triacanthos
Common Name	Honeylocust
Organism Image
Description	Order: Fabales Family: Fabaceae Chromosome Number: 2n = 28
Cross Reference	NCBITaxon:54874

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 Honey Locust (Gleditsia triacanthos)	Trinity; CD-HIT-EST	Aug 26th, 2014

Analysis Details

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

Name	Program	Date Constructed
Honey Locust Ozone Treatments	HTSeq; RPKM	Apr 6th, 2016
Honey Locust (blastx against TrEMBL)	blastx	Apr 21st, 2016
Interpro Analysis of Honey Locust (Gleditsia triacanthos)	InterProScan	Apr 21st, 2016
Honey Locust (blastx against sprot)	blastx	Apr 21st, 2016
de novo Honey Locust (Gleditsia triacanthos)	Trinity; CD-HIT-EST	Aug 26th, 2014

Biological Samples

Name	Tissue	Treatment	Description
HL225	roots	225ppb ozone, varying exposure times	Honeylocust -pooled seedling RNAs, 225 ppb ozone
HL125	roots	125ppb ozone, varying exposure times	Honeylocust -pooled seedling RNAs, 125 ppb ozone
HL80	roots	80ppb ozone, varying exposure times	Honeylocust -pooled seedling RNAs, 80 ppb ozone
HCL0	roots	none	Honeylocust -pooled seedling RNAs, control
HR-R-Contr	root	none	honeylocust seedlings - root sample - control
HL-HR	root	heat(40C)-24hr	honeylocust seedlings - root sample - heat 40C 24hrs
HL-DR	root	drought(<1.0 mpa)	honeylocust seedlings - root sample - drought (<1.0mpa)
HL-CR-24	root	cold(4C)-24hr	honeylocust seedlings - root sample - cold 4C 24hrs
HL-CL-0	root	cold(4C)-immediately	honeylocust seedlings - root sample - cold 4C immediate

Mapping Population

Locations: University of Tennessee, Ames Plantation in Ames, TN and East Tennessee State Nursery

Principal Investigators: Scott Schlarbaum (University of Tennessee), Oliver Gailing (Michigan Tech)

A honeylocust half sibling population has been established at the East Tennessee State Nursery and includes approximately 226 surviving individuals. Seeds were collected from a mother tree from Butternut Valley to develop this population. The population is being maintained by the UT Tree Improvement Program.

Parental analysis at Michigan Tech University identified 149 full siblings from this population. Additional seeds were collected from the mother tree for possible later population expansion. Transfer of the honeylocust full-sibling population from the East Tennessee State Nursery to the East Tennessee Research and Education Center in Knoxville was conducted to better maintain the population for future use. This was possible due to the relatively low number of full siblings (

Genotyping

Genotyping by sequencing is currently ongoing for a subset of this population with the aim to produce a genetic map. The genotypes will be posted when publicly available.

Please contact us for more information or if you are interested in utilizing this population for research. Genotype and phenotype information will be posted here when publicly available.

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	15,327,293
Untrimmed Bases	3,096,113,186
Reconstructed Fragments	13,775,803
Reconstructed Fragments - Bases	2,147,108,245
Dinucleotide repeats with primers	4,084
Trinucleotide repeats with primers	544
Tetranucleotide repeats with primers	87

Download Files:

*The file of extended fragments is not available for download via web browser due to the very large size. In the meantime, please contact the site admin if you would like to download the file.

Polymorphic SSRS

A subset of the predicted genomic SSRs have been screened for polymorphism and published:

Owusu SA, Staton M, Jennings TN, Schlarbaum S, Coggeshall MV, Romero-Severson J, Carlson JE, Gailing O. Development of genomic microsatellites in Gleditsia triacanthos (Fabaceae) using Illumina sequencing. Applications in plant sciences. 2013 Dec;1(12).

Owusu SA, Schlarbaum SE, Carlson JE, Gailing O. Pollen gene flow and molecular identification of full-sib families in small and isolated population fragments of Gleditsia triacanthos L. Botany. 2016 Apr 6(ja).