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
Transcriptome
NameProgramDate Constructed
de novo Honey Locust (Gleditsia triacanthos)Trinity; CD-HIT-ESTAug 26th, 2014
Analysis Details
Provides detailed information on the programs used to assemble and annotate the data.
NameProgramDate Constructed
Honey Locust Ozone TreatmentsHTSeq; RPKMApr 6th, 2016
Honey Locust (blastx against TrEMBL)blastxApr 21st, 2016
Interpro Analysis of Honey Locust (Gleditsia triacanthos)InterProScanApr 21st, 2016
Honey Locust (blastx against sprot)blastxApr 21st, 2016
de novo Honey Locust (Gleditsia triacanthos)Trinity; CD-HIT-ESTAug 26th, 2014
Biological Samples
NameTissueTreatmentDescription
HL225roots225ppb ozone, varying exposure timesHoneylocust -pooled seedling RNAs, 225 ppb ozone
HL125roots125ppb ozone, varying exposure timesHoneylocust -pooled seedling RNAs, 125 ppb ozone
HL80roots80ppb ozone, varying exposure timesHoneylocust -pooled seedling RNAs, 80 ppb ozone
HCL0rootsnoneHoneylocust -pooled seedling RNAs, control
HR-R-Contrrootnonehoneylocust seedlings - root sample - control
HL-HRrootheat(40C)-24hrhoneylocust seedlings - root sample - heat 40C 24hrs
HL-DRrootdrought(<1.0 mpa)honeylocust seedlings - root sample - drought (<1.0mpa)
HL-CR-24rootcold(4C)-24hrhoneylocust seedlings - root sample - cold 4C 24hrs
HL-CL-0rootcold(4C)-immediatelyhoneylocust 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).