Summary
Resource Type
Organism
Abbreviation
F. pennsylvanica
Genus
Fraxinus
Species
pennsylvanica
Common Name
Green Ash
Organism Image
Description

Other Common Names: ash, common ash, British ash
Order: Lamiales
Family: Oleaceae

Image used courtesy of Karan A. Rawlins, University of Georgia, Bugwood.org
licensed under a Creative Commons Attribution-Noncommercial 3.0 License.

Cross Reference
JBrowse

The Green ash (F. pennsylvanica) transcriptome was mapped to the European ash (F. excelsior) genome assembly using GMAP.

Total F. pennsylvanica mrna contigs Contigs mapped to F. excelsior >90% identity >90% coverage
107,611 102,977 80,940 75,379

Reference: Thomas D. Wu and Colin K. Watanabe. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005 21:1859-1875

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Transcriptome
NameProgramDate Constructed
de novo Green ash (Fraxinus pennsylvanica)Trinity; CD-HIT-ESTDec 3rd, 2013
Analysis Details
Provides detailed information on the programs used to assemble and annotate the data.
NameProgramDate Constructed
Green Ash (blastx against TrEMBL)blastxApr 25th, 2016
Green Ash Ozone TreatmentsHTSeq; RPKMJul 18th, 2014
Interpro Analysis of Green Ash (Fraxinus pennsylvanica)InterProScanApr 25th, 2016
Green Ash (blastx against sprot)blastxApr 25th, 2016
de novo Green ash (Fraxinus pennsylvanica)Trinity; CD-HIT-ESTDec 3rd, 2013
Biological Samples
NameTissueTreatmentDescription
FS-12-eggphloem and barkEAB feedingFS Tree 12, fall sample of phloem and bark after EAB feeding
FS-11phloem and barknoneFS Tree 11, summer sample of phloem and bark
FS-10-eggphloem and barkafter EAB damageFS Tree 10, fall sample of phloem and bark after EAB feeding
FS-9phloem and barknoneFS Tree 9, summer sample of phloem and bark
FS-8-eggphloem and barkafter EAB damageFS Tree 8, fall sample of phloem and bark after EAB feeding
FS-7phloem and barknoneFS Tree 7, summer sample of phloem and bark
FS-5phloem and barknoneFS Tree 5, summer sample of phloem and bark
FS-4-eggphloem and barkafter EAB damageFS Tree 4, fall sample of phloem and bark after EAB feeding
FS-3phloem and barknoneFS Tree 3, summer sample of phloem and bark
FS-2-eggphloem and barkafter EAB damageFS Tree 2, fall sample of phloem and bark after EAB feeding

Pages

Mapping Population

Location: University of Missouri, Horticulture and Agroforestry Research Center (HARC) in New Franklin, MO

Principal Investigators: Mark Coggeshall (University of Missouri), Jeanne Romero-Severson (Notre Dame), Jennifer Koch (US Forest Service)

A total of 490 full sibs were produced by Jennifer Koch (USFS, Delaware, OH) in the spring of 2014. Due to some outstanding disease issues, we now have 442 live trees that were outplanted in the spring 2015.

Phenotyping

Leafing date and bud burst phenotyping on these seedlings began in 2015. This population was created specifically to conduct QTL analyses for Emerald Ash Borer
resistance/tolerance, but no funding is yet in place to do this work. If funds permit, we will graft the population and distribute it to one or more additional plantation sites.

Please contact us for more information or if you are interested in utilizing this population for research. 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 36,367,468
Untrimmed Bases 7,346,228,536
Reconstructed Fragments 4,959,578
Reconstructed Fragments - Bases 751,621,434
Dinucleotide repeats with primers 2,161
Trinucleotide repeats with primers 435
Tetranucleotide repeats with primers 54

Download Files:

Polymorphic SSRS

A subset of SSRs have been selected from green ash transcriptome sequences and screened for polymorphism across 14 ash species:

Noakes AG, Best T, Staton ME, Koch J, Romero-Severson J. Cross amplification of 15 EST-SSR markers in the genus Fraxinus. Conservation Genetics Resources. 2014 Dec 1;6(4):969-70.