Fraxinus pennsylvanica

Summary

Reference Genome

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Feature Search

Gene Expression Profiles

Transcriptome

Analysis Details

Biological Samples

Mapping Population

Predicted SSRS (genomic)

Libraries

Physical and Genetic Map

Gene Ontology Browser

KEGG Browser

Summary

Resource Type	Organism
Abbreviation	F. pennsylvanica
Genus	Fraxinus
Species	pennsylvanica
Common Name	Green Ash
Organism Image
Cross Reference	NCBITaxon:56036
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.

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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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.

Gene Expression Profiles

Name	Program	Date Constructed
Green Ash - Abiotic Stress Gene Expression	HTSeq; RPKM	Jul 18th, 2014

Transcriptome

Name	Program	Date Constructed
Fraxinus pennsylvanica - Transcriptome Assembly	Trinity; CD-HIT-EST	Dec 3rd, 2013
[Archived] Fraxinus pennsylvanica - Transcriptome Assembly Ozone	Trinity	Dec 19th, 2012

Analysis Details

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

Name	Program	Date Constructed
Fraxinus pennsylvanica - peptides InterProScan	InterProScan	Apr 25th, 2016
Fraxinus pennsylvanica - mRNA BLASTX against TrEMBL	blastx	Apr 25th, 2016
Fraxinus pennsylvanica - Transcriptome Assembly	Trinity; CD-HIT-EST	Dec 3rd, 2013
Simple Sequence Repeats (SSR) prediction ( F. pennsylvanica)	SSR prediction pipeline	Jul 5th, 2018
Fraxinus pennsylvanica - mRNA BLASTX against SwissProt	blastx	Apr 25th, 2016
Green Ash - Abiotic Stress Gene Expression	HTSeq; RPKM	Jul 18th, 2014
[Archived] Fraxinus pennsylvanica - Transcriptome Assembly Ozone	Trinity	Dec 19th, 2012

Biological Samples

Name	Tissue	Treatment	Description
24-GA-CL	leaf	cold(4C)-24hr	Green ash-open pollinated offspring of Green Ash Mother (6 pooled seedlings)
24-GA-CP	petiole	cold(4C)-24hr	Green ash-open pollinated offspring of Green Ash Mother (6 pooled seedlings)
24-GA-CR	root	cold(4C)-24hr	Green ash-open pollinated offspring of Green Ash Mother (6 pooled seedlings)
FS-1	phloem and bark	none	FS Tree 1, summer sample of phloem and bark
FS-10-egg	phloem and bark	after EAB damage	FS Tree 10, fall sample of phloem and bark after EAB feeding
FS-11	phloem and bark	none	FS Tree 11, summer sample of phloem and bark
FS-12-egg	phloem and bark	EAB feeding	FS Tree 12, fall sample of phloem and bark after EAB feeding
FS-2-egg	phloem and bark	after EAB damage	FS Tree 2, fall sample of phloem and bark after EAB feeding
FS-3	phloem and bark	none	FS Tree 3, summer sample of phloem and bark
FS-4-egg	phloem and bark	after EAB damage	FS Tree 4, fall sample of phloem and bark after EAB feeding

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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)

microsatellite:

There are 484 SSR markers associated with 484 features in this organism.

The complete list of SSR markers, their properties, and primers to amplify then can be found on the corresponding analysis page.

Analysis Name
Simple Sequence Repeats (SSR) prediction ( F. pennsylvanica)

You can search for markers below: the form will return the gene features they are associated with.

Gene Ontology Browser

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KEGG Browser

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Fraxinus pennsylvanica

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