World-wide species

In 2020 we published genome assemblies for many species of ash (Fraxinus) from around the world in Nature Ecology and Evolution. These assemblies and read data are available as shown in Table 1 below.

We have since annotated these assemblies, and improved the assemblies of 13 species de novo using using long mate pair libraries. These unpublished assemblies and annotations can be found here: DOI

We have generated transcriptomic data for Fraxinus mandshurica, Fraxinus ornus, Fraxinus quadrangulata and Fraxinus gooddingii. The reads can be found in Bioproject PRJNA934306 on NCBI SRA.

In 2021 we collaborated in the publication of a major new assembly and annotation of Green ash (Fraxinus pennsylvanica) in Molecular Ecology Resources. This chromosome-level assembly can be downloaded here: DOI . Within this paper we also presented new reference-guided scaffolding of the ash species assemblies published previously. See: DOI andDOI .

Table 1: Genomes in 2020 paper

SpeciesIndividual (sequencing code, accession/genotype number)Reads on ENANCBI Assembly
Fraxinus albicansFRAX26 1901-4706Project: PRJEB20151GCA_903798335.1  
Fraxinus americanaFRAX14 am-6 BProject: PRJEB20151GCA_903798225.1  
Fraxinus angustifolia subsp. angustifoliaFRAX01 56.017Project: PRJEB20151GCA_902829175.1  
Fraxinus angustifolia subsp. oxycarpaFRAX15 31.077Project: PRJEB20151GCA_903798265.1  
Fraxinus angustifolia subsp. syriacaFRAX16 1982-8111Project: PRJEB20151GCA_903798275.1  
Fraxinus anomalaFRAX27 ano-1Project: PRJEB20151GCA_903798345.1  
Fraxinus apertisquamiferaFRAX02 20071420-LN/AUnpublished
Fraxinus baronianaFRAX28 bar-2Project: PRJEB20151GCA_903798355.1   
Fraxinus biltmoreanaFRAX17 5.0463N/AUnpublished
Fraxinus chinensis subsp. rhyncophyllaFRAX18 56.0651N/AUnpublished
Fraxinus cuspidataFRAX31 cusp-5Project: PRJEB20151GCA_903798385.1  
Fraxinus dipetalaFRAX04 20080822-GProject: PRJEB20151GCA_902829195.1  
Fraxinus floribundaFRAX32 flor-ins-12Project: PRJEB20151GCA_903798395.1  
Fraxinus gooddingiiFRAX19 2011-1488Project: PRJEB20151GCA_903798285.1  
Fraxinus greggiiFRAX20 greg-1Project: PRJEB20151GCA_903798315.1  
Fraxinus griffithiiFRAX21 2011/18.O-BProject: PRJEB20151GCA_903798305.1  
Fraxinus lanuginosaFRAX22 20071295 GN/AUnpublished
Fraxinus latifoliaFRAX05 56.0322Project: PRJEB20151GCA_902829145.1  
Fraxinus mandschuricaFRAX06 56.0269Project: PRJEB20151GCA_903772985.1  
Fraxinus nigraFRAX23 19880480-CProject: PRJEB20151GCA_903798295.1  
Fraxinus ornusFRAX07 32.0221Project: PRJEB20151GCA_903798235.1  
Fraxinus paxianaFRAX08 56.0587Project: PRJEB20151GCA_902829205.1  
Fraxinus profundaFRAX24 56.0568N/AUnpublished
F. pennsylvanica [was F. caroliniana]FRAX03 56.0410Project: PRJEB20151GCA_902829185.1  
Fraxinus pennsylvanicaFRAX09 PE_00248Project: PRJEB20151GCA_903798245.1  
Fraxinus pennsylvanicaFRAX10 PE_48Project: PRJEB20151GCA_902829155.1  
Fraxinus platypodaFRAX33 spa-1Project: PRJEB20151GCA_903798405.1  
Fraxinus quadrangulataFRAX11 28.0230Project: PRJEB20151GCA_903798255.1  
Fraxinus sieboldianaFRAX12 32.0516Project: PRJEB20151GCA_902876705.1  
Fraxinus uhdeiFRAX34 uhdei-pontoN/AUnpublished
Fraxinus velutinaFRAX13 56.0256Project: PRJEB20151GCA_902837555.1  
Fraxinus xanthoxyloidesFRAX25 19841432-CProject: PRJEB20151GCA_903798325.1  
Fraxinus sp. 1973-6204 [previously F. bungeana]FRAX29 1973-6204Project: PRJEB20151GCA_903798365.1  
Fraxinus sp.D2006-0159 [previously chinensis subsp. chinensis]FRAX30 F-unk-1Project: PRJEB20151GCA_903798375.1

The first assemblies for the world-wide species were funded by Living with Environmental Change: Tree Health and Plant Biosecurity Initiative – Phase 2 Grant, BB/L012162/1 to Richard Buggs, funded jointly by a grant from BBSRC, Defra, ESRC, the Forestry Commission, NERC and the Scottish Government. This project has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 660003.