Summary
Publication
Sollars, E. S., Harper, A. L., Kelly, L. J., Sambles, C. M., Ramirez-Gonzalez, R. H., Swarbreck, D., ... & Worswick, G. (2017). Genome sequence and genetic diversity of European ash trees. Nature, 541(7636), 212. https://www.nature.com/articles/nature20786
Name
Fraxinus excelsior - Reference Genome
Resource Type
Genome Assembly
Organism
Details
Program, Pipeline, Workflow or Method Name
Maker, Augustus (BATG-0.5, v4). Maker, Augustus
Program Version
n/a
Date Performed
Monday, August 1, 2016 - 21:00
Data Source
Source Name
: BATG-0.5
Source Version
: V3
Source URI
: http://www.ashgenome.org
Cross Reference
Description and Download

Methods from The British Ash Tree Genome Project reproduced below.

Released 29/10/2015 and published in Nature in January 2017, assembled by Lizzy Sollars. Paired reads with insert sizes of: 200bp, 300bp, 500b, 5kb and 454 reads were used to build contigs in CLC Genomics Workbench. Scaffolding was performed using SSPACE with all paired reads (those mentioned in addition to Long Jumping Distance libraries of 3, 8, 20 and 40 kbp). Gaps in the scaffolds were closed using GapCloser and further joining of scaffolds was done using PBJelly with the 454 reads. A major update in this version is that the chloroplast and mitochondrial genomes have been extracted from the nuclear genome; both are located at the end of the assembly file. The chloroplast genome is contained in one contig of 155,498 bp, named 'Cp1'. The mitochondrial genome is present as a draft version in 26 contigs, named 'Mt#' (1-26). Stats for the mitochondrial genome are shown in the table below, along with full stats of the whole genome assembly.

Downloads

Genomic scaffolds
All Gene Models CDS (fasta format)
All Gene Models Protein (fasta format)
All Gene Models GFF (Fasta format)
Citation for all subsequent analysis using this data: Elizabeth S. A. Sollars, Andrea L. Harper, Laura J. Kelly, Christine M. Sambles, Ricardo H. Ramirez-Gonzalez, David Swarbreck, Gemy Kaithakottil, Endymion D. Cooper, Cristobal Uauy, Lenka Havlickova, Gemma Worswick, David J. Studholme, Jasmin Zohren, Deborah L. Salmon, Bernardo J. Clavijo, Yi Li, Zhesi He, Alison Fellgett, Lea Vig McKinney, Lene Rostgaard Nielsen, Gerry C. Douglas, Erik Dahl Kjær, J. Allan Downie, David Boshier, Steve Lee, Jo Clark, Murray Grant, Ian Bancroft, Mario Caccamo and Richard J. A. Buggs (2016) Genome sequence and genetic diversity of European ash trees.Nature doi:10.1038/nature20786 Go to JBrowse
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