Published December 2, 2020 | Version 0.2.1
Dataset Open

Worldwide Fraxinus Genome Assemblies, Annotations, and Gene Families v0.2

  • 1. Kew Gardens

Contributors

Contact person:

Supervisor:

  • 1. Kew Gardens
  • 2. Queen Mary University

Description

The worldwide Fraxinus genome project was conducted to assess the pathogenic resistance of 34 Ash tree species to Ash Dieback and Emerald Ash Borer. The project is led by Dr. Richard Buggs. v0.1 genomes are available at ashgenome.org and on ENA. As part of Josiah Seaman's PhD thesis, he improved the assembly of 13 genomes included here as v0.2. New de novo annotations, gene families, and all associated files are included for future studies and reproducibility. 

Annotations are done with GeMoMa using F. excelsior as a reference (Keilwagen et al. 2016). Gene families are defined as genes originating from a single copy at the last common ancestor with Solanum. Orthofinder outputs reconciled gene trees, aligned CDS, and gene families (Emms and Kelly 2015; Tekaia 2016). Species tree was calibrated based on fossil evidence using r8s, RAxML across 25,182,399 sites (SpeciesTreeAlignment.fa). More methods details can be found in the full Chapter two of Josiah Seaman's PhD thesis (2021).

I'd be happy to talk with you if you'd like any additional information or help visualizing your genomic data. You can find the tools used to browse this data at https://fluentdna.com/ and http://graphgenome.org/ Contact me at josiah@newline.us

Notes

0.2.1 Listed the same data files separately so they could be more easily linked directly.

Files

Annotations.zip

Files (11.7 GB)

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Additional details