Following our past two releases of the European ash (Fraxinus excelsior L.) genome, here we release the genome assembly from an individual with low susceptibility to ash dieback disease (ID: PG5). This genome assembly was generated using Hifiasm with PacBio HiFi reads (details below) as part of work to produce a pangenome for F. excelsior. We hope this release will contribute to ongoing research on ash.
Materials and Methods
Leaf material for the individual ash tree (PG5) was collected from a Forest Research F. excelsior trial site at North Burlingham (tree 185 in plot 57), Norfolk, UK, on 18th May 2022 with permission from the landholders. Genomic DNA was extracted using a CTAB-based protocol in combination with Qiagen Genomic-tips, at Royal Botanic Gardens, Kew. DNA sequencing was conducted by Edinburgh Genomics (The University of Edinburgh, Edinburgh, UK) using a PacBio Revio SMRT cell with HiFi mode, to approximately 32-fold whole genome coverage. We used Hifiasm version 0.19.8-r603 for genome assembly (Cheng et al. 2021, 2022) with the parameters -l3 -s 0.45 -k 61. Hifiasm generated two partially phased assemblies, of which Haplotype 1 (hap1) is released here for download. To evaluate the completeness of the genome assembly, BUSCO v.5.7.1 was used with Eudicots OrthoDB v10 (Manni et al. 2021).
This sequencing and ongoing analysis of the ash genomes at the Royal Botanic Gardens, Kew, is a ‘Centre for Forest Protection’ ash pangenome project, funded by Defra. The Centre for Forest Protection is a unique collaboration led by Forest Research and RBG Kew, focused on the future of forest and tree health. Analyses were conducted using Queen Mary University of London’s HPC facility (Apocrita), supported by QMUL Research-IT (http://doi.org/10.5281/zenodo.438045).
Fraxinus excelsior individual PG5 growing in the Forest Research trial at North Burlingham, Norfolk. Photo Credit: Laura Kelly
Results
- Hifiasm stats for Haplotype 1
| Number of Scaffolds | 1,927 |
| Sum of length (bp) | 847,371,032 |
| Minimum length (bp) | 14,943 |
| Average length (bp) | 439,736 |
| Maximum length (bp) | 55,191,825 |
| GC (%) | 35.22 |
| N50 | 29,329,831 |
| N90 | 217,402 |
- BUSCO results
Download
The haplotype 1 assembly of PG5 is available to download via the link below. Users are free to publish papers dealing with specific genes or small sets of genes (ten or fewer) using the sequence data. If these data are used for publications, please cite this webpage. For complete (whole-genome) analyses of features such as genes/gene families, regulatory elements, repeats or other features, or whole-genome comparisons to other F. excelsior individuals or other species, please contact us (l.kelly@kew.org) prior to downloading the assembly to discuss your plans.
Citations
Cheng, Haoyu, et al. “Haplotype-Resolved de Novo Assembly Using Phased Assembly Graphs with Hifiasm.” Nature Methods, vol. 18, no. 2, Feb. 2021, pp. 170–75. https://doi.org/10.1038/s41592-020-01056-5.
Cheng, Haoyu, et al. “Haplotype-Resolved Assembly of Diploid Genomes without Parental Data.” Nature Biotechnology, vol. 40, no. 9, Sept. 2022, pp. 1332–35. https://doi.org/10.1038/s41587-022-01261-x.
Manni, Mosè, et al. “BUSCO: Assessing Genomic Data Quality and Beyond.” Current Protocols, vol. 1, no. 12, Dec. 2021, p. e323. https://doi.org/10.1002/cpz1.323.
Manni, Mosè, et al. “BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes.” Molecular Biology and Evolution, edited by Joanna Kelley, vol. 38, no. 10, Sept. 2021, pp. 4647–54. https://doi.org/10.1093/molbev/msab199.