The genome of Fraxinus excelsior (European ash)
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Slides presented at the Plant and Animal Genome XXIII conference in San Diego, 11th Jan 2015. The talk includes assembly and annotation of the ash tree genome, as well as analysis of gene sharing with other plants and an preliminary look at the diversity of European ash trees.
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The genome of Fraxinus excelsior (European ash)
- 1. The genome of Fraxinus excelsior (European Ash) Elizabeth Sollars, Laura Kelly, Bernardo Clavijo, David Swarbreck, Jasmin Zohren, David Boshier, Jo Clark, Anika Joecker, Sarah Ayling, Mario Caccamo, Richard Buggs. @LizzySollars
- 2. It’s a tough time to be an ash tree Emerald Ash Borer (Agrilus planipennis) Ash Dieback (Hymenoscyphus fraxineus)
- 3. Workflow DNA RNA Genome AssemblyMitochondrial assembly Ab initio gene prediction Resequencing 37 European trees Functional annotation Gene Sharing Analysis
- 4. Workflow DNA RNA Genome AssemblyMitochondrial assembly Ab initio gene prediction Functional annotation Gene Sharing Analysis Resequencing 37 European trees
- 5. We know… 23 chromosome pairs 880 Mbp genome Selfed We sequenced… Wood tissue 200x coverage Illumina HiSeq + 454 Pairs 200bp – 40 kbp We used… gsAssembler for 454 reads CLC Genomics Workbench SSPACE scaffolder SOAP’s GapCloser We assembled… 875 Mbp in 89,285 scaffolds N50 of 99 kbp 19% in gaps 446 kbp mt. genome 33 complete, 20 incomplete mt. genes
- 6. Repeats, Repeats, Repeats 35% of the genome is classed as repeats. 32% 35% 2% 0.01% 12% 18% 1% LTR Gypsy LTR Copia LINE SINE Class II (DNA transposons) Unclassified Tandem repeats Class I: retrotransposons Laura Kelly, QMUL
- 7. Workflow DNA RNA Genome AssemblyMitochondrial assembly Ab initio gene prediction Functional annotation Gene Sharing Analysis Resequencing 37 European trees
- 8. Workflow DNA RNA Genome AssemblyMitochondrial assembly Ab initio gene prediction Functional annotation Gene Sharing Analysis Resequencing 37 European trees
- 9. Gene finding & Annotation AUGUSTUS with RNA-SeqAUGUSTUS MAKER Repeat-masked genome + protein alignments Evidence Modeller 43,298 genes, 59,154 transcripts. Annotated with BLAST and GO terms David Swarbreck, TGAC
- 10. Gene Completeness David Swarbreck, TGAC
- 11. ashgenome.org The open home of the British Ash Tree Genome project • Genome Assemblies • Transcriptome assemblies • JBrowse • BLAST tool
- 12. Workflow DNA RNA Genome AssemblyMitochondrial assembly Ab initio gene prediction Functional annotation Gene Sharing Analysis Resequencing 37 European trees
- 13. Workflow DNA RNA Genome AssemblyMitochondrial assembly Ab initio gene prediction Functional annotation Gene Sharing Analysis Resequencing 37 European trees
- 14. Gene Sharing Clustering of orthogroups using OrthoMCL • FEXC: Fraxinus excelsior • MGUT: Mimulus guttatus • UGIB: Utricularia gibba • SLYC: Solanum lycopersicum • CROB: Coffea robusta Total orthogroups: 18,870 Laura Kelly, QMUL
- 15. Gene Sharing Clustering of orthogroups using OrthoMCL • FEXC: Fraxinus excelsior • MGUT: Mimulus guttatus • UGIB: Utricularia gibba • SLYC: Solanum lycopersicum • CROB: Coffea robusta The largest ash-specific orthogroups are: • Disease resistance proteins • F-box proteins • Expansin-like proteins Total orthogroups: 18,870 Laura Kelly, QMUL
- 16. Gene Sharing Clustering of orthogroups using OrthoMCL: • FEXC: Fraxinus excelsior • CROB: Coffea robusta • PTRI: Populus trichocarpa • ATRI: Amborella trichopoda • PITA: Pinus taeda In 11-species comparison: • 4,283 groups shared by all • 7,562 shared by all angiosperms A group of laccase proteins were expanded in the woody species: role in lignin degradation. (ash, pine, & poplar) Laura Kelly, QMUL
- 17. Workflow DNA RNA Genome AssemblyMitochondrial assembly Ab initio gene prediction Functional annotation Gene Sharing Analysis Resequencing 37 European trees
- 18. Workflow DNA RNA Genome AssemblyMitochondrial assembly Ab initio gene prediction Functional annotation Gene Sharing Analysis Resequencing 37 European trees
- 20. Diversity Panel In 355 Mb of the reference sequence: • Reads from 37 trees, ~10x coverage each. • Total: 28.7 million polymorphic positions (~ 1 every 12 bp). • Low Frequency Variant Caller in CLC Genomics Workbench 0 5 10 15 20 25 30 Gene SNPs Non-gene SNPs 0 1,000,000 2,000,000 3,000,000 4,000,000 5,000,000 6,000,000 5'UTR SNPs 3' UTR SNPs CDS SNPs Other mRNA & intron 19% 81% 77% 13% 6% 4% 407,911 causing non-synonymous amino acid change 15,689 at splice sites
- 21. Diversity Panel • SNP tree made using SNPhylo • 18.7 million polymorphic positions • Filtered set of 14,000
- 22. Diversity Panel • SNP tree made using SNPhylo • 18.7 million polymorphic positions • Filtered set of 14,000
- 23. Diversity Panel
- 24. Future Work • Gene family expansions – In ash alone – In woody species • Diversity panel – Network analysis – SNP allele frequencies among individuals – SNP verification - KASPAR • Optical mapping using BioNano
- 25. We are the borers… resistance is futile. F. excelsior F. chinensis EAB resistance F. mandschurica EAB and dieback resistance F. quadrangulata Medium EAB resistance F. americana Dieback resistance F. pennsylvanica Medium dieback resistance The Fraxinus genus
- 26. Acknowledgments
Editor's Notes
- Singletons for each species: Fraxinus excelsior (FEXC) 12,265 (28%) Mimulus guttatus (MGUT) 4394 (16%) Solanum lycopersicum (SLYC) 9063 (26%) Utricularia gibba (UGIB) 8701 (31%) Coffea robusta (CROB) 4942 (19%)
- Singletons for each species: Fraxinus excelsior (FEXC) 12,265 (28%) Mimulus guttatus (MGUT) 4394 (16%) Solanum lycopersicum (SLYC) 9063 (26%) Utricularia gibba (UGIB) 8701 (31%) Coffea robusta (CROB) 4942 (19%)
- Singletons for each species: Fraxinus excelsior (FEXC) 12,265 (28%) Mimulus guttatus (MGUT) 4394 (16%) Solanum lycopersicum (SLYC) 9063 (26%) Utricularia gibba (UGIB) 8701 (31%) Coffea robusta (CROB) 4942 (19%)