SlideShare uses cookies to improve functionality and performance, and to provide you with relevant advertising. If you continue browsing the site, you agree to the use of cookies on this website. See our User Agreement and Privacy Policy.
SlideShare uses cookies to improve functionality and performance, and to provide you with relevant advertising. If you continue browsing the site, you agree to the use of cookies on this website. See our Privacy Policy and User Agreement for details.
Successfully reported this slideshow.
Activate your 14 day free trial to unlock unlimited reading.
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.
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.
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
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
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