Improving genome assemblies and capturing...
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Improving genome assemblies and capturing genome variation data for
applied crop improvement.
1
David Edwards
University of Western Australia, Australia
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Outline
• Sequencing wheat chromosome arms
• Chickpea chromosomal genomics
• Skim GBS based genome assembly
• Validation and improvement of the canola genome
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Sequencing wheat chromosome arms
3
Ta 7DS Bd 1
Bd 3
www.wheatgenome.info
Berkman, et al., Plant Biotechnology Journal (2011)
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Sequencing wheat chromosome arms
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Sequencing wheat chromosome arms
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Contig duplication
0.00%
5.00%
10.00%
15.00%
20.00%
25.00%
30.00%
35.00%
40.00%
45.00%
Level of sequence duplication (% of assembled chromosome arm)
IWGSC
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Genes not supported by read data
0
5
10
15
20
25
30
2D
L
1D
L
5A
L
6A
S
5A
S
3A
L
2D
S
2A
L
6D
L
5B
L
4D
L
5B
L
6B
L
3A
S
4D
S
2B
S
1A
S
Number of Genes with no read supporting them
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New assembly
0
100000000
200000000
300000000
400000000
500000000
600000000
Assem
bly
siz
e (
bp
)
Chromosome Arm assembly
Total assembly size
IWGSC
Non-normalizedVelvet
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Chickpea
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Chickpea desi vs kabuli
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Chickpea kabuli reference
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Kabuli reference
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Kabuli reference
Desi Kabuli
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Desi reference
Desi Kabuli Desi WGS
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Skim GBS
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• Determine SNPs by sequencing parents and running SGSautoSNP
• Low coverage skim sequence segregating population
• Map reads to the reference genome
• Call genotype where reads cover previously defined SNP
• Impute and clean to define haplotype blocks
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Genotype calling
16
Call genotype of previously predicted SNPs
A
C/A T/C
A
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Haplotype blocks
TN1 A G G T C C A G G A T A A T
TN2 A G G T C C A G G A T A A T
TN3 T C C A G G C G G A T A A T
TN4 A G G T C C A G G A T A A T
TN5 T C C A G G C T C G C G G C
TN6 A G G T C C A G G A T A A T
TN7 T C C A G G C T C G C G G C
T A G G T C C A G G A T A A T
N T C C A G G C T C G C G G C
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Pre-imputation
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After imputation and cleaning
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Genome assessment with isolated chromosome sequence data A)Heat maps on released genome (chromosome’s) size & quality B-H) Heat maps on improved genome assessment with isolated chromosomes sequence data I) Gene density plots J) SNP density plots
Kabuli improved genome assessment
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Desi improved genome assessment
Genome assessment with isolated chromosome sequence data A)Heat maps on released genome (chromosome’s) size & quality B-H) Heat maps on improved genome assessment with isolated chromosomes sequence data I) Heat map produced with WGS (ICC 4958) J) Gene density plots
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Genome stats
0
10
20
30
40
50
60
70
80
Ca1 Ca2 Ca3 Ca4 Ca5 Ca6 Ca7 Ca8
Kabuli v1.0
Kabuli v2.6.2
Desi v1.0
Desi v1.1
Siz
e in
Mb
p
Chromosomes
Kabuli v2.6.2 overall chromosome length has increased from 303.1 Mbp to 423.2 Mbp by placing 1,987 contigs Desi v1.1 overall chromosome length has increased from 124.3 Mbp to 416.9 Mbp by placing 133,840 contigs
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Desi vs Kabuli comparison
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Improvement of Darmor genome
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GBS using Darmor
• Both parental individuals high coverage (~50x)
• 92 double haploid Tapidor x Ningyou individuals, average coverage 1.6x
• Novel algorithm: contigPlacer
• Uses tagging SNPs per contig and compares genotype patterns with placed contigs, places unplaced contigs
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Darmor genome
• 10 A-chromosomes, 9 C-chromosomes,
• 22 sets of unplaced contigs
• Assembled size: 850.29 Mbp
• 645.95 Mbp placed (75.8%), 204.33 Mbp unplaced contigs
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Darmor improvement
• Identified 1,006,985 SNPs
• ~60% alleles called, after imputation ~80%
• Data in contigPlacer
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Darmor improvement
• Before contigPlacer: 645.95 Mbp placed (75.8%), 204.33 Mbp unplaced contigs
• After contigPlacer: 798.95 Mbp placed (93.9%), 51.33 Mbp unplaced
• 98.5% of unplaced contigs with initial chromosome assignment mapped to the same chromosome
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Resolving minor structural errors
Fixing minor structural errors is important for accurate trait fine mapping
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Conclusions
• Many high quality published genomes can be improved
• Chromosomal genomics, skimGBS and bioinformatics can validate and improve genome assemblies
• Quality genome assemblies improve trait association, they are essential for pan genome assembly and assessment of structural variation
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Acknowledgements
31
Philipp Bayer
Pradeep Ruperao
Juan Montenegro
Kenneth Chan
Michal Lorenc
Agnieszka Golicz
Kaitao Lai
Paul Visendi
Paula Martinez
Jenny Lee
Paul Berkman
Jiri Stiller
Sahana Manoli
Jacqueline Batley
Alice Hayward
Emma Campbell
Jessica Dalton-Morgan
Satomi Hayashi
Reece Tollenaere
Hana Šimková
Marie Kubaláková
Jaroslav Doležel
Tim Sutton
Deepa Jaganathan
Rajeev Varshney
(and colleagues)
Contact: