Daniela Puiu at #ICG12: The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum

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Daniela Puiu in the GigaScience Prize Track at ICG12: The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum. #ICG12, 26th October 2017

Science

The first near-complete assembly of
the hexaploid bread wheat genome,
Tritricum aestivum
Daniela Puiu
Aleksey Zimin, Richard Hall, Sarah Kingan, Bernardo Clavijo, Steven Salzberg
ICG-12
Oct 27 2017

IGC-12The Wheat Genome 2
Sequencing and Assembly of the
Ancestral and Common Wheat
Aegilops tauschii ssp strangulata accession AL8/78
Chinese spring variety (CS42, accession Dv418)
2013-2017

IGC-12The Wheat Genome 3
History of Wheat
~8,000 years ago: spontaneous hybridization
Emmer Wheat + Goat grass = Bread Wheat (World's 3rd
cereal crop)
Triticum turgidum + Aegilops tauschii = Triticum aestivum
AABB + DD = AABBDD
Whole Genome => Assisted Breeding => Improved Yield

IGC-12The Wheat Genome 4
The Wheat Genome
One of the most complex genomes !
1) Genome size: over 15 billion bases
2) Allohexapoild : six copies of each chromosome
3) >90% repeats
Multiple past attempts to assemble =>
assemblies shorter than the estimated genome size.

IGC-12The Wheat Genome 5
New vs Previous Assemblies
Tritricum 3.1
N50
232K

IGC-12The Wheat Genome 6
Data Reduction
Original Reads Number Sum Coverage Accuracy
Illumina 7.06G 1Tb 65x 99.5%
PacBio 55.5M 545Gb 36x 87.5%
Processed Seq Number Sum Coverage Accuracy
super-reads 95.7M 31Gb 2x 99.95%
mega-reads 57M 278Gb 18x 99.65%
MaSuRCA mega-reads
hybrid correction

IGC-12The Wheat Genome 7
MaSuRCA mega-reads Correction

IGC-12The Wheat Genome 8
Assembly Pipeline
MaSuRCA Correction
Illumina
Celera WGS Assembler
Mega-reads
Remove Duplicates
Tritricum 1.0
Tritricum 2.0
FALCON Correction
PacBio
FALCON Assembler
pReads
Arrow Polishing
FALCON Trit 0.5
FALCON Trit 1.0
k-mer Analysis
Merge
Tritricum 3.1

IGC-12The Wheat Genome 9
k-mer Analysis
50M
k-mers missing from the
PacBio assembly only
40M
30M
20M
10M
31-mer frequencies

IGC-12The Wheat Genome 10
Assembly Merge
Merging of the Hybrid and PacBio assembliesMerging of the Hybrid and PacBio assemblies
Tritricum 2.0 contig
FALCON contigA FALCON contigB
Tritricum 3.1
>5Kb >5Kb>5Kb

IGC-12The Wheat Genome 11
Assembly Statistics
Assembly Number Total size
(bp)
N50 size
(bp)
Triticum 2.0 375,328 14,395,027,822 75,599
FALCON Trit 1.0 97,809 12,939,100,857 215,314
Triticum 3.1 279,439 15,344,693,583 232,659

IGC-12The Wheat Genome 12
Run Time: 100 CPU years
Main
Steps
Run
Time
CPUhrs
Wall
Time
Months
MaSuRCA 100K 1.5
Celera WGS 470K 5
FALCON 150K 0.75
ARROW 160K 0.75
total 880K 9
100K CPU hrs=11.5 years
800K CPU hrs=100 years

IGC-12The Wheat Genome 13
Genome Repetitiveness
k-mer uniqueness ratios
WHEAT
FLY
COW
RICE
PINE
Ae tauschii

IGC-12The Wheat Genome 15
Conclusions
The most challenging genome (we) assembled!
Learning experience!
Assembly quality vs computational resources?
Share your data!
The most challenging genome (we) assembled!
Learning experience!
Assembly quality vs computational resources?
Share your data!

IGC-12The Wheat Genome 16
Acknowledgements
Steven Salzberg
Aleksey ZImin
Johns Hopkins University UCDavis Plant Sciences
Jan Dvorak
Earlham Institute
Bernardo Clavijo
Mingcheng Luo

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Daniela Puiu at #ICG12: The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum

1. The first near-complete assembly of the hexaploid bread wheat genome, Tritricum aestivum Daniela Puiu Aleksey Zimin, Richard Hall, Sarah Kingan, Bernardo Clavijo, Steven Salzberg ICG-12 Oct 27 2017

2. IGC-12The Wheat Genome 2 Sequencing and Assembly of the Ancestral and Common Wheat Aegilops tauschii ssp strangulata accession AL8/78 Chinese spring variety (CS42, accession Dv418) 2013-2017

3. IGC-12The Wheat Genome 3 History of Wheat ~8,000 years ago: spontaneous hybridization Emmer Wheat + Goat grass = Bread Wheat (World's 3rd cereal crop) Triticum turgidum + Aegilops tauschii = Triticum aestivum AABB + DD = AABBDD Whole Genome => Assisted Breeding => Improved Yield

4. IGC-12The Wheat Genome 4 The Wheat Genome One of the most complex genomes ! 1) Genome size: over 15 billion bases 2) Allohexapoild : six copies of each chromosome 3) >90% repeats Multiple past attempts to assemble => assemblies shorter than the estimated genome size.

5. IGC-12The Wheat Genome 5 New vs Previous Assemblies Tritricum 3.1 N50 232K

6. IGC-12The Wheat Genome 6 Data Reduction Original Reads Number Sum Coverage Accuracy Illumina 7.06G 1Tb 65x 99.5% PacBio 55.5M 545Gb 36x 87.5% Processed Seq Number Sum Coverage Accuracy super-reads 95.7M 31Gb 2x 99.95% mega-reads 57M 278Gb 18x 99.65% MaSuRCA mega-reads hybrid correction

7. IGC-12The Wheat Genome 7 MaSuRCA mega-reads Correction

8. IGC-12The Wheat Genome 8 Assembly Pipeline MaSuRCA Correction Illumina Celera WGS Assembler Mega-reads Remove Duplicates Tritricum 1.0 Tritricum 2.0 FALCON Correction PacBio FALCON Assembler pReads Arrow Polishing FALCON Trit 0.5 FALCON Trit 1.0 k-mer Analysis Merge Tritricum 3.1

9. IGC-12The Wheat Genome 9 k-mer Analysis 50M k-mers missing from the PacBio assembly only 40M 30M 20M 10M 31-mer frequencies

10. IGC-12The Wheat Genome 10 Assembly Merge Merging of the Hybrid and PacBio assembliesMerging of the Hybrid and PacBio assemblies Tritricum 2.0 contig FALCON contigA FALCON contigB Tritricum 3.1 >5Kb >5Kb>5Kb

11. IGC-12The Wheat Genome 11 Assembly Statistics Assembly Number Total size (bp) N50 size (bp) Triticum 2.0 375,328 14,395,027,822 75,599 FALCON Trit 1.0 97,809 12,939,100,857 215,314 Triticum 3.1 279,439 15,344,693,583 232,659

12. IGC-12The Wheat Genome 12 Run Time: 100 CPU years Main Steps Run Time CPUhrs Wall Time Months MaSuRCA 100K 1.5 Celera WGS 470K 5 FALCON 150K 0.75 ARROW 160K 0.75 total 880K 9 100K CPU hrs=11.5 years 800K CPU hrs=100 years

13. IGC-12The Wheat Genome 13 Genome Repetitiveness k-mer uniqueness ratios WHEAT FLY COW RICE PINE Ae tauschii

14. IGC-12The Wheat Genome 14 Publication

15. IGC-12The Wheat Genome 15 Conclusions The most challenging genome (we) assembled! Learning experience! Assembly quality vs computational resources? Share your data! The most challenging genome (we) assembled! Learning experience! Assembly quality vs computational resources? Share your data!

16. IGC-12The Wheat Genome 16 Acknowledgements Steven Salzberg Aleksey ZImin Johns Hopkins University UCDavis Plant Sciences Jan Dvorak Earlham Institute Bernardo Clavijo Mingcheng Luo

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Daniela Puiu at #ICG12: The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum