Sequencing of the Aegilops tauschii genome

subspecies strangulata accession AL8/78

IOS-1238231

A310

R392

A374

C356

A260

Af369

Tm415Af255

Af335

Af256A295

Af371Af367Af258Af370C347Af368Af261

Af372A263

Af259Af373

A304A264A281

A282

A265A302

A278A280A283A279 I298

A303I364I365

A300

A358

A305A266

I297V424V425

Tm410

C348

Tm418B327

B333Af262

B318I399I400

C349C350

C343C346C345

Tm409Tm411

Tm412

Tm414Tm413

Tm416

V423V420419422I366

V426V421

A357

A271A301

C341C340

A267A268

A270

I403Tm408

A363A273

A359

A360

A375A376

A285

A308

A362A377

A269

A299I381I404

I398B402I407

B315316

B331B326R379

B320B321B317B322B323B324

Af396328B330A277

A274A275

311I401

A294R296A306

A307A361I397

A288A290A276

I391

R389

B390

A293A309B334T286

R388A312A313

R394

B319

R395B314

R382

R384

B325R387

R393

R385

R383R386

197189

124114

125446

9910035

2310974

51721256

26

4113725311925477

6519515

31851801965379

248

31142002504721

11445224

64512918

19166

22108170208

153

2152 2092271143156

207229

202198428

223 225342266373

427186120194 181

187182183184

4136252

154193

Tauschii gene pool

AL8/78

Ae. tauschii ssp. strangulata

Ae. tauschii ssp. tauschii

Hexaploid wheat

Genetic relationships of accession AL8/78

Collection site of AL8/78 and the putative geographic area of hexaploid wheat origin

AL8/78 Hexaploid wheat origin

• ~ 80 to 90% repeated sequences

Aegilops tauschii genome

• Haploid genome ~ 4 to 5 Gbp

Ordered-clone sequencing approach

Aegilops tauschii physical map • 3,578 BAC contigs

• 2,263 anchored contigs (84.2% total contig length)

• MTP = 42,882 BAC clones

Luo et al., PNAS 110, 2013

• 2 = recombination rates • 1 = physical map

• 3 = gene density

Division of labor among participants

By chromosome By task

• Index each pool, combine 48 pools, sequence pools

Tasks

• Validate and pool 8 BAC clones

• Assemble our short pair-end reads together with BGI long pair-end reads

• Construct nanomap and validate scaffolds

• Produce pseudomolecules

• Preliminarily annotate TEs and genes

• Finally annotate TEs and genes

• Conduct community gene annotation

0

2000

4000

6000

8000

10000

12000

14000

16000

18000

1D 2D 3D 4D 5D 6D 7D ? Singletons

Target As of January 2015

MiSeq MTP sequencing and assembly status

Num

bers

of

BAC

clo

nes

Chromosomes

Scaffold assembly v.1

Average number of scaffolds > 2Kb per BAC pool: 18

Total scaffold length: 5.7 Gb

Average Scaffold N50 length: 203 Kb

Assembly pipeline (Poster #577)

Transposable element annotation

Perc

ent

• TE classes and families

Numbers of high-confidence genes

Wheat survey

sequence

Anchored BAC contigs

Corrected for unanchored BAC contigs

A B D

1 3,237 3,808 4,155 4,178 3,772

2 5,499 6,469 5,626 6,196 6,375

3 short 1,763 1,763 1,859 1,906

Ae. tauschii

Gene annotation

Chrom.

Gene annotation validation Manual validation of annotation

• MIPS • TriAnnot • Maker • Other

Annotation pipeline comparisons (Poster #576)

Pseudomolecule assembly

Scaffold validation, ordering, and orientating

Ordering BAC contigs in low recombination regions

Closing gaps

Chalenges

Nanomap

Nanomaps BAC contigs (Hastie et al., PloS ONE e55864, 2013)

Global nanomap of the Ae. tauschii genome

Nanomap construction (Poster #574) M.C. Luo’s presenations in Tuesday’s IWGSC technical workshop

New technologies

Ordering and orienting sequence scaffolds on the global nanomap

ctg1715 6D (76.097 cM)

ctg12344 6D (76.097 cM)

ctg195 6D (75.686 cM)

ctg6115 6D (76.097 cM)

Nanomap contig Sequence scaffolds

PacBio P6 chemistry

5 SMRT cells Total reads 4.1 Gbp Reads > 10 Kb 3.1 Gbp

10 kb 20 kb

Num

ber o

f rea

ds

Read length

Whole genome shotgun sequence

Where can I access data? http://aegilops.wheat.ucdavis.edu/ATGSP/data.php

Batch download of scaffolds also available

BLAST:

Karin Deal Pat McGuire Ming-Cheng Luo Naxin Huo, Yi Wang Chad Jorgensen Tingting Zhu, Sonny Van Lichan Xiao, Luxia Yuan Luis Curiel, Scott Liu JC Rodriguez, Thanh Ngo Armond Murray

Olin Anderson Yong Gu

Katrien Devos Hao Wang Jeffrey Bennetzen

Acknowledgements

Richard McCombie

National Science Foundation Plant Genome

Klaus Mayer Matthias Pfeifer

Steven Salzberg Daniela Puiu Geo Pertea

Thomas Wicker

Jaroslav Doležel

Shuhong Ouyang Yong Liang Zhenzhong Wang Zhiyong Liu Qixin Sun

Zhengqiang Ma

Alex Hastie Andrew Anfora Palak Sheth

Long Mao

Eric Lyons

Frank You Philippe Leroy

Cari Soderlund