The Medicago truncatula genome Nevin Dale Young January 2007 1 Medicago genome sequencing initiative

Nevin Dale YoungJanuary 2007

1The Medicago truncatula genome

Medicago genome sequencing initiative



Medicago as a model legume

Limpens & Bisseling (2003) Curr. Opin. Plant Biol. 6: 343

Choi HK, et al (2004) PNAS 101:15289-15294.Photo: R. Guerts, Wageningen



Sequencing strategy• BAC-by-BAC sequencing of the entire euchromatin of Medicago truncatula, originally estimated at 200 Mbp, now estimated at ~300 Mbp.– >2000 BACs sequenced as of January 2007.

• Goal is high quality “Bermuda standards” sequence throughout the euchromatin.

• Strategy chosen to optimize the utility of the M. truncatula sequence in comparative genomics.

• International consortium of genome centers are responsible for sequencing, distributed by chromosome.

• Initial coordinated, genome-wide assembly generated in August 2006. Analysis is underway and release is planned for early 2007.



M. truncatula assembly — Release 1.0www.medicago.org/genome



M. truncatula genome assembly

Chromosome 1 2 3 4 5 6 7 8 "0" TotalBACs 193 209 257 238 244 117 238 241 89 1826Singletons 14 3 8 23 0 4 10 8 68 138Contigs 39 39 55 46 39 32 36 53 9 348Scaffolds 31 31 42 35 18 30 31 48 9 275Gaps1 44 34 50 57 18 33 40 55 76 407Pseudomolecule2 (kbp) 22,439 23,156 28,918 28,813 29,652 15,021 25,989 28,057 8,965 211,012Pseudomolecule3 (kbp) 26,839 26,456 34,068 34,513 31,352 18,321 29,989 33,557 16,565 251,662Scaffold avg (kbp) 643 731 668 697 1647 475 789 553 260 699Scaffold N-50 (kbp) 516 578 546 482 1353 408 580 415 225 505

1 Gaps between scaffolds2 Pseudomolecule size not including 100,000 nt spacers between scaffolds3 Pseudomolecule size including 100,000 nt spacers between scaffolds



M. truncatula genome assembly



IMGAG Annotation



Confidence of gene models

Full length

Partial EST

Protein similarity

Hypothetical

Low confidence



Confidence of gene models



M. truncatula – Genome statistics

Chr 1 Chr 2 Chr 3 Chr 4 Chr 5 Chr 6 Chr 7 Chr 8 "Chr 0" AllLength (kb) 26,838 26,456 34,068 34,513 31,352 18,321 29,989 33,556 16,565 251,661Gene number 4436 4775 5824 5630 6122 2647 5227 5517 2180 42,358Genes per 100 kb 23.1 23.0 22.4 23.2 23.1 20.9 22.5 22.5 24.5 22.8Avg gene length 1796 1663 1741 1753 1669 1568 1726 1720 1480 1700Avg peptide length 249 240 250 245 237 219 239 241 203 239Exons Number 14,513 14,580 17,536 17,654 18,245 6,759 15,947 17,344 5,498 128,076 Avg per gene 3.3 3.1 3.0 3.1 3.0 2.6 3.1 3.1 2.5 3.0 Avg size (bp) 295 305 336 308 311 385 319 300 374 318Introns Number 10,077 9.803 11,710 12,024 12,123 4,110 10,719 11,826 3,318 85,710 Avg size (bp) 364 355 362 367 373 377 365 361 351 364



M. truncatula – Genome statistics



Chr4 Centromere trace

0

5

1015

20

25

30

3540

45

50

AC148341/CAC135316/CAC147537/BAC144805/HAC146649/HAC174305/CAC124969/HAC174309/CAC147405/CAC144515/HAC159147/C

gene_densitygypsy_densitycopia_density

Mth2-139k12 4-S borderMth2-20l08 4-N border

Gene densityGypsy densityCopia densityTotal TE densityPericentromere

Centromeres & pericentromeres



Legume phylogeny



Medicago & Lotus



Medicago & Glycine



Medicago PoplarArabidopsis

Med

icag

oP

opla

rA

rabi

dops

is

Multi-speciessynteny comparisons



Multi-speciessynteny comparisons



Synteny on different chromosomes

Medicago chromosomes covered by synteny blocks

0.00%

10.00%20.00%

30.00%

40.00%

50.00%60.00%

70.00%

80.00%90.00%

100.00%

Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8Genome

Medicago Chr

Coverage

Mt-At

Pt-Mt

Os-Mt

Mt-Mt



Synteny on differentchromosomes



Summary: The Medicago genome

• BAC-by-BAC sequence by end of 2008• Release 1.0 (~60% complete) in early 2007• Genome features

– Lots of genes; many short, but probably expressed

– Recombination drops nears ends of chromosomes– Chromosome 6 is very different from others– Comparative & evolutionary genomics

• Ten large synteny blocks between Medicago & Lotus• Less internal duplication than At/Pt• Many short, scattered synteny blocks with At/Pt• Synteny varies greatly from region to region

• For more information, visit posters P7 & P221



Sequencing the Medicago genome• EU Medicago Sequencing

– Christine Nicholson (Sanger)– Frederic Debelle (Toulouse)– Jerome Gouzy (Toulouse)– Rene Guerts (Wageningen)– Sean Humphray (Sanger)– Gyorgy Kiss (Hungary)– Klaus Mayer (MIPS)– Giles Oldroyd (JIC)– Frances Quetier (Genoscope)– Stephane Rombauts (Ghent)– Jane Rogers (Sanger)– Thomas Schiex (Toulouse)– Heiko Schoof (MIPS)– Yves van de Peer (Ghent)– Many others…

• Also– Perry Cregan (Beltsville)– David Hyten (Beltsville)

• TIGR– Chris Town– Ryan Althoff– Tammy Arbogast– Foo Cheung– Doug Fadrosch– Erin Hine– Hean Koo– Erin Monaghan– Luke Tallon

• CCGB (Minnesota)– Ernie Retzel– John Crow– Chris Dwan– Michael Heuer– Anne-Francoise Lamblin

• UC-Davis– Doug Cook– Dongjin Kim– Hong-Kyu Choi– Andrew Cook

• Young Lab (Minnesota)– Carine Ameline-Torregrosa– Eric Boehlke– Ryan Bretzel– Steven Cannon (now @ ISU)– Ethy Cannon (now @ ISU)– Ben Chacko– Roxanne Denny– Joann Mudge– Libby Shoop– Bing-Bing Wang– Min Wang– Shelley Wang– Ariel Abell– Atif Ahmed– Chris Alley– Daniel Feldman– Andrew Homan– Shara Johnson– Dana Larsen-Howe– Michael Kantar– Nyaling Moorosi– Michael O’Toole– Jake Pemberton– Diana Rommelfanger– Erica Savage



• Mandi Aycock• Amy Dickey• Kayci Hale• Randy Hine• Aisha Hines• Courtney Johnson• Joey Klebba• Julia Kim• Xiangfei Kong• Karen Marichal• Goldameir Osisanya• Stephen Snow• Aleksandra Stojanoska,• Yonas Tesfai• Graham Wiley• Erica Willis

University of Oklahoma• Bruce Roe• Anh Do• Trang Do• Sara Downard• Mounir Elharam• Ying Fu• Shaoping Lin• Phoebe Loh,• Rose Morales-Diaz• Sulan Qi • Baifang Qin• Chunmei Qu• Ziyun Zao• Doug White• Keqin Wang• Limei Yang• Yang Ye• Liping Zhao

• Steve Kenton• Hongshing Lai• Sean Qian• Jim White• Axin Hua• Fares Najar• Shweta Deshpande• Majesta Seigfried• Irena Vasylenko• Ying Yi• Tammy Womack• KayLynn Hale

Sequencing the Medicago genome



Medicago genome sequencing initiative

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The Medicago truncatula genome Nevin Dale Young January 2007 1 Medicago genome sequencing initiative