Arabidopsis as a model for plant development

Eva Huala

0

1,000

2,000

3,000

4,000

5,000

6,000

P F C P F C P F C P F C P F C P F C P F C P F C P F C

Experimental

S. cer.

(yeast)

D. disc.

(slime mold)

D. mel.

(fly)

C. eleg.

(worm)

D. rer.

(fish)

A. thal.

(plant)

M. mus.

(mouse)

R. nor.

(rat)

H. sap.

(human)

Gen

e pr

oduc

tsGenes with experimental GO annotations by species

P = biological process

F = molecular function

C = subcellular component

0

1,000

2,000

3,000

4,000

5,000

6,000

P F C P F C P F C P F C P F C P F C P F C P F C P F C

Experimental

S. cer.

(yeast)

D. disc.

(slime mold)

D. mel.

(fly)

C. eleg.

(worm)

D. rer.

(fish)

A. thal.

(plant)

M. mus.

(mouse)

R. nor.

(rat)

H. sap.

(human)

Gen

e pr

oduc

tsGenes with experimental GO annotations by species

P = biological process

F = molecular function

C = subcellular component

12 4 3 Rank

0

5,000

10,000

15,000

20,000

25,000

30,000

35,000

40,000

45,000

P F C P F C P F C P F C P F C P F C P F C P F C P F C

All proteins

IEA

Other

Experimental

S. cer.

(yeast)

D. disc.

(slime mold)

D. mel.

(fly)

C. eleg.

(worm)

D. rer.

(fish)

A. thal.

(plant)

M. mus.

(mouse)

R. nor.

(rat)

H. sap.

(human)

Gen

e pr

oduc

tsGenes with GO annotations by evidence and species

65% 12%11%11% 10% 9%7%4% 2%% gene products with exp GO annotations

Arabidopsis as a model plant

• What is the role of Arabidopsis now that we have lots of plant genome sequences?

– Original reasons for using Arabidopsis still hold true

– New genomes make it easier to apply results from Arabidopsis

to other plants

– More knowledge and tools More useful

Arabidopsis as a model plant

• What is the role of Arabidopsis now that we have lots of plant genome sequences?

– Original reasons for using Arabidopsis still hold true

– New genomes make it easier to apply results from Arabidopsis

to other plants

– More knowledge and tools More useful

• The era of genome-hopping is upon us

Populus(cottonwood)

Oryza(rice)

Medicago(clover)Arabidopsis

Physcomitrella(moss)

Land plants

Vascular plants

Seed plants

Dicots

Eurosids II

92

160

400

450

Selaginella(lycophyte)

Arabidopsis

Populus (92 Mya)

Medicago (92 Mya)

Oryza (160 Mya)

Selaginella (400 Mya)

Physcomitrella (450 Mya)

TAIR GBrowse: http://arabidopsis.org/cgi-bin/gbrowse/arabidopsis/

Nucleotide conservation across large evolutionary time spans

Nucleotide conservation across large evolutionary time spans

Phot1 blue light photoreceptorArabidopsis

Populus (92 Mya)

Medicago (92 Mya)

Oryza (160 Mya)

Selaginella (400 Mya)

Physcomitrella (450 Mya)

TAIR GBrowse: http://arabidopsis.org/cgi-bin/gbrowse/arabidopsis/

LBL: http://pipeline.lbl.gov/cgi-bin/textBrowser2?act=hits&run=74-&base=174&pos=chr3:16826523-16836522

Other ways to navigate between genomes: Orthologs and gene families

TAIR GBrowse: http://arabidopsis.org/cgi-bin/gbrowse/arabidopsis/

Other ways to navigate between genomes: Brassica and radish sequences

Brassica - 840,000 ESTs, 2100 cDNAsRaphanus - 287,000 ESTs

Nucleotide alignments to Arabidopsis using CAT (Cross-species Alignment Tool, Li et al 2007) TAIR GBrowse

Spinacia oleracea

Arabidopsis thaliana

Brassica napus

Spinacia oleracea

Glycine max

www.plantcyc.org

Populus(cottonwood)

Oryza(rice)

Medicago(clover)Arabidopsis

Physcomitrella(moss)

Land plants

Vascular plants

Seed plants

Dicots

Eurosids II

92

160

400

450

Selaginella(lycophyte)

Populus(cottonwood)

Oryza(rice)

Medicago(clover)Arabidopsis

Physcomitrella(moss)

Land plants

Vascular plants

Seed plants

Dicots

Eurosids II

92

160

400

450

Selaginella(lycophyte)

A. lyrataC. rubella

Populus(cottonwood)

Oryza(rice)

Medicago(clover)Arabidopsis

Physcomitrella(moss)

Land plants

Vascular plants

Seed plants

Dicots

Eurosids II

92

160

400

450

Selaginella(lycophyte)

A. lyrataC. rubella

Chlamydomonas(green alga)

475

Populus(cottonwood)

Oryza(rice)

Medicago(clover)Arabidopsis

Physcomitrella(moss)

Land plants

Vascular plants

Seed plants

Dicots

Eurosids II

92

160

400

450

Selaginella(lycophyte)

A. lyrataC. rubella

Chlamydomonas(green alga)

475

Porphyra purpurea(red alga)

Populus(cottonwood)

Oryza(rice)

Medicago(clover)Arabidopsis

Physcomitrella(moss)

Land plants

Vascular plants

Seed plants

Dicots

Eurosids II

92

160

400

450

Selaginella(lycophyte)

A. lyrataC. rubella

Chlamydomonas(green alga)

475

Porphyra purpurea(red alga)

Others from JGI:Cassava,

Brachypodium,Pine, Eucalyptus,Monkey flower,Millet, Soybean,

Switchgrass,Sorghum, Cotton

Tanya Berardini Donghui LiDebbie Alexander

Metabolic Pathways: Gene Function/GO:

TAIR Technical Staff:

Bob MullerShanker Singh

Larry PloetzCynthia Lee

Tom MeyerVanessa Kirkup

Raymond Chetty Anjo Chi

Peifen Zhang Kate DreherA.S. KarthikeyanSue Rhee

David SwarbreckPhilippe LameschChris Wilks

Genome Annotation:

AcknowledgementsNAASC

LBL/JGI

Inna Dubchak