Arabidopsis as a model for plant development Eva Huala.
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Arabidopsis as a model for plant development
Eva Huala
0
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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
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