Genome-wide Identification of Lineage Specific Genes in … · Presentation_name. Summary • 192, 641 and 109 species-specific (SS) genes were discovered in Arabidopsis, Oryza Oryza

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GenomeGenome--wide Identification of Lineage wide Identification of Lineage Specific Genes in Specific Genes in ArabidopsisArabidopsis, , OryzaOryza

and and PopulusPopulus

XiaohanXiaohan YangYangSara Sara JawdyJawdy

Timothy Timothy TschaplinskiTschaplinskiGerald Gerald TuskanTuskan

Environmental Sciences DivisionEnvironmental Sciences Division Oak Ridge National LaboratoryOak Ridge National Laboratory

USAUSA

2 Managed by UT-Battellefor the Department of Energy

Identification of Identification of taxontaxon--specific genes specific genes has both scientific and practical value has both scientific and practical value

Conserved function New function(Common) (Unique)

3 Managed by UT-Battellefor the Department of Energy Presentation_name

Plant genome sequences Plant genome sequences

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Ara

bid

op

sis

Ca

ric

a

Me

dic

ag

o

Gly

cin

e

Po

pu

lus

Vit

is

Ze

a

So

rgh

um

Ory

za

Eudicot MonocotEurosids II Eurosids I

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ObjectivesObjectives

••

To identify lineageTo identify lineage--specific genes in specific genes in reference plant speciesreference plant species

••

To explore functions of the specific genes via To explore functions of the specific genes via expression analysisexpression analysis

••

To study the evolution of the lineageTo study the evolution of the lineage--specific specific genes genes

Application of the knowledge gained to Application of the knowledge gained to bioenergy and carbon sequestration research bioenergy and carbon sequestration research

(Candidate genes)(Candidate genes)


Newly-sequenced genomes

192 proteins 641 proteins109 proteins

Arabidopsis

26784

Oryza

56278

Populus

45555


Transcripts of plant species

nr protein database



No-hits, expressed Differential gene (DG)

tBLASTn

BLASTp

No-hits

No-hits

Pairwise BLASTp

BLASTp

No-hits; Species-specific (SS)

ApproachApproach


The percentage of differential genes The percentage of differential genes showing homology to other plantsshowing homology to other plants

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Expression of the Expression of the ArabidopsisArabidopsis SS SS genes genes

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Cluster01 Cluster02 Cluster03 Cluster04







Expression of the Expression of the ArabidopsisArabidopsis SSSS (Cluster01)(Cluster01)

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Cotyledons Hypocotyl Roots, 7d Shoot apexRoots, 17d Rosette leaf # 8 Senescing leaf2nd internodeFlowers stage 10Flowers stage 12 sepal petal stamen carpel Flower stage 15 sepal petal stamen carpel Mature pollen SiliqueSeed


Expression of the Expression of the PopulusPopulus SS genes SS genes

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Expression of the Expression of the PopulusPopulus SS genes SS genes

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Cluster06Cluster14Cluster13


Number of Number of intronsintrons per gene in per gene in ArabidopsisArabidopsis, , OryzaOryza & & PopulusPopulus

•

Intron number per gene:3-or-more introns2 introns1 intron0 intron (Intronless)

•

“+” indicates that genes are over-represented and “-” under-represented at P < 1x10-5, as compared with all genes in the whole genome.

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+

-

+

-

++

-

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qPCRqPCR analysis of expression of analysis of expression of PopulusPopulus-- specific & differential gene setsspecific & differential gene sets


Conserved motifs in Conserved motifs in ArabidopsisArabidopsis-- and and OryzaOryza--specific proteinsspecific proteins


Other species sharing motifs with Other species sharing motifs with ArabidopsisArabidopsis-- and and OryzaOryza--specific genesspecific genes

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SummarySummary

••

192, 641 and 109 species192, 641 and 109 species--specific (SS) genes specific (SS) genes were discovered in were discovered in ArabidopsisArabidopsis, , OryzaOryza and and PopulusPopulus, respectively, respectively

••

Some SS genes were preferentially expressed Some SS genes were preferentially expressed in flowers, roots, xylem (and cambium or upin flowers, roots, xylem (and cambium or up-- regulated by stress, data not shown)regulated by stress, data not shown)

••

Six conserved motifs in Six conserved motifs in ArabidopsisArabidopsis and and OryzaOryza SS proteins were found in other distant SS proteins were found in other distant lineageslineages

••

The SS gene sets were enriched with The SS gene sets were enriched with intronlessintronless genesgenes

•

The Populus-specific genes are likely candidates for carbon sequestration & biofuel


AcknowledgementsAcknowledgements

Gerald Tuskan, Sara Jawdy, Timothy TschaplinskiStan Wullschleger, Udaya Kalluri, Lee Gunter

http://www.esd.ornl.gov/PGG/index.htm

Documents

Genome-wide Identification of Lineage Specific Genes in … · Presentation_name. Summary • 192, 641 and 109 species-specific (SS) genes were discovered in Arabidopsis, Oryza Oryza