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Table 1 Enriched expression of genes in the embryo sac cells was distinguished by their absence of detectable expression in sporophytic and pollen transcriptomes

From: Genetic subtraction profiling identifies genes essential for Arabidopsisreproduction and reveals interaction between the female gametophyte and the maternal sporophyte

    

Orthologous Zm ESTc

Gene ID

Gene description

Studya

Homology to At siliques transcriptomeb

ES

Egg

CC and EN

Transcriptional Regulation

   At5g06070

Zinc Finger (C2H2 Type) Family Protein (RBE)

2

0

0

0

0

   At1g75430

Homeodomain Protein

1

0

0

0

0

   At2g01500

Homeodomain-Leucine Zipper (WOX6, PFA2)

1

0

0

0

1

   At2g24840

MADS-Box Protein Type I (AGL61)

2

0

1

1

1

   At1g02580

MEDEA (MEA)

2

0

0

1

1

   At5g11050

MYB Transcription Factor (MYB64)

1, 2

0

0

0

1

   At3g29020

MYB Transcription Factor (MYB110)

2

0

0

0

1

   At5g35550

MYB Transcription Factor (MYB123) (TT2)

2

1

0

0

1

   At4g18770

MYB Transcription Factor (MYB98)

2

0

0

0

1

Core Signaling Pathways

   At5g12380

Annexin

2

0

1

1

1

   At2g20660

Rapid Alkalinization Factor (RALF)

2

0

0

0

0

RNA Synthesis And Modification

   At1g63070

PPR Repeat-Containing Protein

1

0

0

0

1

   At2g20720

PPR Repeat-Containing Protein

1

0

0

0

0

   At3g54490

RPB5 RNA Polymerase Subunit

2

0

1

1

1

Protein Synthesis And Modification

   At5g11360

Protein Involved in Amino Acid Phosphorylation

2

1

1

0

0

   At4g15040

Subtilase Family Protein, Proteolysis

2

0

1

1

1

   At5g58830

Subtilase Family Protein, Proteolysis

2

1

0

1

1

   At1g36340

Ubiquitin-Conjugating Enzyme

2

1

1

1

1

Enzymes And Metabolism

   At3g30540

(1-4)-Beta-Mannan Endohydrolase Family

2

0

0

0

0

   At1g47780

Acyl-Protein Thioesterase-Related

2

0

1

0

0

   At1g31450

Aspartyl Protease Family Protein

2

0

1

1

1

   At1g69100

Aspartyl Protease Family Protein

2

0

0

1

1

   At2g28010

Aspartyl Protease Family Protein

2

0

0

1

1

   At2g34890

CTP Synthase, UTP-Ammonia Ligase

2

1

1

0

1

   At4g39650

Gamma-Glutamyltransferase

2

1

0

0

0

   At4g30540

Glutamine Amidotransferase

2

0

0

0

1

   At3g48950

Glycoside Hydrolase Family 28 Protein

2

1

0

1

1

   At2g42930

Glycosyl Hydrolase Family 17 Protein

2

0

1

1

1

   At4g09090

Glycosyl Hydrolase Family 17 Protein

2

1

1

1

1

   At1g56530

Hydroxyproline-Rich Glycoprotein

1

0

0

0

0

   At1g06020

Pfkb-Type Carbohydrate Kinase

2

1

0

1

1

   At2g43860

Polygalacturonase

2

0

0

0

1

   At1g78400

Glycoside Hydrolase Family 28 Protein

1

0

0

0

1

   At5g22960

Serine Carboxypeptidase A10 Family Protein

1

0

0

1

1

   At4g21630

Subtilase Family Protein

2

1

1

1

1

   At4g26280

Sulfotransferase Family Protein

2

0

0

0

0

Cell Structure And Transport

   At1g10010

Amino Acid Permease Involved In Transport

2

1

1

0

0

   At4g20800

FAD-Binding Domain-Containing Protein

2

0

0

1

0

   At1g34575

FAD-Binding Domain-Containing Protein

1

1

0

1

0

   At1g48010

Invertase/Pectin Methylesterase Inhibitor Family Protein

2

0

0

0

0

   At3g17150

Invertase/Pectin Methylesterase Inhibitor Family Protein

2

1

0

0

0

   At3g55680

Invertase/Pectin Methylesterase Inhibitor Family Protein

1

0

0

0

0

   At2g47280

Pectinesterase Family Protein

2

0

0

0

0

   At4g00190

Pectinesterase Family Protein

2

0

0

0

0

   At5g18990

Pectinesterase Family Protein

2

0

0

0

0

   At1g56620

Pectinesterase Inhibitor

2

0

0

0

0

   At2g23990

Plastocyanin-Like

2

1

0

0

1

   At1g73560

Lipid Transfer Protein (LTP) Family Protein

2

1

0

0

0

   At5g56480

Lipid Transfer Protein (LTP) Family Protein

2

0

0

0

1

   At1g63950

Lipid Transfer Protein (LTP) Family Protein

2

1

0

0

0

   At3g05460

Sporozoite Surface Protein-Related

2

1

0

0

0

   At5g06170

Sucrose Transporter

2

1

0

0

1

Uncategorized

   At1g24000

Bet V I Allergen Family Protein

2

1

0

0

0

   At3g42130

Glycine-Rich Protein

1

0

0

0

0

   At3g17140

Invertase Inhibitor-Related

2

0

0

0

0

   At5g09360

Laccase-Like Protein Laccase

2

0

1

1

1

   At1g79960

Ovate Protein-Related

2

0

0

0

0

   At3g59260

Pirin

2

0

0

0

0

   At4g30070

Plant Defensin-Fusion Protein

2

1

0

0

0

   At5g38330

Plant Defensin-Fusion Protein

2

0

0

0

0

   At2g01240

Reticulon Family Protein (RTNLB15)

2

0

1

0

0

   At3g17080

Self-Incompatibility Protein-Related

2

0

0

0

0

   At5g12060

Self-Incompatibility Protein-Related

2

1

0

0

0

   At3g28020

Unknown

1

0

0

0

0

   At3g19780

Unknown

1

0

0

0

0

   At5g30520

Unknown

1

0

0

0

0

   At3g45380

Unknown

1

0

0

0

0

   At4g23780

Unknown

1

0

0

0

0

   At1g54926

Unknown

1

0

0

0

0

   At3g23720

Unknown

1

0

0

0

0

   At1g47470

Unknown

1, 2

0

0

0

0

   At1g32680

Unknown

1

0

0

0

0

   At1g11690

Unknown

1

0

0

0

0

   At2g04870

Unknown

1

0

0

0

0

   At2g06630

Unknown

1

0

0

0

0

   At4g09400

Unknown

1

0

0

0

0

   At1g21950

Unknown

2

1

0

0

0

   At4g11510

Unknown

2

1

0

0

0

   At5g25960

Unknown

2

0

0

0

1

   At1g60985

Unknown

2

0

0

0

0

   At1g63960

Unknown

2

0

0

0

0

   At1g78710

Unknown

2

1

1

0

1

   At2g02515

Unknown

2

1

0

0

0

   At2g20070

Unknown

2

0

0

0

0

   At2g21740

Unknown

2

0

0

1

0

   At2g30900

Unknown

2

0

1

0

1

   At3g04540

Unknown

2

0

0

0

0

   At3g13630

Unknown

2

1

0

0

0

   At3g43500

Unknown

2

0

0

0

0

   At3g57850

Unknown

2

0

0

0

0

   At4g07515

Unknown

2

0

0

0

0

   At4g10220

Unknown

2

1

0

0

0

   At4g17505

Unknown

2

0

0

0

1

   At5g17130

Unknown

2

0

0

0

0

   At5g25950

Unknown

2

1

0

0

1

   At5g46300

Unknown

2

1

0

0

0

   At5g64720

Unknown

2

0

0

1

0

   At1g52970

Unknown

2

0

0

0

0

   At5g42955

Unknown

2

0

0

0

0

   At2g21655

Unknown

2

0

0

0

0

   At2g20595

Unknown

2

0

0

0

0

   At1g45190

Unknown

2

0

0

0

0

   At5g43510

Unknown

2

1

0

0

0

   At2g15780

Unknown, Blue Copper-Binding Protein

1

0

0

0

0

   At1g24851

Unknown

1

0

0

0

0

   At1g30030

Non-LTR retrotransposon family (LINE)

1

0

ND

ND

ND

   At2g34130

CACTA-like transposase family

2

0

ND

ND

ND

   At3g42930

CACTA-like transposase family

1

0

ND

ND

ND

  1. Embryo sac-enriched expression for the 1,260 candidate genes was deduced by comparing the transcriptomes of cotyledon, hypocotyls, root, leaf, shoot, petiole, sepal, petal, pedicel, mature siliques, mature seeds, rosettes, and pollen (see Additional data file 6 for details). Note that there were ten more microarray probes that identified expressed genes (At1g75610, At4g04300, At2g13750, At3g32917, At4g05600, At4g07780, At2g23500, At1g78350, At5g34990, and At2g10840), but they were omitted as pseudogenes by the The Arabidopsis Information Resource (TAIR) Gene ontology. See Additional data files 2 and 3 for further details. a'1' indicates coatlique dataset and '2' indicates sporocyteless dataset. b'0' indicates absent and '1' indicates present in Arabidopsis thaliana (At) transcriptomes of immature siliques with globular embryo. Data are derived from Schmid and coworkers [28]. cAppropriate scores were assigned if an Arabidopsis gene is similar (= 1) or not (= 0) to Zea mays (Zm) and wheat expressed sequence tags (ESTs) by basic local alignment search tool (BLAST) analysis at an e-value of 10-8. A total of 10,747 embryo sac (ES) ESTs, 5,925 egg cell ESTs, and 15,677 ESTs from central cell (CC) and immature endosperm (EN) cells (1-6 days after pollination [DAP]) were used in the BLAST analysis. See Additional data file 8 for further details on the ESTs. ND, not determined.
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Genome Biology

ISSN: 1474-760X

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