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Table 1 List of Spodoptera frugiperda genes transcriptionally modified by HdIV infection.

From: Gene expression profiling of Spodoptera frugiperda hemocytes and fat body using cDNA microarray reveals polydnavirus-associated variations in lepidopteran host genes transcript levels

Spodobase ID

Gene Name

Functional class

Number of clones

SAM Fold

GeneANOVA

   

H

F

M

L

 

F gene-cond°

p-value

Hemocytes_HdIV : 72 significant genes, 18 up-regulated and 54 down-regulated

q-value 0.0056

  

Sf1H03393-5-1

Fumarate hydratase

AVI tricarboxylic acid cycle

1

3

0

0

2.24

74

<0.00001

Sf1H00151-5-1

retinol dehydratase; iso-1

AVI catalytic

7

0

0

0

2.11

152

<0.00001

Sf9L04641

90-kDa heat shock protein HSP83

AVII stress. hsp

0

0

2

5

2.19

33

<0.0001

Sf1H03026-5-1

heat shock cognate 70 protein

AVII stress. hsp

1

0

0

0

1.58

62

<0.00001

Sf1H00903-5-1

prefoldin subunit 2

AVIII processing

2

0

1

0

1.88

91

<0.00001

Sf1H00522-5-1

Galectin; iso-1

BIII lectin

3

0

0

0

5.66

161

<0.00001

Sf1H01648-5-1

Galectin; iso-2

BIII lectin

2

0

0

0

5.50

110

<0.00001

Sf1H01841-5-1

lectin (CrV)

BIII lectin

11

0

0

0

1.66

44

<0.00001

Sf1H03263-5-1

MBF2

C regulator

10

3

0

0

2.18

NS

<0.00001

Sf1H00908-5-1

PPO-1 (X 4 spots)

DI PPO

75

0

0

0

[1.9-4.89]

[27–144]

<0.00001

Sf1H00508-5-1

PPO-2 (X 3 spots)

DI PPO

60

0

0

0

[4.02–5.91]

[67–104]

<0.00001

Sf1H01637-5-1

Hypothetical protein A.gambiae

EII

1

0

0

0

2.73

250

<0.00001

Sf9L08591

Hypothetical protein Drosophila

EII

0

0

1

1

2.52

96

<0.00001

Sf1H00837-3-1

No Similarity

EIII

1

0

0

0

2.74

134

<0.00001

Sf1H00871-5-1

No Similarity

EIII

1

0

0

0

2.98

261

<0.00001

Sf1H01434-3-1

No Similarity

EIII

1

0

0

0

3.03

102

<0.00001

Sf1H02673-5-1

No Similarity

EIII

1

0

0

0

1.96

173

<0.00001

Sf1H00201-3-1

NS. similar to Hypothetical protein (5' seq)

EIII

2

0

0

0

2.73

93

<0.00001

Sf1H02439-5-1

Annexin IX-B

AI Ca binding

7

3

0

0

0.62 (-1.61)

66

<0.00001

Sf9L07393

Calmodulin

AI Ca binding

5

2

11

6

0.59 (-1.69)

31

<0.0001

Sf9L07135

Cytochrome C oxydase I

AI electron transport

162

117

232

146

0.62 (-1.61)

30

<0.0001

Sf1H02665-5-1

splicing factor 3a

AII splicing

1

0

0

0

0.48 (-2.08)

196

<0.00001

Sf9L06869

cofilin

AIV actin

16

1

10

2

0.54 (-1.85)

62

<0.00001

Sf1H03446-5-1

profiling

AIV actin

30

2

16

0

0.54 (-1.85)

142

<0.00001

Sf9L03392

Thymosin beta

AIV actin

7

1

3

13

0.45 (-2.22)

33

<0.0001

Sf9L06055

alpha tubulin

AIV tubulin

5

5

7

7

0.56 (-1.80)

56

<0.00001

Sf9L01568

beta-1 tubulin

AIV tubulin

1

2

2

1

0.56 (-1.80)

NS

<0.00001

Sf1H02495-5-1

synaptotagmin-like; granuphilin

AIX exocytosis

2

0

0

0

0.65 (-1.54)

27

<0.0001

Sf9L01210

Ribosomal protein S24

AV ribosomal

1

0

4

21

0.58 (-1.71)

84

<0.00001

Sf1H02303-5-1

kynurenine aminotransferase

AVI biosynthesis

2

0

0

0

0.60 (-1.66)

73

<0.00001

Sf1H01920-5-1

beta glucosidase; iso-1

AVI carbohydrate metabolism

1

1

0

0

0.58 (-1.72)

123

<0.00001

Sf1H01659-5-1

putative carboxylesterase

AVI catalytic

5

1

0

0

0.56 (-1.78)

87

<0.00001

Sf9L07277

enolase

AVI glycolysis

4

1

1

2

0.55 (-1.82)

NS

<0.00001

Sf9L06272

glyceraldehyde-3-phosphate dehydrogenase

AVI glycolysis

1

3

8

3

0.63 (-1.58)

20.82

<0.0001

Sf9L02512

fructose 1 6-bisphosphate aldolase

AVI glycolysis

0

0

0

1

0.64 (-1.56)

64.61

<0.00001

Sf9L02319

Deoxyribose-phosphate aldolase-like

AVI nucleotide metabolism

0

0

0

2

0.64 (-1.56)

72

<0.00001

Sf1H00106-5-1

Scavenger receptor;iso-1 (X 2 spots)

BI receptor

7

0

0

0

[0.32–0.59] [-1.69/-3.11]

[78–159]

<0.00001

Sf9L03085

Cyclophilin 5/peptidyl-propyl isomerase 5

BII PPIase

5

4

4

3

0.61 (-1.64)

34

<0.00001

Sf9L02900

similar to RAS suppressor protein 1

BII Ras signal transduction

0

0

0

2

0.66 (-1.52)

56

<0.00001

Sf1H01096-5-1

hemicentin (X 3 spots)

BIII CAM

11

0

0

0

[0.45–0.48] [-2.10/-2.22]

[117–132]*

<0.00001

Sf9L07414

collagen alpha 1 (IV) (X 2 spots)

BIII ECM

0

0

0

1

[0.27–0.41] [-2.44/-3.70]

[63–207]

<0.00001

Sf1H01457-5-1

collagen alpha 2 (IV)

BIII ECM

1

2

0

0

0.45 (-2.22)

203

<0.00001

Sf9L06099

cobatoxin-like protein; iso-1

DI AMP

0

0

0

2

0.50 (-1.98)

43

<0.00001

Sf1H01136-5-1

lysozyme (X 2 spots)

DI AMP

140

86

18

0

0.46 (-2.17)

114

<0.00001

Sf1H00867-5-1

hemocytin precursor

DI lectin

3

0

0

0

0.52 (-1.93)

111

<0.00001

Sf1H01505-5-1

immulectin-2

DI LPS binding

5

0

0

0

0.52 (-1.93)

99

<0.00001

Sf9L00974

calreticulin

DI multi-function

5

1

0

1

0.51 (-1.96)

38

<0.00001

Sf1H00566-5-1

PPO activating Enzyme

DI PPAE

4

0

0

0

0.45 (-2.22)

196

<0.00001

Sf1H02709-3-1

Hypothetical protein A. gambiae (X 5 spots)

EII

38

0

0

0

[0.44–0.55] [-1.82/-2.27]

[88–140]*

<0.00001

Sf1H02044-5-1

Hypothetical protein Drosophila

EII

1

0

0

0

0.61 (-1.64)

137

<0.00001

Sf9L08287

Hypothetical protein A. gambiae

EII

0

0

0

1

0.50 (-1.99)

47

<0.00001

Sf9L06591

Hypothetical protein Drosophila

EII

0

0

0

1

0.57 (-1.75)

36

<0.00001

Sf9L06826

Hypothetical protein Drosophila

EII

0

0

0

1

0.66 (-1.52)

26

<0.0001

Sf9L00177

similar to calponin; iso-1

EII

4

0

0

7

0.59 (-1.69)

31

<0.0001

Sf1H00681-5-1

similar to LPS-induced TNF-alpha factor (X 2 spots)

EII

15

2

0

1

[0.47–0.52] [-1.92/-2.13]

[123–159]

<0.00001

Sf1H03038-5-1

similar to pancreatic triacylglyceride lipase (X 2 spots)

EII

6

0

0

0

[0.45–0.46] [-2.17/-2.22]

[81–150]

<0.00001

Sf1H00115-5-1

similar to protease inhibitor (AC protein); iso-1

EII

3

0

0

0

0.50 (-2.01)

131

<0.00001

Sf9L04444

similar to Swiprosin

EII

3

0

0

1

0.63 (-1.58)

25

<0.0001

Sf1H00035-3-1

No Similarity

EIII

19

0

0

0

0.31 (-3.19)

88

<0.00001

Sf1H00499-5-1

No Similarity

EIII

11

0

0

0

0.60 (-1.66)

14

<0.001

Sf1H00686-5-1

No Similarity

EIII

10

0

0

0

0.43 (-2.33)

105

<0.00001

Sf1H03014-5-1

No Similarity

EIII

1

2

0

0

0.64 (-1.56)

178

<0.00001

Sf1F00357-5-1

No Similarity

EIII

1

0

0

0

0.59 (-1.68)

21

<0.0001

Sf1H00037-3-1

No Similarity

EIII

1

0

0

0

0.56 (-1.78)

212

<0.00001

Sf1H00879-5-1

No Similarity

EIII

1

0

0

0

0.53 (-1.89)

147

<0.00001

Sf1H01542-3-1

No Similarity

EIII

1

0

0

0

0.43 (-2.33)

348

<0.00001

Sf1H01712-5-1

No Similarity

EIII

1

0

0

0

0.43 (-2.33)

106

<0.00001

Sf1H02105-5-1

No Similarity

EIII

1

0

0

0

0.41 (-2.44)

163

<0.00001

Sf9L00090

No Similarity

EIII

1

0

0

4

0.62 (-1.61)

35

<0.00001

Sf9L01158

No Similarity

EIII

0

0

1

2

0.45 (-2.22)

73

<0.00001

Sf9L06863

No Similarity

EIII

0

0

0

1

0.53 (-1.89)

43

<0.00001

Sf9L08779

No Similarity

EIII

0

0

0

1

0.52 (-1.91)

NS

<0.00001

Fat Body_HdIV : 7 significant genes, down-regulated

q-value 0.077

  

Sf9L07198

cytoplasmic actin A3

AIV actin

27

6

47

2

0.59 (-1.69)

27

0.00001

Sf9L06055

alpha tubulin

AIV tubulin

5

5

7

7

0.45 (-2.22)

135

<0.00001

Sf9L01568

beta-1 tubulin

AIV tubulin

1

2

2

1

0.65 (-1.54)

80

<0.00001

Sf9L07277

enolase

AVI glycolysis

4

1

1

2

0.54 (-1.85)

39

<0.00001

Sf9L02319

Deoxyribose-phosphate aldolase-like

AVI nucleotide metabolism

0

0

0

2

0.51 (-1.96)

82

<0.00001

Sf9L00974

calreticulin

DI multi-function

5

1

0

1

0.38 (-2.63)

85

<0.00001

Sf1F00299-5-1

Hemolymph glycoprotein precursor

DIII unknown

1

17

1

0

0.51 (-1.96)

33

<0.00001

Fat Body_JcDNV : 8 significant genes, up-regulated

q-value 0.056

  

Sf9L00253

mRNA export factor binding

AII transcription coactivator

0

0

0

2

1.87

35

<0.000001

Sf9L07586

Ribosomal protein S27A

AV ribosomal

5

3

8

11

3.82

136

<0.000001

Sf1H03263-5-1

MBF2

C regulator

10

3

0

0

1.54

22

0.00006

Sf9L06099

cobatoxin-like protein; iso-1

DI AMP

0

0

0

2

2.12

70

<0.000001

Sf1H00171-5-1

lysozyme (X 2 spots)

DI AMP

140

86

18

0

[1.59–1.66]

[10–20]

0.0001

Sf9L06812

immunolectin-A precursor

DI LPS binding

0

1

0

2

5.88

137

<0.000001

Sf9L02793

No Similarity

EIII

0

0

0

1

5.46

212

<0.000001

Sf9L03186

No Similarity

EIII

2

1

7

21

5.42

149

<0.000001

  1. List of Spodoptera frugiperda genes for which transcript levels are significantly modified in the hemocytes and in the fat body 24 hours after injection of HdIV, and in the fat body 24 hours after injection of JcDNV, as detected by a modified t-test from the SAM package and an ANOVA based microarray analysis, GeneANOVA. Only the genes with a fold change superior or equal to 1.5 with both a FDR median and 90th percentiles of 0% were kept. For each assay, the SAM q-value (the lowest FDR at which the gene is called significant) is given. For each gene, the F value for "gene-condition" and the p-value calculated by GeneANOVA are given. Single genes for which more than one cDNA was spotted on the glass slide are indicated (x spots), in those cases, only the spot with the best score was kept in the list. Genes are organized according to their functional annotation (see Additional file 2 for legends). Spodobase ID: identity of the arrayed cDNA in the database Spodobase ([61]); Gene Name: annotation of the sequence after BlastX search against the GenBank nr database; Functional class: classes and subclasses to which the sequences belong to, based on the classification described in Shida et al. [114] for the ascidian Ciona intestinalis (details in Additional file 2); Number of clones: distribution of the cDNA clones corresponding to the given gene with available sequences in the different S. frugiperda cDNA libraries (H:hemocytes; F: fat body; M:midgut; L:Sf9 cell line). For genes represented by at least two cDNAs, we reported the interval [min, max] for the SAM fold change and for the F gene-condition from GeneANOVA analysis. Asterisk (*) indicate that one of the spots was non significant for GeneANOVA (clusters Sf1H01096-5-1 and Sf1H02709-3-1). The list of additional clones corresponding to each gene is provided in Additional file 1B.
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BMC Genomics

ISSN: 1471-2164

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