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Table 4 Selected developmental process genes identified in the O. fasciatu s transcriptome.

From: The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus

Process

# Hits

Hit ID (I/C/S)

Length (range)

Normalized

Non-Normalized

GERM PLASM

     

Argonaute 3

2 (1†)

I

2042-2231

Y

Y

germ cell-less

2 (1†)

I

630-1817

Y

Y

maelstrom

1

I

994

Y

Y

nanos

1

I

1961

Y

Y

piwi/aubergine

1

I

2888

Y

Y

pumilio

2

I

424-2574

Y

Y

staufen

3

I

599-2100

Y

Y

Tudor

2

I

2719-3299

Y

Y

vasa

1

C

330

Y

Y

ANTERIOR-POSTERIOR DETERMINATION

GAP

     

hunchback

1

I

1429

Y

Y

Kruppel

1

S

250

N

Y

ocelliless (orthodenticle)

1

S

207

Y

N

TERMINAL GROUP

     

huckebein

1

I

589

Y

Y

torso-like

2 (1†)

I,C

430-1868

Y

Y

PAIR RULE

     

fushi tarazu

1

I

788

Y

Y

hairy (Enhancer of split/HES-1)

1

I

2530

Y

Y

odd skipped

1

C

346

N

Y

SEGMENT POLARITY

     

armadillo

5

I,S

348-3001

Y

Y

cubitus interruptus

3

I,S

225-906

Y

Y

engrailed

1

S

227

Y*

N

fused

2

I

516-1582

Y

Y

pangolin

2

I,C

492-544

N

Y

patched

2

C, S

225-418

N

Y

Wnt family (wingless, Wnts)

6

C,S

207-508

Y

Y

DORSO-VENTRAL AXIS

     

cactus

7

I, C

629-1748

Y

Y

decapentaplegic (BMP2/4)

1

C

547

Y

Y

gastrulation-defective

1

I

1773

Y

Y

nudel

4

I,S

322-1458

Y

Y

pipe

1

C

266

N

Y

short gastrulation

2

C

254-615

Y

Y

snake

1

I

1789

Y

Y

spätzle

2

I

993-3170

Y

Y

Toll

11

I, C, S

215-4323

Y

Y

MOLTING/METAMORPHOSIS

     

cuticular proteins (including CP 49Ae and adult cuticle protein)

4

I,C

404-566

Y

Y

disembodied (ecdysteroidogenic P450)

1

I

1835

Y

Y

Ecdysone receptor

2

I,C

231-1393

Y

Y

E75

3

I,S

257-649

Y

Y

Ecdysone-induced protein 63E

1

I

1479

Y

Y

ecdysoneless

1

I

4158

Y

Y

ftz transcription factor 1

1

I

807

Y

Y

hormone receptor 4

2

I

1003-2114

Y

Y

juvenile hormone acid methyltransferase

5

I

548-2871

Y

Y

juvenile hormone binding protein

1

I

1099

Y

Y

juvenile hormone epoxide hydrolase

5

I,S

255-2859

Y

Y

juvenile hormone esterase

4

I

850-2382

Y

Y

juvenile hormone esterase binding protein

1

I

1057

Y

Y

Juvenile hormone-inducible protein

7

I

456-2757

Y

Y

Methoprene-tolerant

1

I

3415

Y

Y

Nuclear hormone receptor E78

1

I

3150

Y

Y

Nuclear hormone receptor HR3

2

I

529-737

Y

Y

phantom (cytochrome P450 306a1)

2

C

344-575

N

Y

shade (cytochrome 450 314A1)

1

I

2125

Y

Y

shadow (cytochrome 450 315A1)

1

I

1650

Y

Y

takeout

3

I

591-1011

Y

Y

ultraspiracle nuclear receptor

1

C

245

Y*

N

without children

2

I

1155-1357

Y

Y

  1. Hit ID indicates if gene hits were found among isotigs (I), CAP3-assembled contigs (C), or unassembled singletons (S). Sequence length (range) indicates the shortest and longest S, C or I hit sequences for each gene. These results were generated by BLASTing the raw reads from the N and NN samples against the full assembly. When multiple sequences were obtained via name search, they were tested to see whether they could be made to form a contig with Sequencher or CLC Combined Workbench (see Methods). Asterisk indicates hits only present in normalized GS-FLX reads. X(Y†) indicates that the X sequences with hits could be assembled into Y contigs. Boldface indicates genes also present in Table 3.
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BMC Genomics

ISSN: 1471-2164

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