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Table 2 Summary of gene-family phylogenies

From: Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach

Gene family

D. pulexgenes

Protein model name(s)

Scaffold #

Location

previous trees

expansion in pancrustaceans?

visual system specification gene families

Decapentaplegic (Dpp)

1

Dappu-347232

2:2889112-2890686

[93, 94]

No

Engrailed (En)

2

Dappu-290630

106:41493-47422

--

Yes

  

Dappu-290638

106:25280-34404

  

Hedgehog (Hh)

2

Dappu-347555

207:81902-105568

[95]

No

Wnt1

1

Dappu-44743

8:1160125-1175065

[96, 97]

No

Zerknullt (Zen)

0

  

[98]

Yes, fly

retinal determination network gene families

Dachshund (Dac)

1

Dappu- 310049

1:4072756-4116888

[99]

Yes, insects

Eyes-absent (Eya)

1

Dappu- 204955

1:62314-73955

[100]

No

Eyegone (Eyg/Toe)

1

Dappu- 253988

74:25897-37400

--

Yes

Pax-6

2

Dappu- 249978

51:368439-379409

[101, 102]

Yes

  

Dappu-249991

51:427984-441429

  

Six 1/2

1

Dappu-65962

275:49584-50586

[102]

No

photoreceptor differentiation gene families

Epidermal Growth Factor

1

Dappu-324147

60:112587-119018

[103]

Yes

Receptor (EGFR)

 

Dappu- 321139

39:412588-415432

  

Kruppel (Kr)

1

Dappu-290527

2:2312128-2315494

--

No

Glass (Gl)

1

Dappu-234903

4:2598047-2600296

[39]

No

Munster (Mu)**

0

  

--

?

Notch

1

Dappu-328760

108:325324-337022

[90, 104]

No

Spam***

0

  

---

--

Spitz (Spi)

1

Dappu-271304

1714:5914-7575

[103]

Yes

CVC Homeobox (Vsx)

1

Dappu-323346

53:603419-625383

[105]

Yes, silkworm+fly

phototransduction gene families

Arrestin (Arr)

2

Dappu-216585

86:316599-318172

[106]

Yes, beetle

  

Dappu-207575

5:2476074-2477692

  

Gq-alpha

2

Dappu-211929

25:514047-515490

[107]

No

  

Dappu-188187

25:531825-536252

  

R-opsin

30

see Colbourne J et al: Genome Biology of the Model Crustacean Daphnia pulex, submitted

[29]

Yes

Phospholipase-C (PLC)

2

Dappu- 226357

53:369165-377304

[108]

Yes, fly, bee

  

Dappu- 304714

3:1803843-1812297

  

Transient Receptor

2

Dappu-54362

41:27419-33467

--

Yes

Potential Channel (TRPC)

 

Dappu- 309057

9:569391-574613

  
  

Dappu- 309057

56:282882-311121

  
  1. **No genome-scale tree.
  2. ***Only a single member with this domain architecture found.