Table 2

Summary of gene-family phylogenies

Gene family

D. pulex genes

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


**No genome-scale tree.

***Only a single member with this domain architecture found.

Rivera et al. BMC Evolutionary Biology 2010 10:123   doi:10.1186/1471-2148-10-123

Open Data