Skip to main content

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.