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Table 1 Summary of visual opsin sequences analyzed in this study

From: The vertebrate ancestral repertoire of visual opsins, transducin alpha subunits and oxytocin/vasopressin receptors was established by duplication of their shared genomic region in the two rounds of early vertebrate genome duplications

 

Species (genome assembly version)

Sequence names in phylogenetic analyses a

Type b

Chromosome, linkage group, or genomic scaffold

Loc. (Mb)

Sarcopterygians

Mammals

Human

Hsa X OPN1LW

LWS

X

153.41

 

(GRCh37)

Hsa X OPN1MW2

LWS

X

153.49

  

Hsa X OPN1MW

LWS

X

153.45

  

Hsa 3 RHO

RH1

3

129.25

  

Hsa 7 OPN1SW

SWS1

7

128.41

 

Mouse

Mmu X Opn1mw

LWS

X

71.37

 

(NCBIM37)

Mmu 6 Rho

RH1

6

115.88

  

Mmu 6 Opn1sw

SWS1

6

29.33

 

Grey short-tailed opossum

Mdo X LWS

LWS

X

14.66

 

(MonDom5)

Mdo 6 RH1

RH1

6

246.61

  

Mdo 8 SWS1

SWS1

8

188.61

Birds

Chicken

Gga LWS

LWS

c

 
 

(WASHUC2)

Gga 12 RH1

RH1

12

20.16

  

Gga 26 RH2

RH2

26

4.38

  

Gga SWS1

SWS1

c

 
  

Gga SWS2

SWS2

c

 

Non-avian reptiles

Carolina anole lizard

Aca 2 LWS

LWS

2

88.66

 

(AnoCar2.0)

Aca RH1

RH1

GL343273.1

0.64

  

Aca 4 RH2

RH2

4

122.81

  

Aca SWS1

SWS1

GL343828.1

0.11

  

Aca 2 SWS2

SWS2

2

88.63

Amphibians

Western clawed frog

Xtr opn1lw

LWS

GL172911.1

0.21

 

(JGI_4.2)

Xtr rho

RH1

GL172832.1

1.64

  

Xtr opn1sw

SWS1

GL173116.1

0.61

  

Xtr SWS2

SWS2

GL172911.1

0.22

Coelacanths

Coelacanth

Lch RH1

RH1

JH126975.1

0.80

 

(LatCha1)

Lch RH2

RH2

JH126819.1

1.63

  

Lch SWS2

SWS2

JH127263.1

0.54

Actinopterygians

Holostean fishes

Spotted gar

Loc LG1 LWS

LWS

LG1

2.61

 

(LepOcu1)

Loc LG5 RH1-1d

RH1

LG5

40.45

  

Loc LG5 RH1-2

RH1

LG5

23.74

  

Loc LG3 RH2

RH2

LG3

36.55

  

Loc LG8 SWS1-1e

SWS1

LG8

10.39

  

Loc LG8 SWS1-2d

SWS1

LG8

10.40

  

Loc LG1 SWS2

SWS2

LG1

2.62

Teleost fishes

Zebrafish

Dre 11 opn1lw1

LWS

11

26.41

 

(Zv9)

Dre 11 opn1lw2

LWS

11

26.41

  

Dre exorh

RH1

Zv9_NA986

0.130 Kb

  

Dre 8 rho

RH1

8

55.71

  

Dre 11 rhol

RH1

11

19.52

  

Dre 6 opn1mw1

RH2

6

41.11

  

Dre 6 opn1mw2

RH2

6

41.12

  

Dre 6 opn1mw3

RH2

6

41.12

  

Dre 6 opn1mw4

RH2

6

41.13

  

Dre 4 opn1sw1

SWS1

4

12.64

  

Dre 11 opn1sw2

SWS2

11

26.41

 

Three-spined stickleback

Gac XVII LWS

LWS

XVII

10.63

 

(BROADS1)

Gac XII RH1-1d,e

RH1

XII

1.18

  

Gac XII RH1-2

RH1

XII

0.81

  

Gac RH2-1

RH2

scaffold 27

4.15

  

Gac RH2-2

RH2

scaffold 27

4.16

  

Gac SWS1

SWS1

scaffold 90

0.46

  

Gac XVII SWS2

SWS2

XVII

10.62

 

Medaka

Ola 5 LWS-1

LWS

5

27.02

 

(MEDAKA1)

Ola 5 LWS-2

LWS

5

27.01

  

Ola 7 RH1-1

RH1

7

17.43

  

Ola 7 RH1-2

RH1

7

17.10

  

Ola RH2-1

RH2

ultracontig 62

1.61

  

Ola RH2-2

RH2

ultracontig 62

1.62

  

Ola RH2-3

RH2

ultracontig 62

1.62

  

Ola SWS1

SWS1

scaffold 1021

0.04

  

Ola 5 SWS2-1

SWS2

5

27.01

  

Ola 5 SWS2-2

SWS2

5

27.00

 

Spotted green pufferfish

Tni 11 LWS

LWS

11

10.12

 

(TETRAODON8)

Tni 9 RH1-1

RH1

9

6.68

  

Tni 9 RH1-2

RH1

9

6.48

  

Tni 11 RH2

RH2

11

5.97

  

Tni 11 SWS2

SWS2

11

10.12

Cyclostomes

Lampreys

Pouched lamprey

Gau Lws

LWS

  
  

Gau RhA

RH1

  
  

Gau RhB

RH2

  
  

Gau Sws1

SWS1

  
  

Gau Sws2

SWS2

  
  1. aFor the sequence names, species abbreviations are applied as described in Methods, followed by the number of the chromosome or linkage group where the gene is located (if known) and the gene/subtype name. Where available, gene names follow approved symbols by the HUGO Gene Nomenclature Committee and interacting committees, accessed via http://www.genenames.org, and the Zebrafish Model Organism Database (ZFIN), accessed via http://www.zfin.org. Geotria australis gene names follow [36].
  2. bSubtype designations follow the tree topology presented in Figure 1.
  3. cIn the chicken genome assembly available in the Ensembl genome browser (WASHUC2) only two of the five ancestral visual opsin types were identified. However the three missing genes have previously been cloned and are available in the NCBI GenBank database (see Additional file 1).
  4. dSequences manually predicted de novo (see Methods).
  5. eSequence predictions are fragments and do not span the whole length of the alignment.
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BMC Ecology and Evolution

ISSN: 2730-7182

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