Differential expression of duplicated opsin genes in two eye types of ostracod crustaceans

Journal of Molecular Evolution

Volumn 59, Issue 2, 2004, Pages 239-249

  Oakley, Todd H ^a,c   Huber, Daniel R ^a,b  

^a DUKE UNIVERSITY   (United States)

^b UNIVERSITY OF SOUTH FLORIDA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Expression; Gene duplication; Myodocopida; Opsin; Ostracoda; Visual pigment

Indexed keywords

COMPLEMENTARY DNA; OPSIN; VISUAL PIGMENT;

ARTICLE; COMPOUND EYE; CONTROLLED STUDY; CRUSTACEA; DNA SEQUENCE; GENE CONVERSION; GENE DUPLICATION; GENE EXPRESSION; GENE LOCUS; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOTORECEPTOR; RNA SPLICING;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BELIZE; CRUSTACEA; DNA PRIMERS; EYE; GENE EXPRESSION; GENES, DUPLICATE; JAPAN; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; OPSIN; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

CRUSTACEA; INVERTEBRATA; MYODOCOPIDA; OSTRACODA; SKOGSBERGIA; SKOGSBERGIA LERNERI; VARGULA; VARGULA HILGENDORFII;

EID: 4344633861     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-2618-7     Document Type: Article

References (64)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
2. Andersson A (1979) Ultrastructure of ostracod sensory organs. University of Lund, Lund
3. Arikawa K, Kawamata K, Suzuki T, Eguchi E (1987) Daily changes of structure, function and rhodopsin content in the compound eye of the crab Hemigrapsus sanguineus. J Comp Physiol A Sens Neur Behav Physiol (Berlin) 161:161-174
4. Arikawa K, Morikawa Y, Suzuki T, Eguchi E (1988) Intrinsic control of rhabdom size and rhodopsin content in the crab compound eye by a circadian biological clock. Experientia 44:219-220
5. Blackshaw S, Snyder SH (1999) Encephalopsin: A novel mammalian extraretinal opsin discretely localized in the brain. J Neurosci 19:3681-3690
6. Bracho MA, Moya A, Barrio E (1998) Contribution of Taq polymerase-induced errors to the estimation of RNA virus diversity. J Gen Virol 79:2921-2928
7. Briscoe AD (2000) Six opsins from the butterfly Papilla glaucus: molecular phylogenetic evidence for paralogous origins of red-sensitive visual pigments in insects. J Mol Evol 51:110-121
8. Carleton KL, Kocher TD (2001) Cone opsin genes of African cichlid fishes: Tuning spectral sensitivity by differential gene expression. Mol Biol Evol 18:1540-1550
9. Carulli JP, Chen DM, Stark WS, Hartl DL (1994) Phylogeny and physiology of Drosophila opsins. J Mol Evol 38:250-262
10. Chang BS, Crandall KA, Carulli JP, Hartl DL (1995) Opsin phylogeny and evolution: A model for blue shifts in wavelength regulation. Mol Phylogenet Evol 4:31-43
11. Ch'-ng JLC, Badr I (1994) Transcriptional and posttranscriptional mechanisms modulate creatine kinase expression during differentiation of osteoblastic cells. J Biol Chem 269:2336-2341
12. Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate- phenol-chloroform extraction. Anal Biochem 162:156-159
13. Cohen A (1983) Rearing and postembryonic development of the myodocopid ostracode Skogsbergia lerneri from coral reefs of Belize and the Bahamas. J Crust Biol 3:235-256
14. Cohen AC, Morin JG (1990) Morphological relationships of bioluminescent Caribbean species of Vargula. In: Whatley R, Maybury C (eds) Ostracoda and global events. Chapman Hall, New York, pp 381-400
15. Cohen AC, Martin JW, Kornicker LS (1998) Homology of Holocene ostracode biramous appendages with those of other crustaceans: The protopod, epipod, exopod and endopod. Lethaia 31:251-265
16. Crandall KA, Cronin TW (1997) The molecular evolution of visual pigments of freshwater crayfishes (Decapoda: Cambaridae). J Mol Evol 45:524-534
17. Elofsson R (1992) To the question of eyes in primitive crustaceans. Acta Zool 73:369-372
18. Franke RR, Konig B, Sakmar TP, Khorana HG, Hofmann KP (1990) Rhodopsin mutants that bind but fail to activate transducin. Science 250:123-125
19. Franke RR, Sakmar TP, Graham RM, Khorana HG (1992) Structure and function in rhodopsin. Studies of the interaction between the rhodopsin cytoplasmic domain and transducin. J Biol Chem 267:14767-14774
20. Frohman MA, Dush MK, Martin GR (1988) Rapid production of full-length cDNAs from rare transcripts: Amplification using a single gene-specific oligonucleotide primer. Proc Natl Acad Sci USA 85:8998-9002
21. Fryer G (1996) Reflections on arthropod evolution. Biol J Linn Soc 58:1-55
22. Goldman N (1993) Statistical tests of models of DNA substitution. J Mol Evol 36:182-198
23. Gonzales MJ, Dugan JM, Shafer RW (2002) Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN). Bioinformatics 18:886-887
24. Grassly NC, Holmes EC (1997) A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol Biol Evol 14:239-247
25. Green P, Hartenstein A, Hartenstein V (1993) The embryonic development of the Drosophila visual system. Cell Tissue Res 273:583-598
26. Haeussler J, Striebel AM, Assum G, Vogel W, Furneaux H. Krone W (2000) Tumor antigen HuR binds specifically to one of five protein-binding segments in the 3′-untranslated region of the neurofibromin messenger RNA. Biochem Biophys Res Commun 267:726-732
27. Hariyama T, Ozaki K, Tokunaga F, Tsukahara Y (1993) Primary structure of crayfish visual pigment deduced from cDNA. FEBS Lett 315:287-292
28. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160-174
29. Higgins DG, Bleasby AJ, Fuchs R (1992) CLUSTAL V: Improved software for multiple sequence alignment. Comput Appl Biosci 8:189-191
30. Huvard AL (1993) Analysis of visual pigment absorbance and luminescence emission spectra in marine ostracodes. Comp Biochem Physiol A Comp Physiol 104:333-338
31. Ikeya N, Kato M (2000) The life history and culturing of Xestoleberis hanaii (Crustacea, Ostracoda). Hydrobiologia 149-159
32. Kawamura S, Yokoyama S (1996) Molecular characterization of the pigeon P-opsin gene. Gene 182:213-214
33. Kawamura S, Yokoyama S (1997) Expression of visual and non-visual opsins in American chameleon. Vision Res 37:1867-1871
34. Kawamura S, Yokoyama S (1998) Functional characterization of visual and nonvisual pigments of American chameleon (Anolis carolinensis). Vis Res 38:37-44
35. Kitamoto J, Sakamoto K, Ozaki K, Mishina Y, Arikawa K (1998) Two visual pigments in a single photoreceptor cell: Identification and histological localization of three mRNAs encoding visual pigment opsins in the retina of the butterfly Papilio xuthus. J Exp Biol 201:1255-1261
36. Kohn DT, Tsai KC, Cansino VV, Neve RL, Perrone-Bizzozero NI (1996) Role of highly conserved pyrimidine-rich sequences in the 3′ untranslated region of the GAP-43 mRNA in mRNA stability and RNA-protein interactions. Mol Brain Res 36:240-250
37. Kojima D, Fukada Y (1999) Non-visual photoreception by a variety of vertebrate opsins. Novartis Found Symp 224:265-279
38. Kornicker LS (1989) Bathyal and abyssal myodocopid Ostracoda of the Bay of Biscay and vicinity (France, Spain). Smithsonian Contrib Zool 467:1-134
39. Kornicker LS (1992) Myodocopid Ostracoda of the Benthedi Expedition, 1977, to the NE Mozambique channel, Indian Ocean. Smithson Contrib Zool 531:1-243
40. Lee KB, Brooks DJ, Thomas JO (1998) Selection of a cDNA clone for chicken high-mobility-group 1 (HMG1) protein through its unusually conserved 3′-untranslated region, and improved expression of recombinant HMG1 in Escherichia coli. Gene 125:97-105
41. Malpel S, Klarsfeld A, Rouyer F (2002) Larval optic nerve and adult extra-retinal photoreceptors sequentially associate with clock neurons during Drosophila brain development. Development 129:1443-1453
42. Melzer RR, Diersch R, Nicastro D, Smola U (1997) Compound eye evolution: Highly conserved retinula and cone cell patterns indicate a common origin of the insect and crustacean ommatidium. Naturwissenschaften 84:542-544
43. Moguilevsky A (1985) Cytogenetic studies on marine ostracods: The karyotype of Gigantocypris muelleri Skogsberg, 1920 (Ostracoda, Myodocopida). J Micropalaeontol 4:159-164
44. Moguilevsky A (1990) Cytogenetic studies on marine myodocopid Ostracoda: The karyotypes of some species of Vargula Skogsberg, 1920. In: Whatley R, Maybury C (eds) Ostracoda and global events. Chapman and Hall, London
45. Morin JG, Cohen AC (1991) Bioluminescent displays, courtship, and reproduction in ostracods. In: Bauer RT, Martin JW (eds) Crustacean sexual biology. Columbia University Press, New York, pp 1-16
46. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418-426
47. Oakley TH (2003) On homology of arthropod compound eyes. Integr Comp Biol 43:522-530
48. Oakley TH (2004) Myodocopa (Crustacea:Ostracoda) as models for evolutionary studies of light and vision: Multiple origins of bioluminescence and extreme sexual dimorphism. Hydrobiologia (in press)
49. Oakley TH, Cunningham CW (2002) Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye. Proc Natl Acad Sci USA 99:1426-1430
50. Parker AR (1995) Discovery of functional iridescence and its coevolution with eyes in the phylogeny of Ostracoda (Crustacea). Proc R Soc Lond B 262:349-355
51. Pichaud F, Briscoe A, Desplan C (1999) Evolution of color vision. Curr Opin Neurobiol (London) 9:622-627
52. Pollock JA, Benzer S (1988) Transcript localization of four opsin genes in the three visual organs of Drosophila; RH2 is ocellus specific. Nature 333:779-782
53. Posada D, Crandall KW (1998) Modeltest: Testing the model of DNA substitution. Bioinformatics 14:817-818
54. Sakamoto K, Hisatomi O, Tokunaga F, Eguchi E (1996) Two opsins from the compound eye of the crab Hemigrapsus sanguineus. J Exp Biol 199:441-450
55. Smith WC, Price DA, Greenberg RM, Battelle BA (1993) Opsins from the lateral eyes and ocelli of the horseshoe crab Limulus polyphemus. Proc Natl Acad Sci USA 90:6150-6154
56. Swofford DL (1999) PAUP*: Phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland, MA
57. Vannier J, Abe K (1992) Recent and early palaeozoic myodocope ostracodes: Functional morphology, phylogeny, distribution and lifestyles. Palaeontology 35:485-517
58. Vannier J, Abe K (1995) Size, body plan and respiration in the Ostracoda. Palaeontology 38:843-873
59. Wang JK, McDowell JH, Hargrave PA (1980) Site of attachment of 11-cis-retinal in bovine rhodopsin. Biochemistry 19:5111-5117
60. Wilden U, Kuhn H (1982) Light-dependent phosphorylation of rhodopsin: Number of phosphorylation sites. Biochemistry 21:3014-3022
61. Yasuyama K, Meinertzhagen IA (1999) Extraretinal photoreceptors at the compound eye's posterior margin in Drosophila melanogaster. J Comp Neurol 412:193-202
62. Yokoyama S (1996) Molecular evolution of retinal and nonretinal opsins. Genes Cells 1:787-794
63. Zhao Z, Hewett-Emmett D, Li WH (1998) Frequent gene conversion between human red and green opsin genes. J Mol Evol 46:494-496
64. Zhou YH, Li WH (1996) Gene conversion and natural selection in the evolution of X-linked color vision genes in higher primates. Mol Biol Evol 13:780-783