User menu

De novo transcriptome analyses provide insights into opsin-based photoreception in the lanternshark Etmopterus spinax

  • Open access
  • PDF
  • 4.38 M
  1. McEachran John, Aschliman Neil, Phylogeny of Batoidea, Marine Biology (2004) ISBN:9780849315145 p.79-113, 10.1201/9780203491317.ch3
  2. L.J. Compagno, 33 (1990)
  3. L. Compagno, 2005
  4. R.E. Hueter, 325 (2004)
  5. Meredith T. L., Kajiura S. M., Olfactory morphology and physiology of elasmobranchs, 10.1242/jeb.045849
  6. H. Bleckmann, The biology of elasmobranch fish, 300 (1999)
  7. J.L. Cohen, 465 (1990)
  8. G.L. Walls (1942)
  9. A. Rochon-Duvigneaud (1943)
  10. S.H. Gruber, 11 (1978)
  11. HART Nathan S., COLLIN Shaun P., Sharks senses and shark repellents, 10.1111/1749-4877.12095
  12. N.S. Hart, Communication in Fishes, 337 (2006)
  13. Hart N. S., Multiple cone visual pigments and the potential for trichromatic colour vision in two species of elasmobranch, 10.1242/jeb.01314
  14. Theiss Susan M., Lisney Thomas J., Collin Shaun P., Hart Nathan S., Colour vision and visual ecology of the blue-spotted maskray, Dasyatis kuhlii Müller & Henle, 1814, 10.1007/s00359-006-0171-0
  15. Ripps Harris, Dowling John E., Structural features and adaptive properties of photoreceptors in the skate retina, 10.1002/jez.1402560508
  16. Denton E. J., Shaw T. I., The Visual Pigments of Some Deep-Sea Elasmobranchs, 10.1017/s0025315400005245
  17. Denton E. J., Nicol J. A. C., The Chorioidal Tapeta of some Cartilaginous Fishes (Chondrichthyes), 10.1017/s0025315400024760
  18. STEVEN D. M., THE DERMAL LIGHT SENSE, 10.1111/j.1469-185x.1963.tb00783.x
  19. N. Millott (1978)
  20. N. Millott (1968)
  21. Kojima Daisuke, Mano Hiroaki, Fukada Yoshitaka, Vertebrate Ancient-LongOpsin: A Green-Sensitive Photoreceptive Molecule Present in Zebrafish Deep Brain and Retinal Horizontal Cells, 10.1523/jneurosci.20-08-02845.2000
  22. Mano Hiroaki, Kojima Daisuke, Fukada Yoshitaka, Exo-rhodopsin: a novel rhodopsin expressed in the zebrafish pineal gland, 10.1016/s0169-328x(99)00242-9
  23. Wolken Jerome J., Photobehavior of marine invertebrates: Extraocular photoreception, 10.1016/0742-8413(88)90180-6
  24. J.J. Wolken (1995)
  25. Vigh-Teichmann I., Vigh B., Manzano e Silva M.J., Aros B., The pineal organ of Raja clavata: Opsin immunoreactivity and ultrastructure, 10.1007/bf00206272
  26. Davies W. L., Carvalho L. S., Tay B.-H., Brenner S., Hunt D. M., Venkatesh B., Into the blue: Gene duplication and loss underlie color vision adaptations in a deep-sea chimaera, the elephant shark Callorhinchus milii, 10.1101/gr.084509.108
  27. Venkatesh Byrappa, Kirkness Ewen F, Loh Yong-Hwee, Halpern Aaron L, Lee Alison P, Johnson Justin, Dandona Nidhi, Viswanathan Lakshmi D, Tay Alice, Venter J. Craig, Strausberg Robert L, Brenner Sydney, Survey Sequencing and Comparative Analysis of the Elephant Shark (Callorhinchus milii) Genome, 10.1371/journal.pbio.0050101
  28. Venkatesh Byrappa, Lee Alison P., Ravi Vydianathan, Maurya Ashish K., Lian Michelle M., Swann Jeremy B., Ohta Yuko, Flajnik Martin F., Sutoh Yoichi, Kasahara Masanori, Hoon Shawn, Gangu Vamshidhar, Roy Scott W., Irimia Manuel, Korzh Vladimir, Kondrychyn Igor, Lim Zhi Wei, Tay Boon-Hui, Tohari Sumanty, Kong Kiat Whye, Ho Shufen, Lorente-Galdos Belen, Quilez Javier, Marques-Bonet Tomas, Raney Brian J., Ingham Philip W., Tay Alice, Hillier LaDeana W., Minx Patrick, Boehm Thomas, Wilson Richard K., Brenner Sydney, Warren Wesley C., Elephant shark genome provides unique insights into gnathostome evolution, 10.1038/nature12826
  29. Y. Hara, Nature ecology & evolution, 1 (2018)
  30. D.A. Ebert (2013)
  31. Renwart Marie, Delroisse Jérôme, Claes Julien M., Mallefet Jérôme, Ultrastructural organization of lantern shark (Etmopterus spinax Linnaeus, 1758) photophores, 10.1007/s00435-014-0230-y
  32. Renwart Marie, Delroisse Jérôme, Flammang Patrick, Claes Julien M., Mallefet Jérôme, Cytological changes during luminescence production in lanternshark (Etmopterus spinax Linnaeus, 1758) photophores, 10.1007/s00435-014-0235-6
  33. Claes Julien M., Partridge Julian C., Hart Nathan S., Garza-Gisholt Eduardo, Ho Hsuan-Ching, Mallefet Jérôme, Collin Shaun P., Photon Hunting in the Twilight Zone: Visual Features of Mesopelagic Bioluminescent Sharks, 10.1371/journal.pone.0104213
  34. Claes J. M., Kronstrom J., Holmgren S., Mallefet J., Nitric oxide in the control of luminescence from lantern shark (Etmopterus spinax) photophores, 10.1242/jeb.040410
  35. J.M. Claes, Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology, 153, 231 (2011)
  36. Claes J. M., Mallefet J., Hormonal control of luminescence from lantern shark (Etmopterus spinax) photophores, 10.1242/jeb.034363
  37. Claes J. M., Mallefet J., Functional physiology of lantern shark (Etmopterus spinax) luminescent pattern: differential hormonal regulation of luminous zones, 10.1242/jeb.041947
  38. Speiser Daniel I, Pankey M Sabrina, Zaharoff Alexander K, Battelle Barbara A, Bracken-Grissom Heather D, Breinholt Jesse W, Bybee Seth M, Cronin Thomas W, Garm Anders, Lindgren Annie R, Patel Nipam H, Porter Megan L, Protas Meredith E, Rivera Ajna S, Serb Jeanne M, Zigler Kirk S, Crandall Keith A, Oakley Todd H, Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms, 10.1186/s12859-014-0350-x
  39. J. Delroisse, Luminescence: journal of biological and chemical luminescence, 29, 15 (2014)
  40. Delroisse Jérôme, Ullrich-Lüter Esther, Blaue Stefanie, Eeckhaut Igor, Flammang Patrick, Mallefet Jérôme, Fine structure of the luminous spines and luciferase detection in the brittle star Amphiura filiformis, 10.1016/j.jcz.2017.05.001
  41. Delroisse Jérôme, Ullrich-Lüter Esther, Blaue Stefanie, Ortega-Martinez Olga, Eeckhaut Igor, Flammang Patrick, Mallefet Jérôme, A puzzling homology: a brittle star using a putative cnidarian-type luciferase for bioluminescence, 10.1098/rsob.160300
  42. Delroisse Jérôme, Ullrich-Lüter Esther, Ortega-Martinez Olga, Dupont Sam, Arnone Maria-Ina, Mallefet Jérôme, Flammang Patrick, High opsin diversity in a non-visual infaunal brittle star, 10.1186/1471-2164-15-1035
  43. Schnitzler Christine E, Pang Kevin, Powers Meghan L, Reitzel Adam M, Ryan Joseph F, Simmons David, Tada Takashi, Park Morgan, Gupta Jyoti, Brooks Shelise Y, Blakesley Robert W, Yokoyama Shozo, Haddock Steven HD, Martindale Mark Q, Baxevanis Andreas D, Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes, 10.1186/1741-7007-10-107
  44. Tong D., Rozas N. S., Oakley T. H., Mitchell J., Colley N. J., McFall-Ngai M. J., Evidence for light perception in a bioluminescent organ, 10.1073/pnas.0904571106
  45. Delroisse Jérôme, Mallefet Jérôme, Flammang Patrick, De Novo Adult Transcriptomes of Two European Brittle Stars: Spotlight on Opsin-Based Photoreception, 10.1371/journal.pone.0152988
  46. Delroisse Jérôme, Ortega-Martinez Olga, Dupont Sam, Mallefet Jérôme, Flammang Patrick, De novo transcriptome of the European brittle star Amphiura filiformis pluteus larvae, 10.1016/j.margen.2015.05.014
  47. S. Andrews, Reference Source (2010)
  48. Grabherr Manfred G, Haas Brian J, Yassour Moran, Levin Joshua Z, Thompson Dawn A, Amit Ido, Adiconis Xian, Fan Lin, Raychowdhury Raktima, Zeng Qiandong, Chen Zehua, Mauceli Evan, Hacohen Nir, Gnirke Andreas, Rhind Nicholas, di Palma Federica, Birren Bruce W, Nusbaum Chad, Lindblad-Toh Kerstin, Friedman Nir, Regev Aviv, Full-length transcriptome assembly from RNA-Seq data without a reference genome, 10.1038/nbt.1883
  49. Pertea G., Huang X., Liang F., Antonescu V., Sultana R., Karamycheva S., Lee Y., White J., Cheung F., Parvizi B., Tsai J., Quackenbush J., TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets, 10.1093/bioinformatics/btg034
  50. Das Sunetra, Shyamal Sharmishtha, Durica David S., Analysis of Annotation and Differential Expression Methods used in RNA-seq Studies in Crustacean Systems, 10.1093/icb/icw117
  51. Li R., Li Y., Kristiansen K., Wang J., SOAP: short oligonucleotide alignment program, 10.1093/bioinformatics/btn025
  52. Chen Ting-Wen, Gan Ruei-Chi, Fang Yi-Kai, Chien Kun-Yi, Liao Wei-Chao, Chen Chia-Chun, Wu Timothy H., Chang Ian Yi-Feng, Yang Chi, Huang Po-Jung, Yeh Yuan-Ming, Chiu Cheng-Hsun, Huang Tzu-Wen, Tang Petrus, FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation, 10.1038/s41598-017-10952-4
  53. Conesa A., Gotz S., Garcia-Gomez J. M., Terol J., Talon M., Robles M., Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, 10.1093/bioinformatics/bti610
  54. Parra G., Bradnam K., Korf I., CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes, 10.1093/bioinformatics/btm071
  55. M.D. Ramirez, Genome biology and evolution, 8, 3640 (2016)
  56. Kearse M., Moir R., Wilson A., Stones-Havas S., Cheung M., Sturrock S., Buxton S., Cooper A., Markowitz S., Duran C., Thierer T., Ashton B., Meintjes P., Drummond A., Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data, 10.1093/bioinformatics/bts199
  57. Fain Gordon L., Hardie Roger, Laughlin Simon B., Phototransduction and the Evolution of Photoreceptors, 10.1016/j.cub.2009.12.006
  58. Yau King-Wai, Hardie Roger C., Phototransduction Motifs and Variations, 10.1016/j.cell.2009.09.029
  59. Kojima Daisuke, Terakita Akihisa, Ishikawa Toru, Tsukahara Yasuo, Maeda Akio, Shichida Yoshinori, A Novel Go-mediated Phototransduction Cascade in Scallop Visual Cells, 10.1074/jbc.272.37.22979
  60. Koyanagi Mitsumasa, Terakita Akihisa, Kubokawa Kaoru, Shichida Yoshinori, Amphioxus homologs of Go-coupled rhodopsin and peropsin having 11-cis - and all-trans -retinals as their chromophores, 10.1016/s0014-5793(02)03616-5
  61. Su C.-Y., Parietal-Eye Phototransduction Components and Their Potential Evolutionary Implications, 10.1126/science.1123802
  62. S. Kawamura, Journal of Biological Chemistry, 268, 14579 (1993)
  63. Chen Ching-Kang, Inglese James, Lefkowitz Robert J., Hurley James B., Ca-dependent Interaction of Recoverin with Rhodopsin Kinase, 10.1074/jbc.270.30.18060
  64. Klenchin Vadim A., Calvert Peter D., Bownds M. Deric, Inhibition of Rhodopsin Kinase by Recoverin : FURTHER EVIDENCE FOR A NEGATIVE FEEDBACK SYSTEM IN PHOTOTRANSDUCTION, 10.1074/jbc.270.27.16147
  65. Arnold Konstantin, Bordoli Lorenza, Kopp Jürgen, Schwede Torsten, The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling, 10.1093/bioinformatics/bti770
  66. Biasini Marco, Bienert Stefan, Waterhouse Andrew, Arnold Konstantin, Studer Gabriel, Schmidt Tobias, Kiefer Florian, Cassarino Tiziano Gallo, Bertoni Martino, Bordoli Lorenza, Schwede Torsten, SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information, 10.1093/nar/gku340
  67. F. Kiefer, Nucleic acids research, 37, D387 (2008)
  68. Katoh K., Standley D. M., MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, 10.1093/molbev/mst010
  69. Gasteiger E., ExPASy: the proteomics server for in-depth protein knowledge and analysis, 10.1093/nar/gkg563
  70. E. Gasteiger (2005)
  71. D'Aniello S., Delroisse J., Valero-Gracia A., Lowe E.K., Byrne M., Cannon J.T., Halanych K.M., Elphick M.R., Mallefet J., Kaul-Strehlow S., Lowe C.J., Flammang P., Ullrich-Lüter E., Wanninger A., Arnone M.I., Opsin evolution in the Ambulacraria, 10.1016/j.margen.2015.10.001
  72. Feuda R., Hamilton S. C., McInerney J. O., Pisani D., Metazoan opsin evolution reveals a simple route to animal vision, 10.1073/pnas.1204609109
  73. Feuda Roberto, Rota-Stabelli Omar, Oakley Todd H., Pisani Davide, The Comb Jelly Opsins and the Origins of Animal Phototransduction, 10.1093/gbe/evu154
  74. Criscuolo Alexis, Gribaldo Simonetta, BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, 10.1186/1471-2148-10-210
  75. Ronquist Fredrik, Teslenko Maxim, van der Mark Paul, Ayres Daniel L., Darling Aaron, Höhna Sebastian, Larget Bret, Liu Liang, Suchard Marc A., Huelsenbeck John P., MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space, 10.1093/sysbio/sys029
  76. Gooding Jane M., Yap Kyoko L., Ikura Mitsuhiko, The cadherin-catenin complex as a focal point of cell adhesion and signalling: new insights from three-dimensional structures, 10.1002/bies.20033
  77. Nagafuchi A., The roles of catenins in the cadherin-mediated cell adhesion: functional analysis of E-cadherin-alpha catenin fusion molecules, 10.1083/jcb.127.1.235
  78. Read Timothy D., Petit Robert A., Joseph Sandeep J., Alam Md. Tauqeer, Weil M. Ryan, Ahmad Maida, Bhimani Ravila, Vuong Jocelyn S., Haase Chad P., Webb D. Harry, Tan Milton, Dove Alistair D. M., Draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus Smith 1828, 10.1186/s12864-017-3926-9
  79. Chana-Munoz Andres, Jendroszek Agnieszka, Sønnichsen Malene, Kristiansen Rune, Jensen Jan K., Andreasen Peter A., Bendixen Christian, Panitz Frank, Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation, 10.1371/journal.pone.0182756
  80. Dratz Edward A., Hargrave Paul A., The structure of rhodopsin and the rod outer segment disk membrane, 10.1016/0968-0004(83)90235-9
  81. S.S. Karnik, Journal of Biological Chemistry, 265, 17520 (1990)
  82. Sakmar T. P., Franke R. R., Khorana H. G., Glutamic acid-113 serves as the retinylidene Schiff base counterion in bovine rhodopsin., 10.1073/pnas.86.21.8309
  83. Cohen George B., Yang Tong, Robinson Phyllis R., Oprian Daniel D., Constitutive activation of opsin: Influence of charge at position 134 and size at position 296, 10.1021/bi00074a024
  84. Sakmar Thomas P., Fahmy Karim, Properties and Photoactivity of Rhodopsin Mutants, 10.1002/ijch.199500034
  85. Ovchinnikov Yu.A., Abdulaev N.G., Bogachuk A.S., Two adjacent cysteine residues in the C-terminal cytoplasmic fragment of bovine rhodopsin are palmitylated, 10.1016/0014-5793(88)80628-8
  86. Terakita Akihisa, 10.1186/gb-2005-6-3-213
  87. Arendt D., Ciliary Photoreceptors with a Vertebrate-Type Opsin in an Invertebrate Brain, 10.1126/science.1099955
  88. Koyanagi M., Takada E., Nagata T., Tsukamoto H., Terakita A., Homologs of vertebrate Opn3 potentially serve as a light sensor in nonphotoreceptive tissue, 10.1073/pnas.1219416110
  89. Velarde Rodrigo A., Sauer Colin D., O. Walden Kimberly K., Fahrbach Susan E., Robertson Hugh M., Pteropsin: A vertebrate-like non-visual opsin expressed in the honey bee brain, 10.1016/j.ibmb.2005.09.001
  90. Haltaufderhyde Kirk, Ozdeslik Rana N., Wicks Nadine L., Najera Julia A., Oancea Elena, Opsin Expression in Human Epidermal Skin, 10.1111/php.12354
  91. Setty Subba Rao, Opsin3—A Link to Visible Light-Induced Skin Pigmentation, 10.1016/j.jid.2017.09.025
  92. J. Delroisse, Cah Biol, 54, 721 (2013)
  93. Wang Zhong, Gerstein Mark, Snyder Michael, RNA-Seq: a revolutionary tool for transcriptomics, 10.1038/nrg2484
  94. Claes Julien M., Aksnes Dag L., Mallefet Jérôme, Phantom hunter of the fjords: Camouflage by counterillumination in a shark (Etmopterus spinax), 10.1016/j.jembe.2010.03.009
  95. J. Delroisse, Cah Biol, 54, 721 (2013)
  96. VIHTELIC THOMAS S., DORO CHRISTOPHER J., HYDE DAVID R., Cloning and characterization of six zebrafish photoreceptor opsin cDNAs and immunolocalization of their corresponding proteins, 10.1017/s0952523899163168
  97. Lan Yi, Sun Jin, Xu Ting, Chen Chong, Tian Renmao, Qiu Jian-Wen, Qian Pei-Yuan, De novo transcriptome assembly and positive selection analysis of an individual deep-sea fish, 10.1186/s12864-018-4720-z
Bibliographic reference Delroisse, Jérôme ; Duchatelet, Laurent ; Flammang, Patrick ; Mallefet, Jérôme. De novo transcriptome analyses provide insights into opsin-based photoreception in the lanternshark Etmopterus spinax. In: PLoS One, Vol. 13, no.12, p. e0209767 (2018)
Permanent URL http://hdl.handle.net/2078.1/209304