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Ancient origin of the rod bipolar cell pathway in the vertebrate retina

Nature Ecology & Evolution (2024)Cite this article

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Abstract

Vertebrates rely on rod photoreceptors for vision in low-light conditions. The specialized downstream circuit for rod signalling, called the primary rod pathway, is well characterized in mammals, but circuitry for rod signalling in non-mammals is largely unknown. Here we demonstrate that the mammalian primary rod pathway is conserved in zebrafish, which diverged from extant mammals ~400 million years ago. Using single-cell RNA sequencing, we identified two bipolar cell types in zebrafish that are related to mammalian rod bipolar cell (RBCs), the only bipolar type that directly carries rod signals from the outer to the inner retina in the primary rod pathway. By combining electrophysiology, histology and ultrastructural reconstruction of the zebrafish RBCs, we found that, similar to mammalian RBCs, both zebrafish RBC types connect with all rods in their dendritic territory and provide output largely onto amacrine cells. The wiring pattern of the amacrine cells postsynaptic to one RBC type is strikingly similar to that of mammalian RBCs and their amacrine partners, suggesting that the cell types and circuit design of the primary rod pathway emerged before the divergence of teleost fish and mammals. The second RBC type, which forms separate pathways, was either lost in mammals or emerged in fish.

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Fig. 1: Comparison of single-cell gene expression identified two possible rod bipolar cells in zebrafish.
Fig. 2: Transgenic labelling of clusters 14 and 19 revealed morphological features of these BCs.
Fig. 3: RBC1 and RBC2 connect to rods and red cones but differ in dendritic and axonal synaptic arrangements.
Fig. 4: Rod input to RBC1 is mediated by mGluR6 receptors.
Fig. 5: Identification of RBC1 and RBC2, and their postsynaptic neuron types in an SBFSEM volume.
Fig. 6: The circuit diagram of RBC1 is similar to the mammalian RBC pathway.

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Data availability

No new scRNA-seq data were generated in this paper.

Code availability

Computational scripts detailing scRNA-seq analysis reported in this paper are available on GitHub at https://github.com/shekharlab/ZebrafishBC. We have also provided R markdown (Rmd) files that show step-by-step reproduction of the key results on GitHub at https://github.com/shekharlab/ZebrafishBC.

References

  1. Baylor, D. A., Lamb, T. D. & Yau, K. W. Responses of retinal rods to single photons. J. Physiol. 288, 613–634 (1979).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Baylor, D. A., Nunn, B. J. & Schnapf, J. L. The photocurrent, noise and spectral sensitivity of rods of the monkey Macaca fascicularis. J. Physiol. 357, 575–607 (1984).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Field, G. D. & Rieke, F. Nonlinear signal transfer from mouse rods to bipolar cells and implications for visual sensitivity. Neuron 34, 773–785 (2002).

    Article  CAS  PubMed  Google Scholar 

  4. Field, G. D. & Rieke, F. Mechanisms regulating variability of the single photon responses of mammalian rod photoreceptors. Neuron 35, 733–747 (2002).

    Article  CAS  PubMed  Google Scholar 

  5. Ingram, N. T., Sampath, A. P. & Fain, G. L. Why are rods more sensitive than cones? J. Physiol. 594, 5415–5426 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Yang, X.-L. & Wu, S. M. Response sensitivity and voltage gain of the rod- and cone-bipolar cell synapses in dark-adapted tiger salamander retina. J. Neurophysiol. 78, 2662–2673 (1997).

    Article  CAS  PubMed  Google Scholar 

  7. Ashmore, J. F. & Falk, G. Absolute sensitivity of rod bipolar cells in a dark-adapted retina. Nature 263, 248–249 (1976).

    Article  CAS  PubMed  Google Scholar 

  8. Kolb, H. & Famiglietti, E. V. Rod and cone pathways in the inner plexiform layer of cat retina. Science 186, 47–49 (1974).

    Article  CAS  PubMed  Google Scholar 

  9. Field, G. D., Sampath, A. P. & Rieke, F. Retinal processing near absolute threshold: from behavior to mechanism. Annu. Rev. Physiol. 67, 491–514 (2005).

    Article  CAS  PubMed  Google Scholar 

  10. Strettoi, E. in The Senses: A Comprehensive Reference (eds Masland, R. H. et al.) 303–311 (Academic Press, 2008).

  11. Wu, S. M. Synaptic organization of the vertebrate retina: general principles and species-specific variations: the Friedenwald lecture. Invest. Ophthalmol. Vis. Sci. 51, 1264–1274 (2010).

    Article  PubMed Central  Google Scholar 

  12. Strettoi, E., Masri, R. A. & Grünert, U. AII amacrine cells in the primate fovea contribute to photopic vision. Sci. Rep. 8, 16429 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Lee, S. C. S., Martin, P. R. & Grünert, U. Topography of neurons in the rod pathway of human retina. Invest. Ophthalmol. Vis. Sci. 60, 2848–2859 (2019).

    Article  CAS  PubMed  Google Scholar 

  14. Tsukamoto, Y., Morigiwa, K., Ueda, M. & Sterling, P. Microcircuits for night vision in mouse retina. J. Neurosci. 21, 8616–8623 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Behrens, C., Schubert, T., Haverkamp, S., Euler, T. & Berens, P. Connectivity map of bipolar cells and photoreceptors in the mouse retina. eLife 5, e20041 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Kolb, H. & Nelson, R. Rod pathways in the retina of the cat. Vis. Res. 23, 301–312 (1983).

    Article  CAS  PubMed  Google Scholar 

  17. Dacheux, R. F. & Raviola, E. The rod pathway in the rabbit retina: a depolarizing bipolar and amacrine cell. J. Neurosci. 6, 331–345 (1986).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Freed, M. A., Smith, R. G. & Sterling, P. Rod bipolar array in the cat retina: pattern of input from rods and GABA-accumulating amacrine cells. J. Comp. Neurol. 266, 445–455 (1987).

    Article  CAS  PubMed  Google Scholar 

  19. Ashmore, J. F. & Falk, G. Transmission of visual signals to bipolar cells near absolute threshold. Vis. Res. 19, 419–423 (1979).

    Article  CAS  PubMed  Google Scholar 

  20. Ashmore, J. F. & Falk, G. Responses of rod-bipolar cells in the dark-adapted retina of the dogfish, Scyliorhinus canicula. J. Physiol. 300, 115–150.4 (1980).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Joselevitch, C. & Kamermans, M. Interaction between rod and cone inputs in mixed-input bipolar cells in goldfish retina. J. Neurosci. Res. 85, 1579–1591 (2007).

    Article  CAS  PubMed  Google Scholar 

  22. Joselevitch, C. & Kamermans, M. Retinal parallel pathways: seeing with our inner fish. Vis. Res. 49, 943–959 (2009).

    Article  PubMed  Google Scholar 

  23. Lamb, T. D. Evolution of phototransduction, vertebrate photoreceptors and retina. Prog. Retin. Eye Res. 36, 52–119 (2013).

    Article  CAS  PubMed  Google Scholar 

  24. Franke, K. et al. Inhibition decorrelates visual feature representations in the inner retina. Nature 542, 439–444 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Ghosh, K. K., Bujan, S., Haverkamp, S., Feigenspan, A. & Wässle, H. Types of bipolar cells in the mouse retina. J. Comp. Neurol. 469, 70–82 (2004).

    Article  PubMed  Google Scholar 

  26. Grünert, U. & Martin, P. R. Cell types and cell circuits in human and non-human primate retina. Prog. Retin. Eye Res. 5, 100844 (2020).

  27. Peng, Y.-R. et al. Molecular classification and comparative taxonomics of foveal and peripheral cells in primate retina. Cell 176, 1222–1237.e22 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Shekhar, K. et al. Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics. Cell 166, 1308–1323.e30 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Masland, R. H. The neuronal organization of the retina. Neuron 76, 266–280 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Hahn, J. et al. Evolution of neuronal cell classes and types in the vertebrate retina. Nature 624, 415–424 (2023).

  31. Strettoi, E., Dacheux, R. F. & Raviola, E. Synaptic connections of rod bipolar cells in the inner plexiform layer of the rabbit retina. J. Comp. Neurol. 295, 449–466 (1990).

    Article  CAS  PubMed  Google Scholar 

  32. Zhang, C., Hellevik, A., Takeuchi, S. & Wong, R. O. Hierarchical partner selection shapes rod–cone pathway specificity in the inner retina. iScience 25, 105032 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  33. Strettoi, E., Raviola, E. & Dacheux, R. F. Synaptic connections of the narrow-field, bistratified rod amacrine cell (AII) in the rabbit retina. J. Comp. Neurol. 325, 152–168 (1992).

    Article  CAS  PubMed  Google Scholar 

  34. Dunn, F. A. & Rieke, F. Single-photon absorptions evoke synaptic depression in the retina to extend the operational range of rod vision. Neuron 57, 894–904 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Grimes, W. N., Hoon, M., Briggman, K. L., Wong, R. O. & Rieke, F. Cross-synaptic synchrony and transmission of signal and noise across the mouse retina. eLife 3, e03892 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  36. Pang, J.-J., Gao, F. & Wu, S. M. Light-evoked current responses in rod bipolar cells, cone depolarizing bipolar cells and AII amacrine cells in dark-adapted mouse retina. J. Physiol. 558, 897–912 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Demb, J. B. & Singer, J. H. Intrinsic properties and functional circuitry of the AII amacrine cell. Vis. Neurosci. 29, 51–60 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  38. Strettoi, E., Dacheux, R. F. & Raviola, E. Cone bipolar cells as interneurons in the rod pathway of the rabbit retina. J. Comp. Neurol. 347, 139–149 (1994).

    Article  CAS  PubMed  Google Scholar 

  39. Vitorino, M. et al. Vsx2 in the zebrafish retina: restricted lineages through derepression. Neural Dev. 4, 14 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  40. Križaj, D., Cordeiro, S. & Strauß, O. Retinal TRP channels: cell-type-specific regulators of retinal homeostasis and multimodal integration. Prog. Retin. Eye Res. 92, 101114 (2023).

    Article  PubMed  Google Scholar 

  41. Wässle, H., Yamashita, M., Greferath, U., Grünert, U. & Müller, F. The rod bipolar cell of the mammalian retina. Vis. Neurosci. 7, 99–112 (1991).

    Article  PubMed  Google Scholar 

  42. Wässle, H., Puller, C., Müller, F. & Haverkamp, S. Cone contacts, mosaics, and territories of bipolar cells in the mouse retina. J. Neurosci. 29, 106–117 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  43. Morris, A. C., Schroeter, E. H., Bilotta, J., Wong, R. O. L. & Fadool, J. M. Cone survival despite rod degeneration in XOPS-mCFP transgenic zebrafish. Invest. Ophthalmol. Vis. Sci. 46, 4762–4771 (2005).

    Article  PubMed  Google Scholar 

  44. Vihtelic, T. S., Doro, C. J. & Hyde, D. R. Cloning and characterization of six zebrafish photoreceptor opsin cDNAs and immunolocalization of their corresponding proteins. Vis. Neurosci. 16, 571–585 (1999).

    Article  CAS  PubMed  Google Scholar 

  45. Chinen, A., Hamaoka, T., Yamada, Y. & Kawamura, S. Gene duplication and spectral diversification of cone visual pigments of zebrafish. Genetics 163, 663–675 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Thoreson, W. B. & Dacey, D. M. Diverse cell types, circuits, and mechanisms for color vision in the vertebrate retina. Physiol. Rev. 99, 1527–1573 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Sandell, J. H., Masland, R. H., Raviola, E. & Dacheux, R. F. Connections of indoleamine-accumulating cells in the rabbit retina. J. Comp. Neurol. 283, 303–313 (1989).

    Article  CAS  PubMed  Google Scholar 

  48. Bloomfield, S. A. & Völgyi, B. The diverse functional roles and regulation of neuronal gap junctions in the retina. Nat. Rev. Neurosci. 10, 495–506 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Quint, W. H. et al. Loss of Gap Junction Delta-2 (GJD2) gene orthologs leads to refractive error in zebrafish. Commun. Biol. 4, 676 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Li, H., Chuang, A. Z. & O’Brien, J. Photoreceptor coupling is controlled by connexin 35 phosphorylation in zebrafish retina. J. Neurosci. 29, 15178–15186 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Miller, A. C. et al. A genetic basis for molecular asymmetry at vertebrate electrical synapses. eLife 6, e25364 (2017).

  52. Gamlin, C. R., Zhang, C., Dyer, M. A. & Wong, R. O. L. Distinct developmental mechanisms act independently to shape biased synaptic divergence from an inhibitory neuron. Curr. Biol. 30, 1258–1268.e2 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Marc, R. E., Anderson, J. R., Jones, B. W., Sigulinsky, C. L. & Lauritzen, J. S. The AII amacrine cell connectome: a dense network hub. Front. Neural Circuits 8, 104 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  54. Tsukamoto, Y. & Omi, N. Functional allocation of synaptic contacts in microcircuits from rods via rod bipolar to AII amacrine cells in the mouse retina. J. Comp. Neurol. 521, 3541–3555 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  55. Hahn, J. et al. Evolution of neuronal cell classes and types in the vertebrate retina. Nature 624, 415–424 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Wang, J. et al. Molecular characterization of the sea lamprey retina illuminates the evolutionary origin of retinal cell types. Preprint at bioRxiv https://doi.org/10.1101/2023.12.10.571000 (2023).

  57. Li, Y. N., Tsujimura, T., Kawamura, S. & Dowling, J. E. Bipolar cell-photoreceptor connectivity in the zebrafish (Danio rerio) retina. J. Comp. Neurol. 520, 3786–3802 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  58. Zimmermann, M. J. Y. et al. Zebrafish differentially process color across visual space to match natural scenes. Curr. Biol. 28, 2018–2032.e5 (2018).

    Article  CAS  PubMed  Google Scholar 

  59. Zhou, M. et al. Zebrafish retinal ganglion cells asymmetrically encode spectral and temporal information across visual space. Curr. Biol. 30, 2927–2942.e7 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Yoshimatsu, T., Schröder, C., Nevala, N. E., Berens, P. & Baden, T. Fovea-like photoreceptor specializations underlie single UV cone driven prey-capture behavior in zebrafish. Neuron 107, 320–337.e6 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Schröder, C., Oesterle, J., Berens, P., Yoshimatsu, T. & Baden, T. Distinct synaptic transfer functions in same-type photoreceptors. eLife 10, e67851 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  62. Yan, W. et al. Cell atlas of the human fovea and peripheral retina. Sci. Rep. 10, 9802 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Günther, A. et al. Double cones and the diverse connectivity of photoreceptors and bipolar cells in an avian retina. J. Neurosci. 41, 5015–5028 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  64. Yamagata, M., Yan, W. & Sanes, J. R. A cell atlas of the chick retina based on single-cell transcriptomics. eLife 10, e63907 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Baden, T. & Osorio, D. The retinal basis of vertebrate color vision. Annu. Rev. Vis. Sci. 5, 177–200 (2019).

    Article  CAS  PubMed  Google Scholar 

  66. Sherry, D. M. & Yazulla, S. Goldfish bipolar cells and axon terminal patterns: a golgi study. J. Comp. Neurol. 329, 188–200 (1993).

    Article  CAS  PubMed  Google Scholar 

  67. Behrens, U. D., Borde, J., Mack, A. F. & Wagner, H.-J. Distribution of phosphorylated protein kinase C alpha in goldfish retinal bipolar synaptic terminals: control by state of adaptation and pharmacological treatment. Cell Tissue Res. 327, 209–220 (2007).

    Article  CAS  PubMed  Google Scholar 

  68. DeVries, S. H., Li, W. & Saszik, S. Parallel processing in two transmitter microenvironments at the cone photoreceptor synapse. Neuron 50, 735–748 (2006).

    Article  CAS  PubMed  Google Scholar 

  69. Kim, M.-H. & von Gersdorff, H. Postsynaptic plasticity triggered by Ca2+-permeable AMPA receptor activation in retinal amacrine cells. Neuron 89, 507–520 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Vigh, J., Vickers, E. & von Gersdorff, H. Light-evoked lateral GABAergic inhibition at single bipolar cell synaptic terminals is driven by distinct retinal microcircuits. J. Neurosci. 31, 15884–15893 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Vigh, J. & von Gersdorff, H. Prolonged reciprocal signaling via NMDA and GABA receptors at a retinal ribbon synapse. J. Neurosci. 25, 11412–11423 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Grimes, W. N., Zhang, J., Graydon, C. W., Kachar, B. & Diamond, J. S. Retinal parallel processors: more than 100 independent microcircuits operate within a single interneuron. Neuron 65, 873–885 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Burrone, J. & Lagnado, L. Electrical resonance and Ca2+ influx in the synaptic terminal of depolarizing bipolar cells from the goldfish retina. J. Physiol. 505, 571–584 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Protti, D. A., Flores-Herr, N. & von Gersdorff, H. Light evokes Ca2+ spikes in the axon terminal of a retinal bipolar cell. Neuron 25, 215–227 (2000).

    Article  CAS  PubMed  Google Scholar 

  75. Powers, M. K. & Easter, S. S. Absolute visual sensitivity of the goldfish. Vis. Res. 18, 1137–1147 (1978).

    Article  CAS  PubMed  Google Scholar 

  76. Tsukamoto, Y. & Omi, N. Classification of mouse retinal bipolar cells: type-specific connectivity with special reference to rod-driven AII amacrine pathways. Front. Neuroanat. 11, 92 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  77. Pang, J.-J., Gao, F. & Wu, S. M. Stratum-by-stratum projection of light response attributes by retinal bipolar cells of Ambystoma. J. Physiol. 558, 249–262 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Balaji, V. et al. Immunohistochemical characterization of bipolar cells in four distantly related avian species. J. Comp. Neurol. 531, 561–581 (2023).

    Article  CAS  PubMed  Google Scholar 

  79. Caminos, E., Velasco, A., Jarrı́n, M., Aijón, J. & Lara, J. M. Protein kinase C-like immunoreactive cells in embryo and adult chicken retinas. Dev. Brain Res. 118, 227–230 (1999).

    Article  CAS  Google Scholar 

  80. Frederiksen, R., Fain, G. L. & Sampath, A. P. A hyperpolarizing rod bipolar cell in the sea lamprey, Petromyzon marinus. J. Exp. Biol. 225, jeb243949 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  81. Wong, K. Y., Cohen, E. D. & Dowling, J. E. Retinal bipolar cell input mechanisms in giant Danio. II. Patch-clamp analysis of ON bipolar cells. J. Neurophysiol. 93, 94–107 (2005).

    Article  PubMed  Google Scholar 

  82. Yoshimatsu, T. et al. Ancestral circuits for vertebrate color vision emerge at the first retinal synapse. Sci. Adv. 7, eabj6815 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Morshedian, A. & Fain, G. L. The evolution of rod photoreceptors. Phil. Trans. R. Soc. B 372, 20160074 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  84. Ishida, A. T., Stell, W. K. & Lightfoot, D. O. Rod and cone inputs to bipolar cells in goldfish retina. J. Comp. Neurol. 191, 315–335 (1980).

    Article  CAS  PubMed  Google Scholar 

  85. Connaughton, V. P. & Nelson, R. Axonal stratification patterns and glutamate-gated conductance mechanisms in zebrafish retinal bipolar cells. J. Physiol. 524, 135–146 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Pang, J.-J. et al. Direct rod input to cone BCs and direct cone input to rod BCs challenge the traditional view of mammalian BC circuitry. Proc. Natl Acad. Sci. USA 107, 395–400 (2010).

    Article  CAS  PubMed  Google Scholar 

  87. Whitaker, C. M., Nobles, G., Ishibashi, M. & Massey, S. C. Rod and cone connections with bipolar cells in the rabbit retina. Front. Cell. Neurosci. 15, 662329 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Carter-Dawson, L. D. & LaVail, M. M. Rods and cones in the mouse retina. I. Structural analysis using light and electron microscopy. J. Comp. Neurol. 188, 245–262 (1979).

    Article  CAS  PubMed  Google Scholar 

  89. Famiglietti, E. V. & Sharpe, S. J. Regional topography of rod and immunocytochemically characterized ‘blue’ and ‘green’ cone photoreceptors in rabbit retina. Vis. Neurosci. 12, 1151–1175 (1995).

    Article  CAS  PubMed  Google Scholar 

  90. Nadal-Nicolás, F. M. et al. True S-cones are concentrated in the ventral mouse retina and wired for color detection in the upper visual field. eLife 9, e56840 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  91. Kimura, Y., Satou, C. & Higashijima, S. V2a and V2b neurons are generated by the final divisions of pair-producing progenitors in the zebrafish spinal cord. Development 135, 3001–3005 (2008).

    Article  CAS  PubMed  Google Scholar 

  92. Randlett, O. et al. Cellular requirements for building a retinal neuropil. Cell Rep. 3, 282–290 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Suzuki, S. C. et al. Cone photoreceptor types in zebrafish are generated by symmetric terminal divisions of dedicated precursors. Proc. Natl Acad. Sci. USA 110, 15109–15114 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Kölsch, Y. et al. Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior. Neuron 109, 645–662.e9 (2021).

    Article  PubMed  Google Scholar 

  95. La Manno, G. et al. RNA velocity of single cells. Nature 560, 494–498 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  96. Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20, 296 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Becht, E. et al. Dimensionality reduction for visualizing single-cell data using UMAP. Nat. Biotechnol. 37, 38–44 (2019).

    Article  CAS  Google Scholar 

  98. Bernardos, R. L., Barthel, L. K., Meyers, J. R. & Raymond, P. A. Late-stage neuronal progenitors in the retina are radial Müller glia that function as retinal stem cells. J. Neurosci. 27, 7028–7040 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Hörnberg, H. et al. RNA-binding protein Hermes/RBPMS inversely affects synapse density and axon arbor formation in retinal ganglion cells in vivo. J. Neurosci. 33, 10384–10395 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  100. Sandell, J. H., Martin, S. C. & Heinrich, G. The development of GABA immunoreactivity in the retina of the zebrafish (Brachydanio rerio). J. Comp. Neurol. 345, 596–601 (1994).

    Article  CAS  PubMed  Google Scholar 

  101. Abalo, X. M. et al. Circadian regulation of phosphodiesterase 6 genes in zebrafish differs between cones and rods: implications for photopic and scotopic vision. Vis. Res. 166, 43–51 (2020).

    Article  PubMed  Google Scholar 

  102. Kolosov, D., Bui, P., Chasiotis, H. & Kelly, S. P. Claudins in teleost fishes. Tissue Barriers 1, e25391 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  103. Kwan, K. M. et al. The Tol2kit: a multisite gateway-based construction kit forTol2 transposon transgenesis constructs. Dev. Dyn. 236, 3088–3099 (2007).

    Article  CAS  PubMed  Google Scholar 

  104. Morris, A. C., Scholz, T. L., Brockerhoff, S. E. & Fadool, J. M. Genetic dissection reveals two separate pathways for rod and cone regeneration in the teleost retina. Dev. Neurobiol. 68, 605–619 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  105. Huang, Y.-Y., Haug, M. F., Gesemann, M. & Neuhauss, S. C. F. Novel expression patterns of metabotropic glutamate receptor 6 in the zebrafish nervous system. PLoS ONE 7, e35256 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Choi, H. M. T. et al. Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust. Development 145, dev165753 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank the Vision Core at the University of Washington for processing zebrafish retina samples and acquiring serial images for SBFSEM, and R. N. Swanstrom for helping with cell tracing of the EM volume. Funding was provided by the MCSA fellowship (‘ColourFish’ 748716) from the EU Horizon 2020 and Research to Prevent Blindness Career Development Award to T.Y.; the NIH EY14358 to R.O.W.; U01MH105960 and R01 EY022073 to J.R.S.; EY01730 (Vision Core grant, PI M. Neitz) Developmental Biology Training Grant HD07183 to F.D.D.; the Wellcome Trust 220277/Z20/Z, European Research Council ERC-StG 677687, UKRI BBSRC, BB/R014817/1 and BB/W013509/1, Leverhulme Trust PLP-2017-005, RPG-2021-026 to T.B.; NIH grant R00EY028625, Hellmann Foundation Fellowship, and the McKnight Foundation Fellowship to K.S.; the DFG through TRR-274, TP C04 (project ID 408885537) to L.G.; travel grant from the Graduate School in Systemic Neuroscience to Y.K., and from the Max Planck Society to Y.K. and H.B.

Author information

Author notes

  1. These authors contributed equally: Ayana M. Hellevik, Philip Mardoum, Joshua Hahn.

Authors and Affiliations

  1. Department of Biological Structure, University of Washington, Seattle, WA, USA

    Ayana M. Hellevik, Philip Mardoum, Florence D. D’Orazi, Sachihiro C. Suzuki, Owen Lawrence & Rachel O. Wong

  2. Department of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute; Vision Sciences Graduate Program; California Institute of Quantitative Biosciences (QB3), University of California Berkley, Berkeley, CA, USA

    Joshua Hahn & Karthik Shekhar

  3. Department Genes – Circuits – Behavior, Max Planck Institute for Biological Intelligence, Martinsried, Germany

    Yvonne Kölsch & Herwig Baier

  4. Institute of Neuronal Cell Biology, Technische Universität München, Munich, Germany

    Leanne Godinho

  5. Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA

    Fred Rieke

  6. Vision Science Center, University of Washington, Seattle, WA, USA

    Fred Rieke

  7. Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    Karthik Shekhar

  8. Department of Molecular and Cellular Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA

    Joshua R. Sanes

  9. School of Life Sciences, University of Sussex, Brighton, UK

    Tom Baden

  10. Institute of Ophthalmic Research, University of Tübingen, Tübingen, Germany

    Tom Baden

  11. Department of Ophthalmology and Visual Sciences, Washington University in St Louis School of Medicine, St Louis, MO, USA

    Takeshi Yoshimatsu

  12. BioRTC, Yobe State University, Damatsuru, Yobe, Nigeria

    Takeshi Yoshimatsu

Authors
  1. Ayana M. Hellevik
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  2. Philip Mardoum
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  3. Joshua Hahn
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  4. Yvonne Kölsch
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  5. Florence D. D’Orazi
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  6. Sachihiro C. Suzuki
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  7. Leanne Godinho
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  8. Owen Lawrence
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  9. Fred Rieke
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  10. Karthik Shekhar
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  11. Joshua R. Sanes
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  12. Herwig Baier
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  13. Tom Baden
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  14. Rachel O. Wong
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  15. Takeshi Yoshimatsu
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Contributions

A.M.H., P.M., J.H., Y.K., K.S., J.R.S., H.B., T.B., R.O.W. and T.Y. designed the study; Y.K. performed scRNA-seq under the supervision of H.B. and J.R.S. with guidance from K.S.; J.H. processed and analysed the scRNA-seq data under the supervision of K.S.; the data were further interpreted by J.H., K.S., H.B. and J.R.S.; T.Y., S.C.S. and L.G. generated new plasmids; T.Y. and F.D.D. generated novel lines; T.Y. performed experiments, collected and analysed the data for light microscopy with help from O.L.; P.M. and F.R. performed whole-cell patch recordings and interpreted the data; F.D.D. prepared the sample for SBFSEM; A.M.H., O.L. and T.Y. traced the EM images; T.Y. analysed and interpreted the EM data; all results including transcriptional, physiological and anatomical analysis were further interpreted by K.S., J.R.S., H.B., T.B., R.O.W. and T.Y.; T.Y. wrote the manuscript with input from all authors.

Corresponding author

Correspondence to Takeshi Yoshimatsu.

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The authors declare no competing interests.

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Nature Ecology & Evolution thanks Silke Haverkamp, Stephan Neuhauss and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data

Extended Data Fig. 1 Expression patterns of the identified marker genes in BC clusters.

The size of each circle depicts the percentage of cells in the cluster in which the marker was detected (≥1 UMI), and its grey scale depicts the scaled average expression level of cells within the cluster.

Extended Data Fig. 2 Dendritic tiling of RBC1 and RBC2 BCs across the retina.

a,b, Confocal images of retinal flat mount at outer plexiform layer level from Tg(vsx1:memCerulean)q19 (vsx1:memCer) (a) and Tg(vsx2:memCerulean)wst01 (vsx2:memCer) (b). Note that the vsx1:memCer line occasionally labels OFF BCs. These BCs were distinguished by tracing the cells to the axon terminals in the confocal image volumes.

Extended Data Fig. 3 RBC1 and RBC2 are ON BCs.

Example traces of voltage responses of RBC1 and RBC2 after a cone activating light flash (arrow heads). Inhibitory neurotransmitter receptors were blocked (inh lock) by a bath application of gabazine, strychnine, and TPMPA ((1,2,5,6-Tetrahydropyridin-4-yl)methylphosphinic acid).

Extended Data Fig. 4 Identification of RBC1 and RBC2 postsynaptic neurons in SBFSEM volume.

a, A partial image of an example SEM image of an adult zebrafish retina. OPL (outer plexiform layer), INL (inner nuclear layer), IPL (inner plexiform layer), GCL (ganglion cell layer). b, Magnified image of the region within the black box in a at the bottom layer of the IPL. Characteristic large bipolar cell axons are painted in light yellow and green. c, Ribbon synapse distributions in a RBC1 and a RBC2. The locations of ribbon synapses are marked in red. Arrow heads indicate the locations of example ribbon synapses (arrows) shown in the insets. d, Reconstruction of all RBC1s and RBC2s in the EM volume. Postsynaptic neurons of a centrally located RBC1 (open arrow head) and RBC2 (closed arrow head) were reconstructed in Figs. 5, 6, and S5–9. e,f, Traces of neuronal processes and the location of somas of cells that are post-synaptic to RBC1 and RBC2 cells. Individual cells were color coded. IPL: inner plexiform layer.

Extended Data Fig. 5 Gallery of mono-stratifying AC making reciprocal synapses with RBC1.

En face and side views of individual cells. The numbers of input (open bar) and output (closed bar) synapses with each RBC1 (blue) and RBC2 (red) terminal are indicated as the height of the bars.

Extended Data Fig. 6 Gallery of mono-stratifying AC without reciprocal synapses with RBC1.

En face and side views of individual cells. The numbers of input (open bar) and output (closed bar) synapses with each RBC1 (blue) and RBC2 (red) terminal are indicated as the height of the bars.

Extended Data Fig. 7 Gallery of bi-stratifying AC and RGC contacted to RBC1.

En face and side views of individual cells. The numbers of input (open bar) and output (closed bar) synapses with each RBC1 (blue) and RBC2 (red) terminal are indicated as the height of the bars.

Extended Data Fig. 8 Gallery of mono-stratifying AC connected to RBC2.

En face and side views of individual cells. The numbers of input (open bar) and output (closed bar) synapses with each RBC1 (blue) and RBC2 (red) terminal are indicated as the height of the bars.

Extended Data Fig. 9 Gallery of bi-stratifying AC and RGC connected to RBC2.

En face and side views of individual cells. The numbers of input (open bar) and output (closed bar) synapses with each RBC1 (blue) and RBC2 (red) terminal are indicated as the height of the bars.

Extended Data Fig. 10 Cx35 is highly expressed in two layers of the IPL and co-localizes with ON stratifying BC axon terminals.

a, Confocal images of retinal slices from Tg(vsx1:memCerulean)q19 (vsx1:memCer). Immunolabeling for Connexin35 (cx35) and PKCα are in cyan and magenta, respectively. IPL: inner plexiform layer. b, Distribution patterns of Cx35 immunostaining across the IPL. Cx35 labeling is enriched in the layers where A2-like AC dendrites stratify (grey shades). The blue thick line is mean values and shades are S.E.M. n=3 animals. c, Distribution of cx35 puncta in the PKCα positive ON BC axons. Cx35 labeling outside the axons was digitally masked (removed) in the image on the right.

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Hellevik, A.M., Mardoum, P., Hahn, J. et al. Ancient origin of the rod bipolar cell pathway in the vertebrate retina. Nat Ecol Evol (2024). https://doi.org/10.1038/s41559-024-02404-w

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