TY - JOUR
T1 - Partitioning of gene expression among zebrafish photoreceptor subtypes
AU - Ogawa, Yohey
AU - Corbo, Joseph C.
N1 - Funding Information:
We thank L. Volkov, D. Murphy, and M. Toomey for their comments on the manuscript. Tg(rho:EGFP)ja2Tg and Tg(gnat2:EGFP)ja23Tg fish lines were a generous gift from Dr. Yoshitaka Fukada (University of Tokyo). Tg(-5.5opn1sw1:EGFP)kj9Tg, Tg(-3.5opn1sw2:EGFP)kj11Tg, and Tg(opn1mw2:EGFP)kj4Tg fish lines were kindly provided by Dr. Shoji Kawamura (University of Tokyo). Tg(thrb:Tomato)q22Tg fish were kindly provided by Dr. Rachel Wong (University of Washington, Seattle). TgBAC(vsx1:GFP)nns5Tg were kindly provided by Dr. Ryan B. MacDonald (University College London). We also thank the Genome Technology Access Core (GTAC) in the Department of Genetics at Washington University in St. Louis for 10× library preparation and next generation sequencing, and the Flow Cytometry Core in the Department of Pathology and Immunology at Washington University in St. Louis for FACS services. This work was supported by the Japan Society for the Promotion of Science Overseas Research Fellowship (202060618 to YO) and the National Institutes of Health (EY030075 to JCC). Funding for this project was also provided by the Children’s Discovery Institute of Washington University and St. Louis Children’s Hospital.
Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12
Y1 - 2021/12
N2 - Vertebrate photoreceptors are categorized into two broad classes, rods and cones, responsible for dim- and bright-light vision, respectively. While many molecular features that distinguish rods and cones are known, gene expression differences among cone subtypes remain poorly understood. Teleost fishes are renowned for the diversity of their photoreceptor systems. Here, we used single-cell RNA-seq to profile adult photoreceptors in zebrafish, a teleost. We found that in addition to the four canonical zebrafish cone types, there exist subpopulations of green and red cones (previously shown to be located in the ventral retina) that express red-shifted opsin paralogs (opn1mw4 or opn1lw1) as well as a unique combination of cone phototransduction genes. Furthermore, the expression of many paralogous phototransduction genes is partitioned among cone subtypes, analogous to the partitioning of the phototransduction paralogs between rods and cones seen across vertebrates. The partitioned cone-gene pairs arose via the teleost-specific whole-genome duplication or later clade-specific gene duplications. We also discovered that cone subtypes express distinct transcriptional regulators, including many factors not previously implicated in photoreceptor development or differentiation. Overall, our work suggests that partitioning of paralogous gene expression via the action of differentially expressed transcriptional regulators enables diversification of cone subtypes in teleosts.
AB - Vertebrate photoreceptors are categorized into two broad classes, rods and cones, responsible for dim- and bright-light vision, respectively. While many molecular features that distinguish rods and cones are known, gene expression differences among cone subtypes remain poorly understood. Teleost fishes are renowned for the diversity of their photoreceptor systems. Here, we used single-cell RNA-seq to profile adult photoreceptors in zebrafish, a teleost. We found that in addition to the four canonical zebrafish cone types, there exist subpopulations of green and red cones (previously shown to be located in the ventral retina) that express red-shifted opsin paralogs (opn1mw4 or opn1lw1) as well as a unique combination of cone phototransduction genes. Furthermore, the expression of many paralogous phototransduction genes is partitioned among cone subtypes, analogous to the partitioning of the phototransduction paralogs between rods and cones seen across vertebrates. The partitioned cone-gene pairs arose via the teleost-specific whole-genome duplication or later clade-specific gene duplications. We also discovered that cone subtypes express distinct transcriptional regulators, including many factors not previously implicated in photoreceptor development or differentiation. Overall, our work suggests that partitioning of paralogous gene expression via the action of differentially expressed transcriptional regulators enables diversification of cone subtypes in teleosts.
UR - http://www.scopus.com/inward/record.url?scp=85113842508&partnerID=8YFLogxK
U2 - 10.1038/s41598-021-96837-z
DO - 10.1038/s41598-021-96837-z
M3 - Article
C2 - 34462505
AN - SCOPUS:85113842508
VL - 11
JO - Scientific Reports
JF - Scientific Reports
SN - 2045-2322
IS - 1
M1 - 17340
ER -