Single-cell profiling of photoreceptor cells in adult zebrafish

Vertebrate vision is mediated by two kinds of photoreceptors, rods and cones, responsible for dim- and bright-light vision, respectively. Gene expression differences among cone subtypes remain poorly understood compared with rods. We generated single-cell transcriptome data using a droplet-based approach to reveal the extent of gene expression diversity among adult zebrafish photoreceptor subtypes. Populations of photoreceptor cells were enriched by using the transgenic zebrafish lines, Tg(rho:EGFP)ja2Tg and Tg(gnat2:EGFP)ja23Tg, which express GFP in rods and all cone subtypes, respectively. By analyzing the single-cell transcriptomes, we found that in addition to the four canonical zebrafish cone types (ultraviolet, blue, green and red), there exist subpopulations of green and red cones in the ventral retina that express red-shifted opsin paralogs (opn1mw4 and opn1lw1). This work lays a foundation for future studies aimed at understanding how molecular differences among cone subtypes affect photoreceptor function. Overall design: GFP-positive cells collected from two transgenic zebrafish, Tg(rho:EGFP)ja2Tg and Tg(gnat2:EGFP)ja23Tg were combined into one sample. A small percentage of GFP-negative cells was also included in the sample.

脊椎动物的视觉由两类光感受器介导：视杆细胞（rods）与视锥细胞（cones），二者分别负责暗光视觉与亮光视觉。相较于视杆细胞，目前学界对视锥细胞亚型间的基因表达差异仍知之甚少。本研究采用基于微滴的技术手段获取单细胞转录组（single-cell transcriptome）数据，以解析成年斑马鱼光感受器亚型间的基因表达多样性程度。研究通过两种转基因斑马鱼品系Tg(rho:EGFP)ja2Tg与Tg(gnat2:EGFP)ja23Tg富集光感受器细胞群体：前者可在视杆细胞中表达绿色荧光蛋白（GFP），后者可在所有视锥细胞亚型中表达GFP。通过对单细胞转录组数据的分析，本研究发现：除斑马鱼经典的四类视锥细胞亚型（紫外敏感、蓝敏感、绿敏感与红敏感型）外，腹侧视网膜（ventral retina）中还存在表达红移视蛋白旁系同源基因opn1mw4与opn1lw1的绿敏感与红敏感视锥细胞亚群。本研究为后续探索视锥细胞亚型间的分子差异如何影响光感受器功能的相关研究奠定了基础。实验设计概述：从两种转基因斑马鱼Tg(rho:EGFP)ja2Tg与Tg(gnat2:EGFP)ja23Tg中分离得到的GFP阳性细胞被合并为一个样本，同时样本中也包含了少量GFP阴性细胞。