A single-cell transcriptome atlas of the maturing zebrafish telencephalon

Abstract

The zebrafish telencephalon is composed of highly specialized subregions that regulate complex behaviors such as learning, memory, and social interactions. The transcriptional signatures of the neuronal types in the telencephalon and the timeline of their emergence from larva to adult remain largely undescribed. Using an integrated analysis of single-cell transcriptomes of approximately 64,000 cells obtained from 6 days post-fertilization (dpf), 15 dpf, and adult telencephalon, we delineated nine main neuronal types in the pallium and eight in the subpallium and nominated novel marker genes. Comparing zebrafish and mouse neuronal types revealed both conserved and absent types and marker genes. Mapping of cell types onto a spatial larval reference atlas created a resource for anatomical and functional studies. Using this multi-age approach, we discovered that while most neuronal subtypes are established early in the 6 dpf fish, some emerge or expand in number later in development. Analyzing the samples from each age separately revealed further complexity in the data, including several cell types that expand substantially in the adult forebrain and do not form clusters at the larval stages. Together, our work provides a comprehensive transcriptional analysis of the cell types in the zebrafish telencephalon and a resource for dissecting its development and function.

Molecular logic of neuromodulatory systems in the zebrafish telencephalon

“…4E, F). While these clusters expressed eomesa , we did not detect emx2 at significant levels, consistent with another single-cell sequencing study that failed to detect cell types co-expressing eomesa and emx2 37 . While cell types associated with Dp, Dl or Dm were organized in distinct neighborhoods in UMAP space, clusters associated with Dc were either adjacent to Dm-related clusters or interspersed with the clusters representing Dl (Fig.…”

“…For example, neurons could be identified by the expression of snap25a 29 and further subdivided into GABAergic and glutamatergic cells using the marker genes slc32a1 and slc17a6a 30,31 . Ependymoglial cells were identified by expression of gfap 32 , oligodendrocyte precursor cells (OPCs) by olig1 33 , differentiating oligodendrocytes by gpr17 34 , and mature oligodendrocytes by mbpa 35 , all consistent with previous results from zebrafish 28,36,37 and other species 27,38,39 . We also found a few cells with characteristic signatures of habenular neurons ( kiss1 + / gng8 + ), presumably because the dissected tissue contained parts of the habenula.…”

“…The expression domain of pvalb7 has previously been localized to the posterolateral edge of the dorsal pallium, adjacent to the region described as Dp in the atlas. This area has been proposed to be part of an extended olfactory integration complex 37,47 .…”

Conservation and Diversification of Pallial Cell Types across Vertebrates: An Evo-Devo Perspective

“…Furthermore, Satb2, which is generally thought of as an isocortical upper layer (callosal) marker, has been shown to be transiently expressed in PT neurons during embryonic development and necessary for CST formation [Leone et al, 2015]. FezF2, Ctip2, and Sox5 are expressed in areas of the pallium with extratelencephalic projections in several vertebrates including lamprey, zebrafish, amphibians, and amniotes [Tosches et al, 2018;Hodge et al, 2019;Lamanna et al, 2022;Woych et al, 2022;Pandey et al, 2023]. It is likely that the core transcriptional network of the generic PT-type neuron was inherited by mammals through evolution, and the CST specificity probably evolved with further changes in the interactive regulation of these transcription factors, which demonstrates yet another case of diversification and added functionality.…”

“…Thus, transcriptomics is a powerful way of interrogating evolutionary relationships. With the advent of scRNAseq, there has been a wealth of data generated on molecular expression in adult pallial structures in several vertebrate species [Tosches et al, 2018;Hodge et al, 2019;Yao et al, 2021;Hain et al, 2022;Lamanna et al, 2022;Woych et al, 2022;Pandey et al, 2023]. The overarching impression seems to be that when considering at the level of the pallium, comparison of expression patterns of transcription factors (terminal selectors) and effector genes which determine cell-type identity and their molecular phenotype, respectively, all pallial (cortical/nuclear) ENs are derived from ancestral cell types established at the dawn of vertebrates [Lamanna et al, 2022;Briscoe and Ragsdale, 2018;Suryanarayana et al, 2022c] and express genes associated with the core projection types (input/ output/IT).…”