Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity ofClytiaMedusa Cell Types

Abstract

We present an organism-wide, transcriptomic cell atlas of the hydrozoan medusa Clytia hemisphaerica, and determine how its component cell types respond to starvation. Utilizing multiplexed scRNA-seq, in which individual animals were indexed and pooled from control and perturbation conditions into a single sequencing run, we avoid artifacts from batch effects and are able to discern shifts in cell state in response to organismal perturbations. This work serves as a foundation for future studies of development, function, and plasticity in a genetically tractable jellyfish species. Moreover, we introduce a powerful workflow for high-resolution, whole animal, multiplexed single-cell genomics (WHAM-seq) that is readily adaptable to other traditional or non-traditional model organisms.

Functional modules within a distributed neural network control feeding in a model medusa

“…They also have regenerative capacity, a likely feature of ancestral nervous systems (Tanaka and Ferretti, 2009). Clytia have remarkable abilities to regenerate and recover behaviorally following injury (Kamran et al, 2017;Sinigaglia et al, 2020), and also are continuously integrating newborn neurons into their nervous system without disrupting organismal function (Chari et al, 2021). The local network interactions and modular systems that we have described here may facilitate such growth and repair.…”

Past, present and future of Clytia hemisphaerica as a laboratory jellyfish

“…Until recently, the diversity of different cell types comprising the Clytia jellyfish was underexplored. A significant addition to available resources is a cell type atlas documenting the presence, distribution and transcriptomes of 36 distinct cell types (Chari et al, 2021). This cell atlas was derived from analysis of single cell transcriptome data (scRNAseq) combined with in situ hybridisation to localize the expression of marker genes.…”

“…In female medusae, daily batches of small oocytes grow from around 50µm diameter to the full size of around 180 µm ready for the spawning cue Jessus et al 2020;Figure 2A). The four gonads hang as pouches beneath the medusa bell, with the gonad gastrodermis derived from localized thickening of the radial canals and made up of specialized digestive-absorptive and secretory cell types (Figure 2A, D) (Chari et al, 2021).…”

“…As in other hydrozoan jellyfish, two nerve rings running around the bell margin play a central role in integrating sensory inputs to coordinate behavioural responses, while subpopulations of neural cells also occupy epidermal and gastrodermal layers of the manubrium and gonads. Analysis of scRNAseq data (Chari et al, 2021) revealed at least 12 mature neural cell types expressing different neuropeptides, whose precise morphologies, locations and roles mainly remain to be determined. A recent pioneering functional study shows that RFamide-expressing neurons in the subumbrella mediate the oriented flexing of the bell that brings prey captured by the tentacle to the mouth (Weissbourd et al, 2021).…”

The single-cell transcriptional landscape of the axolotl

“…To study typical thyroid hormone-induced cell-type shifts and perturbations, we adopted the L1 distance to determine the gene perturbation of newly generated cell types in metamorphosed skin 61 . The most noticeable difference was observed in skin (Figure 4B).…”