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Single-cell analyses of tissue regeneration in two true jellyfish.

Overview

Authors: Yiqian Li1, Sean T S Law1, Wenyan Nong1, Wai Lok So1, Yichun Xie1, Thomas C N Leung2, Tse Ho Li2, Joyce Tse2, Ho Yin Yip1, Oli Jin3, Jordan Zhang3, Apple P Y Chui4, Kwok Fai Lau5, Akbar John6, Zhen-peng Kai7, William G Bendena8, Alexander Hayward9, Yingying Wei10, Ting Fung Chan2, Sai Ming Ngai2, Jerome H L Hui1
ORCID iDs: Yiqian Li, Sean T S Law, Yichun Xie, Thomas C N Leung, Joyce Tse, Ho Yin Yip, Jordan Zhang, Apple P Y Chui, Kwok Fai Lau, Akbar John, Zhen-peng Kai, William G Bendena, Alexander Hayward, Yingying Wei, Ting Fung Chan, Sai Ming Ngai, Jerome H L Hui
  1. School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong SAR, China
  2. School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
  3. Dovetail Genomics, Scotts Valley, CA, USA
  4. School of Life Sciences, Simon F.S. Li Marine Science Laboratory, The Chinese University of Hong Kong, Hong Kong SAR, China
  5. School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
  6. Sharjah Marine Science Research Centre, College of Marine Science and Aquatic Biology, University of Khorfakkan, Sharjah, United Arab Emirates
  7. School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
  8. Department of Biology, Queen's University, Kingston, Canada
  9. Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, UK
  10. Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China
Institutions: Chinese University of Hong Kong (Hong Kong SAR China); Dovetail Genomics (United States) (United States); University of Khorfakkan (United Arab Emirates); Shanghai Institute of Technology (China); Queen's University (Canada); University of Exeter (United Kingdom)
Journal: Molecular biology and evolution, volume 43, issue 6, article msag128
Dates: received 11 August 2025; accepted 11 May 2026; published online 29 May 2026; in print June 2026
Type: Research article · Language: English
License: CC BY-NC
Identifiers: DOI 10.1093/molbev/msag128 · PMID 42212572 · PMCID PMC13308536 · OpenAlex W7162771121
Open access: gold, a free copy (OpenAlex)
Status: empty repository
Categories: genetics / omics (modality), other (organism), cellular / molecular (subfield)
Methods: Smoothing, state filtering, decompositions
Keywords: cnidarians, lineage-specific genes, regeneration, single cell
MeSH: Regeneration*, Scyphozoa*, Animals, Single-Cell Analysis, Single-Cell Gene Expression Analysis (* major topic)
Topic: Marine Invertebrate Physiology and Ecology (Paleontology, Earth and Planetary Sciences), according to OpenAlex
Funding: Hong Kong Research Grant Council General Research Fund (14102224, 14103823); TUYF Charitable Trust; Collaborative Research Fund (C4015-20EF)
Citations: not cited yet (Europe PMC); 77 references in the paper

Abstract

The phylum Cnidaria is the outgroup of Bilateria and includes sea anemones, corals, hydroids, and jellyfish. Cnidarians play crucial ecological roles in marine ecosystems, including the formation of highly diverse and productive coral reefs, and acting as important predator and prey species. They are also well known for their remarkable regeneration capacities. Here, we report single-cell RNA sequencing of bell tissue remodeling/regeneration after amputation in two species of scyphozoans or “true jellyfish,” the Asian moon jelly, Aurelia coerulea, and the flame jellyfish, Rhopilema esculentum. We delineated 12 cell populations in Aurelia and Rhopilema and revealed their respective marker genes and enriched gene pathways. During this process, conserved transcription factor Otx, TFAP2A, Erg, NFIA, and Wnt/β-catenin signaling pathway genes were identified. Additionally, we discovered two conserved, sequentially activated patterns, with putative proliferative cells, gastrodermal cells, neural cells, and secretory gland cells modulated in the first phase, followed by cnidocytes in the second phase. Further comparison among cnidarian genomes identified a suite of lineage-specific scyphozoan genes, a subset of which were frequently significantly expressed in cnidocytes in both jellyfish species. Using powerful single-cell RNA sequencing approaches, this study elucidates the evolution of lineage-specific genetic networks and biological processes in true jellyfish, which remain comparatively poorly studied, and in particular provides key insights into the molecular pathways underlying their remarkable regenerative capacity.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Code

No file of the authors' code could be read here: it is described below, and read at its source.

fanny-bio/jellyfish.rg.scrna

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 61736b4134390253d831396a915d7a659d5c93f0, 3 December 2025
Size: 37 files, 0 scripts
Software Heritage: not archived
Found in: “Data availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
At the source: github.com/Fanny-bio/Jellyfish.rg.scRNA/tree/main

The paper's code and data availability statement is in the Data section.

Tracing map

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  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
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  • no match between paragraphs and code yet;
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Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data availability

The raw reads generated in this study have been deposited in the NCBI database under BioProject accession numbers PRJNA1229829 (PacBio HiFi and Omni-C reads of Aurelia), PRJNA1049062 (single-cell sequencing data of Aurelia), and PRJNA1045829 (single-cell data of Rhopilema). The genome and genome annotation files have been deposited in the Figshare dataset (https://figshare.com/s/f89fdf550cf68d97a541) and CUHK Research Data Repository (https://doi.org/10.48668/JVK8SW). The scripts used in this study can also be found at GitHub repository (https://github.com/Fanny-bio/Jellyfish.rg.scRNA/tree/main) and CUHK Research Data Repository.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 21 authors, 4 keywords, 5 MeSH terms, 3 funders, 77 references.

Cite

This paper

Li, Y., Law, S. T. S., Nong, W., So, W. L., Xie, Y., Leung, T. C. N., Li, T. H., Tse, J., Yip, H. Y., Jin, O., Zhang, J., Chui, A. P. Y., Lau, K. F., John, A., Kai, Z.-p., Bendena, W. G., Hayward, A., Wei, Y., Chan, T. F., . . . Hui, J. H. L. (2026). Single-cell analyses of tissue regeneration in two true jellyfish. Molecular biology and evolution, 43(6), msag128. https://doi.org/10.1093/molbev/msag128

BibTeX

@article{li2026single,
author = {Li, Yiqian and Law, Sean T S and Nong, Wenyan and So, Wai Lok and Xie, Yichun and Leung, Thomas C N and Li, Tse Ho and Tse, Joyce and Yip, Ho Yin and Jin, Oli and Zhang, Jordan and Chui, Apple P Y and Lau, Kwok Fai and John, Akbar and Kai, Zhen-peng and Bendena, William G and Hayward, Alexander and Wei, Yingying and Chan, Ting Fung and Ngai, Sai Ming and Hui, Jerome H L},
title = {{Single-cell analyses of tissue regeneration in two true jellyfish}},
journal = {Molecular biology and evolution},
year = {2026},
month = jun,
volume = {43},
number = {6},
pages = {msag128},
publisher = {Oxford University Press},
issn = {0737-4038},
doi = {10.1093/molbev/msag128},
url = {https://doi.org/10.1093/molbev/msag128},
pmid = {42212572},
pmcid = {PMC13308536}
}

RIS

TY - JOUR
AU - Li, Yiqian
AU - Law, Sean T S
AU - Nong, Wenyan
AU - So, Wai Lok
AU - Xie, Yichun
AU - Leung, Thomas C N
AU - Li, Tse Ho
AU - Tse, Joyce
AU - Yip, Ho Yin
AU - Jin, Oli
AU - Zhang, Jordan
AU - Chui, Apple P Y
AU - Lau, Kwok Fai
AU - John, Akbar
AU - Kai, Zhen-peng
AU - Bendena, William G
AU - Hayward, Alexander
AU - Wei, Yingying
AU - Chan, Ting Fung
AU - Ngai, Sai Ming
AU - Hui, Jerome H L
TI - Single-cell analyses of tissue regeneration in two true jellyfish
T2 - Molecular biology and evolution
J2 - Mol Biol Evol
PY - 2026
DA - 2026/06/01
VL - 43
IS - 6
SP - msag128
SN - 0737-4038
PB - Oxford University Press
DO - 10.1093/molbev/msag128
UR - https://doi.org/10.1093/molbev/msag128
LA - en
ER -

CSL-JSON

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