Gene Gain and Loss Inform the Evolution of Cnidocytes and Lineage-Specific Traits in Cnidaria
ABSTRACT:
Cnidarians—the group of animals including jellyfish, sea anemones, and corals—are characterized by complex life histories, symbiotic relationships, and cnidocytes: specialized stinging cells unique to Cnidaria. Previous comparative genomic studies have highlighted the importance of gene gain and loss in the evolutionary origins of novel traits. Using genome-scale data from seventy-two species, in this research study we reconstructed the timing of gene family gain and loss throughout cnidarian evolution and characterized the functions of key bursts of gain and loss. Single-cell RNA sequencing (scRNA-seq) is an emerging technique that measures gene expression in individual cells. We integrated scRNA-seq datasets from five species: Hydra vulgaris, Aurelia coerulea, Xenia sp., Nematostella vectensis, and Acropora millepora, to examine the collective expression patterns of genes gained at key evolutionary nodes, such as the ancestor of all cnidarians, and to uncover the history of gene gain that led to the evolution and diversification of cnidocytes. Our analyses highlight a significant burst of gene gain in the lineage leading to sea anemones and corals, which is enriched in functions related to nutrient uptake, cell communication and adhesion, and signaling, possibly underpinning adaptations for symbiosis, a defining trait for this group. In endocnidozoans, a group of parasitic cnidarians with reduced morphological complexity, we observed significant losses in functions essential for free-living cnidarians such as immunity, cell communication, and development. Significant gains in cell localization, communication, and division occurring in the lineage leading to jellyfish and other related species are expressed in stem cells, possibly reflecting the increased biosynthetic demands of the free-swimming medusa life history stage. This study both identifies candidate genes that are potentially important for the evolution of characteristic traits in Cnidaria and outlines novel methods that can be used to better understand the evolution of other lineages.
The Hamel Center for Undergraduate Research provided funding for this project through a Summer Undergraduate Research Fellowship and a Research Presentation Grant. We acknowledge Sabrina Pankey and Hannah Pare as coauthors on this project. Additionally, we thank the members of Plachetzki Lab for providing suggestions on methodology and figures, Premise High-Performance Computing Cluster for access to computing resources, Dr. ZJ Dong for kindly providing Aurelia coerulea scRNA-seq data, and other research groups who have made their data publicly accessible.
Author and Mentor Bios
Olivia Tatro is from Moultonborough, New Hampshire, and graduated from UNH in May 2026 as a biology major and genetics minor. At UNH, she conducted research projects in both Adrienne Kovach's molecular ecology lab and Dave Plachetzki's comparative genomics lab. Olivia will continue her studies of cnidarians in Nat Clarke's lab at the University of Miami, where she will focus on studying the role of cell adhesion molecules in the formation of both battery complexes and synapses in the model jellyfish: Clytia hemisphaerica. &²Ô²ú²õ±è;
David Plachetzki is an associate professor in the Department of Molecular, Cellular, and Biomedical Sciences at the Â鶹app. With a focus on interdisciplinary work, Plachetzki combines molecular biology with computational genomics to study how complex traits such as the senses, microbiomes or defense mechanisms have evolved over millions of years. In addition to his lab work, Plachetzki conducts field research, collecting marine specimens through SCUBA diving expeditions in the Gulf of Maine, Caribbean and Galapagos Islands.
Copyright 2026 © Olivia Tatro
