Comparative Genomic Studies on the Evolution of Morphological Complexity

National Human Genome Research Institute

Investigators

Linked publications, trials & patents

Abstract

Genomic sequencing of non-bilaterian animal species has provided invaluable insight into the molecular innovations that have fueled the outbreak of diversity and complexity in the early evolution of animals. The cnidarians are organisms unified in a single phylum based on their use of cnidocytes (stinging cells) for capturing prey and defense from predators, and they occupy a key phylogenetic position as the sister group to bilaterian animals. Cnidarian genomes are remarkably similar to the human genome in terms of gene content and structure, and what makes these organisms particularly attractive for study is our observation that the genomes of cnidarians encode more homologs to human disease genes than do classic invertebrate models (1). We are leading efforts to establish selected cnidarians as new model organisms that have the potential to inform important questions in human biology and human health, laying the groundwork for translational studies focused on specific human diseases. To that end, we have sequenced and annotated the genome of Hydractinia, a colonial marine hydroid known for its extraordinary ability to regenerate its entire body throughout its lifetime, facilitated by its adult migratory stem cells, called i-cells (2). We conducted a detailed analysis of the genomic structure and gene content of two Hydractinia species, H. symbiolongicarpus and H. echinata, comparing them within an evolutionary framework alongside other cnidarian genomes. Most evolutionarily conserved single-copy orthologs were easily identified in these assemblies. Analyses of these whole-genome sequencing data have already provided valuable insights into the evolution of chromatin compaction and animal neurogenesis. Additionally, we generated and annotated a single-cell transcriptomic atlas for adult male H. symbiolongicarpus, identifying cell type markers for all major cell types, including key i-cell markers. Orthology analyses revealed that Hydractinia’s i-cells are highly enriched in genes common across animals despite Hydractinia having a higher proportion of phylum-specific genes compared to the 41 other animals in our analysis. This suggests that Hydractinia's stem cells and early progenitor cells utilize a toolkit shared with all animals, highlighting its potential as a model organism for studying stem cell biology and regenerative medicine. The genomic and transcriptomic resources developed will facilitate further research into the mechanisms underlying regeneration and self/non-self recognition. We also generated an updated Hydractinia single-cell atlas by integrating new datasets from fixed cells with previously published live-cell data, capturing over 47,000 cells from feeding polyps and stolon tissue (3). This expanded atlas refines major somatic cell lineages, including cnidocytes, neurons, gland cells, epithelial cells, and stem cells (i-cells), and identifies a novel population of putative immune cells. We validated all major cell types and several cell states by investigating spatial expression patterns of selected marker genes. Our analyses uncovered a previously undescribed neural subtype, two spatially distinct gland cell populations, a stolon-specific cell type, and a putative immune cell cluster. Additionally, we explored a complete Hydractinia cnidocyte trajectory with two distinct endpoints, supported by spatial marker gene expression reflecting the developmental progression of cnidoblasts. Subclustering of somatic i-cells revealed putative progenitor states and a potential population of true stem cells. This atlas significantly advances our understanding of Hydractinia cellular diversity and dynamics, generating new hypotheses and providing a valuable resource for the cnidarian research community and beyond. Given Hydractinia’s exceptional regenerative abilities and capacity to distinguish self from non-self, the availability of well-annotated multi-omic data and visualization tools is crucial for exploring the relationship between genomic and morphological complexity, the evolution of multicellularity, and the emergence of novel cell types. To that end, we developed the Hydractinia Genome Project Portal, a comprehensive resource providing genomic, transcriptomic, and proteomic datasets for two widely studied Hydractinia species. The Portal includes extensive sequence, structure, and functional annotations not available elsewhere, alongside interactive visualization tools such as genome browsers, a single-cell gene expression atlas, a protein structure viewer, and a custom BLAST implementation. We also demonstrated how structure-based deep learning methods like Deep Functional Residue Identification (DeepFRI) can enhance the functional annotation of previously unannotated i-cell (stem cell) markers. The Portal is freely accessible at https://research.nhgri.nih.gov/hydractinia, providing an essential resource for advancing the use of Hydractinia in biomedical research. Mnemiopsis. We also generated a proteome-scale dataset of predicted protein structures for the comb jelly Mnemiopsis leidyi, a ctenophore with complex cell types like neurons and muscle cells. Despite the genome being sequenced, a comprehensive dataset for the Mnemiopsis proteome was lacking, with few experimentally determined structures available. Recognizing the potential of such a dataset for advancing developmental biology, evolutionary biology, proteomics, and human health, we leveraged recent advances in protein structure prediction (specifically, AlphaFold) and NIH's Biowulf supercomputing resource to predict 15,333 Mnemiopsis structures representing the organism’s proteome (4). We demonstrated the utility of these predictions through comparisons with experimentally determined structures for the light-sensitive protein mnemiopsin 1 and the ionotropic glutamate receptor (iGluR). The availability of these structural predictions will enhance the use of non-bilaterian species like Mnemiopsis as powerful model systems for studying early animal evolution and human health. Genomic Structure. Conserved noncoding elements (CNEs) are DNA sequences outside of protein-coding genes that remain under purifying selection for hundreds of millions of years, primarily functioning as regulatory elements. In vertebrates, many CNEs act as enhancers controlling the expression of homeodomain transcription factors and other crucial genes for embryonic development. To extend our understanding of CNEs across the animal kingdom, we conducted a large-scale characterization in over 50 genomes from Cnidaria, Mollusca, and Arthropoda. We identified hundreds of thousands of CNEs, traced their temporal dynamics, and mapped their genomic distribution. Our findings reveal that CNEs consistently evolve around the same genes across Metazoa, particularly around homeodomain genes, other transcription factors, and genes involved in neural development. Additionally, we demonstrate that transposons are a significant source of CNEs, supporting previous observations in vertebrates and suggesting their pivotal role in shaping developmental gene regulatory mechanisms throughout animal evolution. This study enhances our understanding of the evolutionary dynamics of CNEs and their impact on gene regulation across diverse animal lineages (5). Gene Expression. Traditional gene expression analysis disrupts normal cell interactions, making animal models like zebrafish, which allow high-resolution visualization and genetic manipulation, quite valuable. However, methods like RNAseq require cell dissociation, which can alter transcriptional states. To address this, our collaborators at NICHD/DIR developed transgenic zebrafish lines for profiling endothelial gene expression while preserving native states using translating ribosome affinity purification techniques. These lines enable rapid mRNA isolation, and our analyses have revealed novel endothelial genes and signatures in different organs, providing powerful tools for studying gene expression changes during development, disease, or repair (6). 1. Maxwell, E.K. et al. BMC Evolutionary Biology 14: 212, 2014 2. Schnitzler, C.E. et al. Genome Res. 34: 498-513, 2024 3. Song, J. et al. bioRxiv, doi.org/10.1101/2025.06.03.657738, 2024 4. Moreland et al., Proteomics e2300397, 2024. 5. Gonzalez et al., Genome Biol. Evol. 16: evae052, 2024 6. Miller et al., Angiogenesis 28: 40, 2025