Transposable elements (TEs) are pervasive components of eukaryotic genomes and major drivers of genome evolution, yet their contribution to cell-type-specific regulatory landscapes remains poorly understood, particularly in non-model marine invertebrates. Here, we integrated single-cell RNA sequencing with pseudo-aligned TE expression profiling to examine how TE transcription relates to cell type identity in the reef-building coral Acropora hemprichii. We constructed a cell atlas comprising 4,716 cells across eight major cell types. Notably, TE expression alone was sufficient to accurately resolve all major cell types, indicating that cell-type-specific transcriptional states are robustly reflected in TE activity patterns. We identified 9,759 expressed TEs, of which 333 exhibited strong cell-type-specific activity. These differentially expressed TE features were associated with nearby expressed genes and transcription factor loci, suggesting a relationship between cell-type-specific TE activity and local gene regulatory programs. Genes associated with cell-type-specific TEs were enriched for core coral physiological processes, including calcification, metabolite transport, and symbiosis-related functions. Together, these findings indicate that TE transcription is structured along coral cell-type identity and physiological specialization. Our study provides a single-cell-resolved framework for investigating TE-gene relationships in early-diverging metazoans and a community resource for future functional interrogation in reef-building corals.
Zhong, H., Konciute, M. K., Hu, J., Menzies, J., Cui, G., Aranda, M.
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