Dinoflagellates are ecologically important marine phytoplankton whose remarkable adaptability has been linked to their unusual genomic organization and transcriptional regulation. To investigate the molecular basis underlying this adaptability, we generated a near chromosome-level genome assembly of the harmful algal bloom-forming dinoflagellate Amphidinium carterae using long-read sequencing and Hi-C technology and are currently advancing toward a telomere-to-telomere assembly.

Building upon this genomic resource, we integrated transcriptomics, active transcription profiling, and nascent RNA analyses to reconstruct the transcriptional landscape of A. carterae. We found that at least 70% of protein-coding genes undergo trans-splicing and possess conserved trans-splice acceptor sites. Furthermore, integrated genomic and transcriptomic evidence supports a transcription initiation model in which transcription preferentially originates from divergent strand-switch regions (dSSRs) associated with gene clusters, rather than from independent promoters of individual genes. These findings provide genome-wide evidence supporting the long-standing hypothesis of extensive polycistronic transcription and reveal a gene cluster-dependent transcriptional architecture in dinoflagellates.

Our results suggest that coordinated regulation of clustered genes may represent an efficient mechanism for transcriptional reprogramming and environmental responsiveness, providing new insights into the molecular basis of ecological adaptation in marine dinoflagellates under global environmental change.