Unveiling the functional nature of retrogenes in dinoflagellates

TL;DR

This study explores how retrogenes in dinoflagellates function and contribute to stress responses and adaptation.

Contribution

The study provides new evidence of widespread functional retrogenes in dinoflagellates and their role in cellular processes.

Findings

Retrogenes are widespread in dinoflagellates and linked to stress-related processes like post-translational modifications and cell signaling.

Retrogenes are associated with symbiosis and toxin production, highlighting their role in adaptation.

Retrogenes show expression and codon patterns similar to protein-coding genes, indicating functional status.

Abstract

Retroposition is a gene duplication mechanism that uses RNA molecules as intermediaries to generate new gene copies. Dinoflagellates are proposed as an ideal model for exploring this process due to the tagging of retrogenes with DNA-encoded remnants of the dinoflagellate-specific splice-leader motif at their 5′ end. We conducted a comprehensive search for retrogenes in dinoflagellate transcriptomes to uncover their functional nature and the processes underlying their redundancy. We obtained a high-confidence set of hypothetical functional retrogenes widespread through the dinoflagellate lineage. Through annotations and gene ontology enrichment analysis, we found that the functional diversity of retrogenes reflects the most prevalent and active processes during stress periods, particularly those involving post-translational modifications and cell signalling pathways. Additionally, the significant presence of retrogenes linked to specific biological processes involved in symbiosis and toxin production underscores the role of retrogenes in adaptation. The expression profile and codon composition similar to protein-coding genes confirm the operational status of retrogenes and strengthen the idea that retrogenes recapitulate parental gene expression and function. This study provides new evidence supporting widespread gene retroposition across dinoflagellates and highlights the functional link of retrogenes with the core activity of the cell.

Figures