Abstract
Trans-splicing mechanisms have been documented in many lineages that are widely distributed phylogenetically, including dinoflagellates. The spliced leader (SL) sequence itself is conserved in dinoflagellates, although its gene sequences and arrangements have diversified within or across different species. In this study, we present 18 Fugacium kawagutii SL genes identified from stranded RNA-seq reads. These genes typically have a single SL but can contain several partial SLs with lengths ranging from 103 to 292 bp. Unexpectedly, we find the SL gene transcripts contain sequences upstream of the canonical SL, suggesting that generation of mature transcripts will require additional modifications following trans-splicing. We have also identified 13 SL-like genes whose expression levels and length are comparable to Dino-SL genes. Lastly, introns in these genes were identified and a new site for Sm-protein binding was proposed. Overall, this study provides a strategy for fast identification of SL genes and identifies new sequences of F. kawagutii SL genes to supplement our understanding of trans-splicing.
Highlights
Dinoflagellates are a large group of ecologically important unicellular algae
The sequences of the spliced leader are conserved within each lineage but varies among different groups
Several lineages have more than one consensus spliced leader (SL) sequence; for example, euglenozoans can have as many as 14 SL sequences [6]
Summary
Dinoflagellates are a large group of ecologically important unicellular algae. Many members in this lineage play critical roles in marine ecosystems as primary producers, contributors to red tides, and symbionts of reef corals and other invertebrates. The sequences of the spliced leader are conserved within each lineage but varies among different groups. Different roles of trans-splicing have been proposed, which include translation regulation (enhancing or blocking), mRNA stabilization, 5 UTR sanitization, protein retargeting, as well as creating or destroying upstream open reading frames [3,4,5]. Despite the conservation of SL within this phylum, the arrangements of SL RNA genes are rather diverse. In these organisms, SL genes were clustered alone or mixed with 5S rRNA.
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