<i>Fugacium</i> Spliced Leader Genes Identified from Stranded RNA-Seq Datasets

• Main Authors: Yue Song, Bahareh Zaheri, Min Liu, Sunil Kumar Sahu, Huan Liu, Wenbin Chen, Bo Song, David Morse
• Format: Article
• Language: English
• Published: MDPI AG 2019-06-01
• Series: Microorganisms
• Subjects: dinoflagellates; <i>Symbiodinium</i>; <i>Fugacium</i>; <i>trans</i>-splicing; spliced leader
• Online Access: https://www.mdpi.com/2076-2607/7/6/171

<i>Trans</i>-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 <i>Fugacium kawagutii</i> 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 <i>trans</i>-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 <i>F. kawagutii</i> SL genes to supplement our understanding of <i>trans</i>-splicing.