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Open AccessArticle

Fugacium Spliced Leader Genes Identified from Stranded RNA-Seq Datasets

1
Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
2
BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
3
BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
4
State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
5
China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
6
Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, QC H1X 2B2, Canada
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Microorganisms 2019, 7(6), 171; https://doi.org/10.3390/microorganisms7060171
Received: 10 May 2019 / Revised: 27 May 2019 / Accepted: 5 June 2019 / Published: 11 June 2019
(This article belongs to the Special Issue Dinoflagellate Biology in the Omics Era)
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. View Full-Text
Keywords: dinoflagellates; Symbiodinium; Fugacium; trans-splicing; spliced leader dinoflagellates; Symbiodinium; Fugacium; trans-splicing; spliced leader
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MDPI and ACS Style

Song, Y.; Zaheri, B.; Liu, M.; Sahu, S.K.; Liu, H.; Chen, W.; Song, B.; Morse, D. Fugacium Spliced Leader Genes Identified from Stranded RNA-Seq Datasets. Microorganisms 2019, 7, 171.

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