Unique features of conventional and nonconventional nuclear pre-mRNA introns in Euglena gracilis

Abstract

Abstract Background Nuclear precursor messenger RNA introns in Euglenida have been understudied. This study aims to address this question by identifying a large number of introns in Euglena gracilis (E. gracilis), including cis-spliced conventional and nonconventional introns, as well as trans-spliced outrons. We also examine the sequence characteristics of these introns. Results A total of 28,337 introns and 11,921 outrons were identified. Conventional and nonconventional introns have distinct splice site features with the former harbor the canonical GT/C-AG splice sites, whereas the latter are capable of forming structured motifs with their terminal sequences. We notice that short introns are observed to prefer the canonical GT-AG introns. Notably, conventional introns and outrons in E. gracilis exhibit a distinct cytidine-rich polypyrimidine tract, in contrast to a thymidine-rich one observed in other organisms. Furthermore, the SL-RNAs in E. gracilis, as well as in other trans-splicing species, can form, with the respective U6s, a recently discovered motif called the extended U6/5' ss duplex. We also describe a novel type of alternative splicing pattern in E. gracilis. Tandem repeat sequences of introns in this protist are also determined and their content is comparable to that in human. Conclusions Our findings highlight the unique features of E. gracilis introns and provide insights into the splicing mechanism of these introns, as well as the genomics and evolution of Euglenida.