背景:对Euglenida中核内含子的研究不足。本研究旨在通过识别Euglenagracilis中的大量内含子来研究Euglenida中的核内含子(E.gracilis),包括顺式剪接的常规和非常规内含子,以及交叉剪接的外突。我们还检查了这些内含子的序列特征。
结果:共鉴定出28,337个内含子和11,921个外端。常规和非常规内含子具有不同的剪接位点特征;前者是典型的GT/C-AG剪接位点,而后者能够与其末端序列形成结构化基序。我们观察到短内含子对规范的GT-AG内含子具有偏好。值得注意的是,普通E.gracilis中的常规内含子和反离子表现出明显的富含胞苷的聚嘧啶束,与在其他生物体中观察到的富含胸苷的区域相反。此外,E.gracilis中的SL-RNA,以及其他反式剪接物种,可以与相应的U6形成一个最近发现的主题,称为扩展的U6/5\'ss双工。我们还描述了一种新型的可变剪接模式。确定了该原生生物中内含子的串联重复序列,它们的含量与人类相当。
结论:我们的发现突出了E.gracilis内含子的独特特征,并提供了对这些内含子剪接机制的见解,以及Euglenida的基因组学和进化。
BACKGROUND: Nuclear introns in Euglenida have been understudied. This study aimed to investigate nuclear introns in Euglenida 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 examined 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; the former harbour canonical GT/C-AG splice sites, whereas the latter are capable of forming structured motifs with their terminal sequences. We observed that short introns had a preference for canonical GT-AG introns. Notably, conventional introns and outrons in E. gracilis exhibited a distinct cytidine-rich polypyrimidine tract, in contrast to the thymidine-rich tracts observed in other organisms. Furthermore, the SL-RNAs in E. gracilis, as well as in other trans-splicing species, can form a recently discovered motif called the extended U6/5\' ss duplex with the respective U6s. We also describe a novel type of alternative splicing pattern in E. gracilis. The tandem repeat sequences of introns in this protist were determined, and their contents were comparable to those in humans.
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.