Splice site diversity and abundance of non-canonical introns in diplonemids (Diplonemea, Euglenozoa)

Abstract

Non-coding introns are a unifying feature of protein-coding genes in virtually all extant eukaryotes, with most lineages following the canonical intron structure. However, euglenozoans, unicellular flagellates that include free-living euglenids, human pathogenic kinetoplastids, and highly diverse and abundant marine diplonemids, are a notable exception. Euglenozoan genomes range from extremely intron-poor kinetoplastids to euglenid genomes containing both canonical and non-canonical introns. Here, we present a comprehensive analysis of splice sites and spliceosomal components in six species of understudied diplonemids. All diplonemids examined contain a nearly complete set of spliceosomal snRNP components indicating the presence of a functional U2-type spliceosome. However, the majority of introns in the hemistasiid diplonemids Artemidia motanka and Namystynia karyoxenos are non-canonical and lack conserved GT-AG terminal dinucleotides typical for U2-type introns. These non-canonical introns are capable of extensive base pairing, which brings intron ends into close proximity. Thus, while the splicing apparatus is conserved in diplonemids, the splice sites are highly variable among individual species.