Heterogeneity of intron presence/absence in Olifantiella sp. (Bacillariophyta) contributes to the understanding of intron loss

Abstract

Although hypotheses have been proposed and developed to interpret the origins and functions of introns, substantial controversies remain about the mechanism of intron evolution. The availability of introns in the intermediate state is quite helpful for resolving this debate. In this study, a new strain of diatom (denominated as DB21-1) was isolated and identified as Olifantiella sp., which possesses multiple types of 18S rDNAs (obtained from genomic DNA; lengths ranged from 2,056 bp to 2,988 bp). Based on alignments between 18S rDNAs and 18S rRNA (obtained from cDNA; 1,783 bp), seven intron insertion sites (IISs) located in the 18S rDNA were identified, each of which displayed the polymorphism of intron presence/absence. Specific primers around each IIS were designed to amplify the introns and the results indicated that introns in the same IIS varied in lengths, while terminal sequences were conserved. Our study showed that the process of intron loss happens via a series of successive steps, and each step could derive corresponding introns under intermediate states. Moreover, these results indicate that the mechanism of genomic deletion that occurs at DNA level can also lead to exact intron loss.

Annotated 18S and 28S rDNA reference sequences of taxa in the planktonic diatom family Chaetocerotaceae

“…The short ones comprise spliceosomal introns ([59]; [60]) based on rRNA sequence details. Spliceosomal introns are generally found in eukaryotic protein-coding genes but have also been detected in the ribosomal genes of Ascomycetes [59], and now also of diatoms ([61]; this study). The two longer inserts at locations #14 and #15 exhibit the typical spliceosomal 5′-end (GTAATA and GTACGT, respectively), but their exact nature is not clear.…”

Species detection and delineation in the marine planktonic diatoms Chaetoceros and Bacteriastrum through metabarcoding: making biological sense of haplotype diversity

“…Clade Na12A3 could be due to intra‐individual variation in presence of such an intron, which is supported by forward and reverse Sanger reads of the reference sequence becoming illegible from the position of the intron onwards (Gaonkar et al ., ). Intraspecific variation in the presence of introns has been reported in other diatoms as well (Han et al ., ).…”

Determination of genetic variation within the <i>DYRK2</i> gene and its associations with milk traits in cattle

“…There have been some studies on DYRK2, but InDels are often neglected, particularly in introns and UTR (untranslated region) mutations (Maddika et al, 2009;Taira et al, 2012;Yang et al, 2016;Ju et al, 2020). Here, we identified InDel in introns, and there were insertion and deletion mutations as well (Hu et al, 2011;Liu et al, 2015). To the best of our knowledge, this is the first identification of a candidate gene, DYRK2, associated with milk traits in XJBC.…”