Is there any intron sliding in mammals?

Abstract

Background Eukaryotic protein-coding genes consist of exons and introns. Exon–intron borders are conserved between species and thus their changes might be observed only on quite long evolutionary distances. One of the rarest types of change, in which intron relocates over a short distance, is called "intron sliding", but the reality of this event has been debated for a long time. The main idea of a search for intron sliding is to use the most accurate genome annotation and genome sequence, as well as high-quality transcriptome data. We applied them in a search for sliding introns in mammals in order to widen knowledge about the presence or absence of such phenomena in this group. Results We didn’t find any significant evidence of intron sliding in the primate group (human, chimpanzee, rhesus macaque, crab-eating macaque, green monkey, marmoset). Only one possible intron sliding event supported by a set of high quality transcriptomes was observed between EIF1AX human and sheep gene orthologs. Also, we checked a list of previously observed intron sliding events in mammals and showed that most likely they are artifacts of genome annotations and are not shown in subsequent annotation versions as well as are not supported by transcriptomic data. Conclusions We assume that intron sliding is indeed a very rare evolutionary event if it exists at all. Every case of intron sliding needs a lot of supportive data for detection and confirmation.

The Evolution of Hemocyanin Genes in Caenogastropoda: Gene Duplications and Intron Accumulation in Highly Diverse Gastropods

“…The obtained phylogenies of caenogastropod hemocyanins are in accordance with the currently accepted systematic relationships of the four groups Muricidae, Littorinida, Cerithiida and Ampullariida (Fig. 2; Bouchet et al 2017;Ponder et al 2019). The phylogenies obtained by maximum likelihood and MrBayes both reveal that the multiple hemocyanin genes from different analyzed species resulted from independent gene duplications that occurred after the diversification of Caenogastropoda into Ampullariida, Cerithiida and Hypsogastropoda (orange arrows in Fig.…”

“…Positions of nearby FU-internal introns within the analyzed hemocyanin genes of Caenogastropoda vary by at least six nucleotides (Supplement 2). Furthermore, intron sliding most likely contributes little to gene structure evolution (Poverennaya et al 2020 ; Stoltzfus et al 1997 ). It should be noted that the presence of some introns within an ancestor cannot be assessed because the two possible scenarios would have taken the same number of evolutionary steps (smaller arrows in a hypothetical gene precursor, Fig.…”

“…Gene duplications, as we have identified for hemocyanins in Tectipleura and Caenogastropoda (Fig. 3), play a major role in genomic complexity and evolution (Magadum et al 2013;Ohno 1970). They are a driving force in organismal diversity (Lynch and Conery 2000) and can promote adaptation (Qian and Zhang 2014).…”

“…Additionally, we characterized hemocyanins from Littorina saxatilis, a species that belongs to the same large group of Hypsogastropoda as the Muricidae R. venosa and N. lapillus but does not belong to the siphonate clade (Fig. 2; Ponder et al 2019).…”

“…5Maximum parsimony scenario of exon-intron architecture evolution within gastropod hemocyanins. The phylogenetic tree on the left shows the relation of gastropod species with known hemocyanin gene architectures(Ponder et al 2019). For groups of Apogastropoda, the number of included species according to the WoRMS Editorial Board (2020) is also shown.…”