Irina V Poverennaya1,2, Nadezhda A Potapova3,4, Sergey A Spirin5,6,7. 1. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia. ipoverennaya@gmail.com. 2. Institute of Mathematical Problems of Biology RAS-The Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia. ipoverennaya@gmail.com. 3. Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia. 4. Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia. 5. Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Moscow, Russia. 6. Federal Science Center System Research Institute of the Russian Academy of Sciences, Moscow, Russia. 7. National Research University Higher School of Economics, Moscow, Russia.
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.
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 EIF1AXhuman 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.
Authors: Stepan V Denisov; Georgii A Bazykin; Roman Sutormin; Alexander V Favorov; Andrey A Mironov; Mikhail S Gelfand; Alexey S Kondrashov Journal: Genome Biol Evol Date: 2014-05-14 Impact factor: 3.416