Intron sliding and length variability of genes enriched of phase 1 long introns

I. V. Poverennaya ; D. D. Gorev ; T. V. Astakhova ; I. I. Tsitovich ; V. V. Yakovlev ; M. A. Roytberg

Matematičeskaâ biologiâ i bioinformatika, Tome 12 (2017) no. 2, pp. 302-316.

Résumé

Due to high mutagenesis of intron sequences, intron evolution is usually considered in terms of evolution of exon-intron structures (EIS). The shifting of intron over short distances (rare evolutionary event called intron sliding) could lead to the change of intron phase, i.e. the intron position relative to the open reading frame. Here we analyze the EIS from four datasets of eukaryotic orthologues in order to find out the preferable choice of intron phase during sliding and to study the correlation between orthologous intron lengths. To identify the orthologous introns we have constructed the alignments of EIS of orthologous genes. Several sliding events with intron phase change were revealed from the analysis; however, our initial hypothesis that in the process of sliding introns prefer to change its phase to $0$ more frequently, was not been confirmed. Nevertheless, it is necessary to expand the analysis on a larger dataset for making a proper conclusions. Despite high variability of intron length, some taxonomic groups share the similar length values. Moreover, some length conservation could be observed if instead of intron length L we consider a normalized length $N = (L-A)/A$, where $A$ is an average length within an orthologous intron group. E.g. for ptprd genes of birds ($28$ species) the normalized value is in the interval $(-0.15, 0.15)$ for $85.2 \%$ of introns what is significantly higher than the values for random lengths set in accordance with the intron lengths distribution. That length “conservation” leads us to the question what intron length was in the ancient introns.

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