G-quadruplexes in genomes of viruses infecting eukaryotes or prokaryotes are under different selection pressures from hosts

G-quadruplexes in viral genomes can be applied as the targets of antiviral therapies, which has attracted wide interest. However, it is still not clear whether the pervasive number of such elements in the viral world is the result of natural selection for functionality. In this study, we identified putative quadruplex-forming sequences (PQSs) across the known viral genomes and analyzed the abundance, structural stability, and conservation of viral PQSs. A Viral Putative G-quadruplex Database (http://jsjds.hzau.edu.cn/MBPC/ ViPGD/index.php/home/index) was constructed to collect the details of each viral PQS, which provides guidance for selecting the desirable PQS. The PQS with two putative G-tetrads (G(2)-PQS) was significantly enriched in both eukaryotic viruses and prokaryotic viruses, whereas the PQSs with three putative G-tetrads (G(3)-PQS) were only enriched in eukaryotic viruses and depleted in prokaryotic viruses. The structural stability of PQSs in prokaryotic viruses was significantly lower than that in eukaryotic viruses. Conservation analysis showed that the G(2)-PQS, instead of G(3)-PQS, was highly conserved within the genus. This suggested that the G(2)-quadruplex might play an important role in viral biology, and the difference in the occurrence of G-quadruplex between eukaryotic viruses and prokaryotic viruses may result from the different selection pressures from hosts. Copyright (C) 2021, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Limited and Science Press. All rights reserved.

Automated summary

G-quadruplexes in viral genomes can be targeted for antiviral therapies. This study identified putative quadruplex-forming sequences (PQSs) in viral genomes and analyzed their abundance, structural stability, and conservation. A database was constructed to collect details of each viral PQS. The results showed an enrichment of G(2)-PQS in both eukaryotic and prokaryotic viruses, while G(3)-PQS was only enriched in eukaryotic viruses and depleted in prokaryotic viruses. Structural stability of PQSs was lower in prokaryotic viruses compared to eukaryotic viruses.