Using networks to analyze and visualize the distribution of overlapping genes in virus genomes

Abstract

Gene overlap occurs when two or more genes are encoded by the same nucleotides. This phenomenon is found in all taxonomic domains, but is particularly common in viruses, where it may increase the information content of compact genomes or influence the creation of new genes. Here we report a global comparative study of overlapping open reading frames (OvRFs) of 12,609 virus reference genomes in the NCBI database. We retrieved metadata associated with all annotated open reading frames (ORFs) in each genome record to calculate the number, length, and frameshift of OvRFs. Our results show that while the number of OvRFs increases with genome length, they tend to be shorter in longer genomes. The majority of overlaps involve +2 frameshifts, predominantly found in dsDNA viruses. Antisense overlaps in which one of the ORFs was encoded in the same frame on the opposite strand (−0) tend to be longer. Next, we develop a new graph-based representation of the distribution of overlaps among the ORFs of genomes in a given virus family. In the absence of an unambiguous partition of ORFs by homology at this taxonomic level, we used an alignment-free k-mer based approach to cluster protein coding sequences by similarity. We connect these clusters with two types of directed edges to indicate (1) that constituent ORFs are adjacent in one or more genomes, and (2) that these ORFs overlap. These adjacency graphs not only provide a natural visualization scheme, but also a novel statistical framework for analyzing the effects of gene- and genome-level attributes on the frequencies of overlaps.

Transcriptional analysis in bacteriophage Fc02 ofPseudomonas aeruginosarevealed two overlapping genes with exclusion activity

“…1700 nucleotides) includes upstream genes. The upstream transcript region includes two overlapped genes, olg 1 in frame +0 and olg 2 in frame +1 of the DNA forward strand(Lèbre and Gascuel, 2017, Muñoz-Baena and Poon, 2022) and two smaller ORFs not studied in this work. Interestingly olg1-olg2 overlapped region, in turn completely overlaps gene 10, and part of the 3’-end of ner -like gene, on the reverse strand.…”

“…In dsDNA viruses is frequent the incidence of overlapping genes, but these systems are often not well characterized. Either there is no proof that the genes involved are expressed, or their function is not clearly known(Muñoz-Baena and Poon, 2022, Schlub and Holmes, 2020). Three-gene overlapping configuration, like the one described here, is a very rare instance but is known to occur in phages (Fiddes and Godson, 1979).…”

“…In bacteria and their bacteriophages numerous cases of extensive overlapped genes have been described(Zehentner et al, 2020, Muñoz-Baena and Poon, 2022, Scherbakov and Garber, 2000). However, frequently the evidence provided is partial, the function of one or both overlapped genes is unknown or is not clear whether the corresponding mRNA is transcribed and translated into protein.…”

Transcriptional analysis in bacteriophage Fc02 of Pseudomonas aeruginosa revealed two overlapping genes with exclusion activity

“…In bacteria and their bacteriophages, numerous cases of extensively overlapped genes have been described (Scherbakov and Garber, 2000;Zehentner et al, 2020;Muñoz-Baena and Poon, 2022). However, frequently the evidence provided is partial, the function of one or both overlapped genes is unknown, or is not clear whether the corresponding mRNA is transcribed and translated into protein.…”

HexSE: Simulating evolution in overlapping reading frames

“…They have been documented across all taxonomic domains including bacteria, vertebrates and fungi (Pallejà et al, 2008; Ribrioux et al, 2008; Chung et al, 2007; Gerads and Ernst, 1998). OvRFs are particularly abundant in virus genomes and examples can be found in all Baltimore classes (Muñoz-Baena and Poon, 2022). In viruses, OvRFs may provide a mechanism to store more information in smaller genomes, to make purifying selection more efficient at removing deleterious mutations, or to facilitate the de novo creation of genes (Willis and Masel, 2018; Sabath et al, 2012; Belshaw et al, 2008; Krakauer and Plotkin, 2002; Chirico et al, 2010).…”