A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences

Schlub, Timothy E; Buchmann, Jan P; Holmes, Edward C

Simple Method to Detect Candidate Overlapping Genes . doi:10.1093/molbev/msy155 MBE movement protein, is overlapping. I870_gp1 is 665 codons long, is located on frame þ2, and is largely contained within the larger (1832 codon) I870_gp2 gene that encodes the enzymes necessary for virus replication (methyltransferase, endopeptidase, helicase, and polymerase) ( fig. 2A ). We calculated the distribution of expected ORF lengths on frames þ1 and þ2 using the codon permutation test. The distributions of these lengths are shown with the shading in figure 2B and C. The actual ORF lengths on frames þ1 and þ2 on the unpermuted I870_gp2 gene are represented by black dots on top of the theoretical distribution. For frame þ1, we observe 37 ORFs, all of which have lengths within expected ranges (P ¼ 0.92). A different picture is observed in frame 2þ. Although there are 62 ORFs, 61 of which have lengths within the expected range, there is a single ORF whose length far exceeds the expected distribution of lengths (P < 0.0001); this is correctly identified as I870_gp2. The synonymous mutation test produces similar results in this example.