Benchmark dataset of 27 overlapping genes with known genealogy.

(1)<p>gene overlaps described previously (see reference <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003162#pcbi.1003162-Rancurel1" target="_blank">[3]</a>).</p>(2)<p>additional overlaps collected for this study.</p>(3)<p>The function is that of the overlapping region of the protein; if it is not known, the field is left blank.</p>(4)<p>The NS2 proteins of <i>brevidensoviruses</i> and that of <i>densoviruses</i> are not homologous (they are encoded in different frames relative to NS1).</p>(5)<p>The <i>alphacarmotetravirus</i> polymerase and <i>machlomovirus</i> capsid have originated by horizontal transfer and thus the two corresponding overlaps are not part of the benchmark dataset, although we perform the same analyses on them than on other overlaps(see text).</p><p>Abbreviations: AAP, assembly-activating protein; dsRNA, double-stranded RNA; C-term, C-terminal; L, large envelope protein; MP, movement protein; NABP, nucleic-acid binding protein; NS, non-structural protein; NSs, non-structural protein of the small RNA segment; N-term, N-terminal; Pog, predicted overlapping gene; Pol, Polymerase; SAT, small alternatively translated protein; ssDNA, single-stranded DNA; ssRNA, single-stranded RNA (+, positive or −, negative); TGBp2, Triple Gene Block protein 2; TGBp3, Triple Gene Block protein 3; VP, viral protein.