Fig. 1: Comparison of gene “inversion” definitions and detection methods.

The two studies use different definitions of “gene inversion”. For clarity, we use “Gene Flip” to mean any change-of-orientation event. Gene flips have two subtypes resulting in a gene having a negative GC Skew (upper graphs) or a positive GC skew (lower graphs). The Merrikh and Zhang definitions agree in the first scenario (upper graphs), but conflict in the second (lower graphs). As both gene orientation and GC skew sign (±) are important considerations, there are four possible circumstances (numbered 1–4) indicated under the GC skew plots. In case 1, a natively leading strand gene (indicated by the positive GC skew) undergoes a flip resulting in a GC skew inversion. In 2, a natively lagging-strand gene undergoes a flip, also resulting in a GC skew inversion. In 3, a leading strand gene with a negative GC skew flips, resulting in a GC skew reversion. In 4, a lagging-strand gene with a negative GC skew flips, resulting a GC skew reversion.