Using reciprocally retained gene families to detect whole-genome multiplications in plants

Traces of ancient whole-genome multiplications (WGMs) have been observed all over the plant kingdom and have been associated with various evolutionary processes, such as increased evolvability, speciation, adaptation to changing environments, domestication and the origin of evolutionary novelties. However, understanding the impact of WGMs on plant evolution requires accurate detection of WGM events, which is challenging because of rapid signal erosion due to genome rearrangements, sequence divergence and the occurrence of additional large- and small-scale duplications.

Here, we investigate whether reciprocally retained gene families, i.e. gene families that preferentially expand through WGM and rarely exhibit small-scale duplications, can be used as WGM markers in angiosperms. Using stochastic birth-death modeling of gene families' gene count profiles across species to test for WGM presence or absence, we demonstrate that strongly reciprocally retained gene families have higher power to detect true WGMs and to reject false WGMs than non-reciprocally retained gene families.

Although none of the reciprocally retained gene families is a perfect WGM marker on its own, we show that using an extended set of such families as input for birth-death and $K_{\text{S}}$ distribution modeling approaches leads to better WGM detection performance than using entire genomes. A pipeline to use reciprocally retained gene families for $K_{\text{S}}$ distribution-based WGM inference in angiosperms has been implemented in ksrates v2.0.