  Measuring gene expression simultaneously in both hosts and symbionts offers a
powerful approach to explore the biology underlying species interactions. Such
dual or simultaneous RNAseq approaches have primarily been used to gain insight
into gene function in model systems, but there is opportunity to expand and
apply these tools in new ways to understand ecological and evolutionary
questions. By incorporating genetic diversity in both hosts and symbionts and
studying how gene expression is correlated between partner species, we can gain
new insight into host-symbiont coevolution and the ecology of species
interactions. In this perspective, we explore how these relatively new tools
could be applied to study such questions. We review the mechanisms that could
be generating patterns of cross-species gene coexpression, including indirect
genetic effects and selective filters, how these tools could be applied across
different biological and temporal scales, and outline other methodological
considerations and experiment possibilities.
