Symbionts
We initially expected that symbiont gene expression would primarily depend on its own abundance within the host. Instead, in bothCladocopium and Durusdinium , gene expression was similar when the genus was either the overwhelming majority or minority, but was highly distinct when the relative proportion of the two genera were close to equal (codominant state, Fig 1). Functional analysis of the codominant state revealed upregulation of translation and photosynthesis machinery in both symbiont genera (Fig. 2, 3). Association between high growth rate and high concentrations of ribosomes has been demonstrated in a variety of organisms, including multicellular plants, green algae (Giordiano et al., 2015), insects, crustaceans (Elser et al., 2003), bacteria (Bosdriez et al., 2015), and yeast (López-Maury et al., 2008). We therefore believe that the observed functional signal indicates higher growth rate in both symbiont genera in the codominant state.