Genomic insights into host–Endozoicomonadaceae cophylogeny

The congruence between host and symbiont phylogenies reflects the evolutionary links among ecologically important interactions. As potential key symbionts, the members affiliated to the family <i>Endozoicomonadaceae</i> have previously been investigated for the cophylogenetic relationship with their hosts using their 16S rRNA gene sequences. However, this approach neglects the genomic features of symbionts that may influence the long-term associations between <i>Endozoicomonadaceae</i> members and their hosts. Here, we collected available high-quality genomes of <i>Endozoicomonadaceae</i> from diverse hosts and investigated their genomic features, including genome size, phages, insertion elements and the composition of functional genes. We also tested the host<i>-Endozoicomonadaceae</i> cophylogeny and examined the correlation between the cophylogenetic squared residuals and the genomic features of <i>Endozoicomonadaceae</i> members. Our results revealed a cophylogenetic pattern between members of the <i>Endozoicomonadaceae</i> family and their various hosts. Moreover, we found that the investigated genomes of <i>Endozoicomonadaceae</i> members were differentially eroded by phages and insertion elements. Additionally, <i>Endozoicomonadaceae</i> members with smaller, more eroded genomes tended to exhibit lower cophylogenetic residuals with their hosts. Gene function analysis further revealed that <i>Endozoicomonadaceae</i> members with closer associations with their hosts carried specific genes related to infection processes and host-symbiont interactions. This study suggests that the genomic features of <i>Endozoicomonadaceae</i> members may influence long-term host<i>-Endozoicomonadaceae</i> intimate associations.