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 Endozoicomonadaceae 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 Endozoicomonadaceae members and their hosts. Here, we collected available high-quality genomes of Endozoicomonadaceae 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-Endozoicomonadaceae cophylogeny and examined the correlation between the cophylogenetic squared residuals and the genomic features of Endozoicomonadaceae members. Our results revealed a cophylogenetic pattern between members of the Endozoicomonadaceae family and their various hosts. Moreover, we found that the investigated genomes of Endozoicomonadaceae members were differentially eroded by phages and insertion elements. Additionally, Endozoicomonadaceae members with smaller, more eroded genomes tended to exhibit lower cophylogenetic residuals with their hosts. Gene function analysis further revealed that Endozoicomonadaceae 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 Endozoicomonadaceae members may influence long-term host-Endozoicomonadaceae intimate associations.