Fig. 1: Phylogenomic relationships and genome characteristics of the Endozoicomonadaceae family.

All genomes, MAGs and SAGs shown here are available on NCBI¹²⁶, IMG¹¹⁸ or RAST¹¹⁷ (accessed March 2024) and, according to GTDB-tk classification¹²¹, belong to the family Endozoicomonadaceae (N = 50) or Zooshikellaceae (N = 4). All genomes, MAGs, and SAGs shown here have an overall quality score (% Completeness–5\(\times\) % Contamination), above 50%¹²⁷. Three genomes of the family Hahellaceae serve as an outgroup to root the tree (Hahella ganghuensis DSM 17046^T, H. chejuensis KCTC 2396^T, and Allohahella marinimesophila JCM 17555^T). The phylogenomic tree was calculated using the SpeciesTreeBuilder version 0.1.4 application with the function ‘Insert Set of Genomes into Species Tree’ of the DOE Systems Biology Knowledgebase (KBase) online platform¹¹⁹ after annotating the genomes with Prokka¹²² within KBase. Sequences were aligned based on a multiple sequence alignment using a set of 49 core clusters of orthologous groups (COGs) of proteins. The FastTree2 algorithm¹²³ was used with the maximum likelihood (ML) method and Jukes–Cantor evolutionary model with a CAT approximation to generate a tree with 1000 repetitions to estimate bootstrap support values¹²³. Filled circles on the branches indicate that the respective nodes have a bootstrap value above 70%. Strains highlighted in blue belong to the family Endozoicomonadaceae, while those in yellow represent the family Zooshikellaceae, as indicated at the corresponding nodes. Known parasitic strains are marked with a red asterisk next to their names and genome accession numbers. Vertical bars next to the tree indicate Endozoicomonas clade A and clade B. Endozoicomonadaceae and Zooshikellaceae origin, genome sizes, GC contents (%) and their secondary metabolite encoding biosynthetic gene clusters (BGCs) are plotted next to the tree. BGCs were annotated with the antiSMASH 7.0 bacterial version online platform¹²⁴. The category ‘Other’ BGCs refers to BGCs that appear only once among all genomes. MAG metagenome assembled genome, SAG single amplified genome, RiPP ribosomally synthesized and post-translationally modified peptide products, NRPS non-ribosomal peptide synthetase, CDPS cyclodipeptide synthase, NAGGN N-acetylglutaminylglutamine amide, PKS polyketide synthase. More detailed information on genome quality, general genome features, and BGC annotations can be found in Supplementary Data 1–3.