Fig. 3

Functional characterization of the methane-oxidizing endosymbiont clades and influences of TEs on clade-specific functional differentiation. a Venn diagram showing numbers of orthologous genes shared and unique across the endosymbiont clades. b Box plot showing nonsynonymous to synonymous polymorphisms (pN/pS) in the core genes and the clade-specific genes in seep and vent populations. c COG terms enriched in the orthologous core and clade-specific genes. d Heatmap showing the percentage of environmental-related orthologs within the three clades. e Box plots showing gene density and transposase density in the 3-kb sequences flanking the core and clade-specific genes. f Synteny analysis of the scaffold regions around a clade-specific gene (here, sulfite exporter TauE/SafE family protein and the copper efflux pump cusCBA) in the three clades (C1.1, C2.1, and C3.1), showing that the insertion of a transposase results in the disruption, rearrangement, and non-functionalization of the corresponding gene. g Synteny analysis of the scaffold regions around clade-specific genes inserted by larger transposon carrying cargo genes (here, the mer operon)