Data for "Metagenomic analyses reveal three supergroups of Wolbachia in a single genus of feather-feeding lice (Penenirmus)" by Ember B. Clodfelter, Jorge Doña, Kimberly K. O. Walden, and Kevin P. Johnson

Abstract: Insects with nutritionally limited diets often harbor bacterial endosymbionts that supplement their nutritional requirements. However, not all interactions between bacteria and insects are mutually beneficial. <i>Wolbachia</i> is a genus of bacteria that frequently causes cytoplasmic incompatibility and other reproductive parasitic effects on many of its arthropod hosts. In nematodes and some insects, however, <i>Wolbachia</i> is a nutritional mutualist. A lineage of <i>Wolbachia</i> closely related to mutualist strains has previously been identified in parasitic lice, including the louse genus <i>Penenirmus </i>(Ischnocera), which specializes in feeding on feathers. In this study, we used genome-resolved metagenomics to examine the diversity of <i>Wolbachia</i> across the genus <i>Penenirmus</i>, with a focus on evidence of long term associations with their hosts, which could indicate a mutualistic relationship. Phylogenomic analysis of over 100 genes from <i>Wolbachia</i> provided a well-resolved phylogeny of this bacterial genus. Across diverse species of the louse genus <i>Penenirmus,</i> genome-resolved metagenomic assemblies of <i>Wolbachia</i> from these insects revealed the presence of three different supergroups (B, F, and V). Supergroup V had not previously been known from lice. Cophylogenetic analysis revealed significant congruence between the <i>Wolbachia</i> and louse trees, although some branches showed incongruence.The <i>Wolbachia</i> in <i>Penenirmus </i>species from supergroups F and B showed evidence of potential mutualism by having long branches, cophylogenetic congruence with their louse hosts, and comparatively smaller genome sizes. Long branch attraction may be affecting the phylogenetic position of two lineages of <i>Wolbachia</i>, but the relative position of all other samples was comparatively stable.