Genome sequencing and assembly
We sequenced the Polyplax lice pooled sample on one lane of Illumina HiSeq2000 (GeneCore, Heidelberg, Germany) using 2×100 paired-end reads. Read quality was checked using FastQC (Andrews, 2010) and quality trimming was performed using the BBtools package (https://jgi.doe.gov/data-and-tools/bbtools). The resulting dataset contained 309 892 186 reads. We used SPAdes assembler 3.10 (Bankevich et al., 2012) to build the assembly, implementing careful options and enabling mismatch corrections. To check for bacterial plasmid(s) we submitted the complete assembly (124 985 contigs) to the PlasmidFinder (Carattoli et al., 2014) with sensitivity set to three different thresholds (95%, 85%, and 60%). We identified bacterial contigs by blasting Snodgrassella alvi wkB2 genome against the assembly using custom blast in the program Geneious (Kearse et al., 2012). This procedure retrieved 39 contigs which were putatively assigned to Neisseriales and their origin was further confirmed by blast analyses of individual genes as specified below.
To sequence a complete Hoplopleura acanthopus lice metagenome, we employed Illumina MiSeq (GeneCore, Heidelberg, Germany) and Oxford-Nanopore (University of Urbana, Illinois, USA) technology. We constructed the Illumina library from the total DNA of 35 individuals and sequenced it in four runs of Illumina MiSeq using V2 500 cycle chemistry. We used the same procedure for quality checking and filtering as described for the Polyplax data set. The resulting number of reads was 34 406 078. We used high molecular weight DNA from 5 H. acanthopus as a template for Oxford-Nanopore sequencing on GridIONx5. The total number of reads was 1 653 194. The quality of Nanopore reads was checked using NanoPack tools (De Coster, D’Hert, Schultz, Cruts, & Van Broeckhoven, 2018) and quality filtering was performed using Filtlong (https://github.com/rrwick/Filtlong). To assemble theH. acanthopus metagenome, we employed a hybrid approach combining the Illumina and Nanopore data (for details see SupplementaryInformation/SupplementaryText).
We annotated genomes of both Neisseria -related symbionts using RAST (Aziz et al., 2008) and deposited them in GenBank under the accession numbers CP046107 (closed genome of the symbiont from H. acanthopus ) and WNLJ00000000 (draft genome of Polyplax serratasymbiont in 39 contigs). To assess phylogenetic origin of individual genes, we blasted each gene against the nr database and categorised its putative origin based on the returned hits (for details see SupplementaryInformation/SupplementaryText).