Parasitic lice have unique mitochondrial (mt) genomes characterized by rearranged gene orders, variable genome structures, and less AT content compared to most other insects. However, relatively little is known about the mt genomes of Amblycera, the suborder sister to all other parasitic lice. Comparing among nine different genera (including representative of all seven families), we show that Amblycera have variable and highly rearranged mt genomes. Some genera have fragmented genomes that vary considerably in length, whereas others have a single mt chromosome. Notably, these genomes are more AT-biased than most other lice. We also recover genus-level phylogenetic relationships among Amblycera that are consistent with those reported from large nuclear datasets, indicating that mt sequences are reliable for reconstructing evolutionary relationships in Amblycera. However, gene order data cannot reliably recover these same relationships. Overall, our results suggest that the mt genomes of lice, already know to be distinctive, are even more variable than previously thought.

We obtained these data from mitochondrial genomes of lice in the suborder Amblycera that we assembled from paired-end Illumina sequence reads. We assembled the genomes using a combination of de novo (aTRAM, SPAdes) and mapping (MITObim) approaches. We annotated the resulting assemblies using MITOS2 and by comparing to published louse mitochondrial genomes. Following annotation, we used protein coding genes and ribosomal RNA genes to estimate phylogenetic relationships among the suborder Amblycera. For these analyses, we included data from previously published mitochondrial genomes of lice to serve as outgroups and to increase our representation of Amblycera. We used both maximum likelihood and Bayesian phylogenetic approaches on different subsets of the sequence alignments (all codon positions, 1st and 2nd codon positions only, cox1 only). We also compared nucleotide composition among the mitochondrial genomes of lice. To do this, we calculated AT%, AT skew, and GC-skew for all publicly available mitochondrial genomes of lice. We also compared these values between lice and all other insect mitochondrial genomes available on NCBI.