![]() We isolated all reads that were incorporated into the assembly of each bacterial contig identified in the de novo assembly described above. Before reconstruction of these bacterial genomes, we needed to separate sequence data belonging to each bacterial genome. One was an alphaproteobacterium belonging to the genus Rickettsia, and the other was a gammaproteobacterium that shared high sequence similarity to Sodalis glossinidius. Our initial alignment of contigs to bacterial genomes suggested that two species of bacteria were present in the lice. Contigs showing significant similarity (determined by an expected value approaching zero) to these bacterial genomes were considered to be part of an endosymbiont genome that had assembled into contigs independently of the louse genome. laumondii gi37524032 Yersinia pestis gi31795333 Bacillus subtilis subsp. ![]() To identify contigs representing the endosymbiont genome, all contigs were compared to a library of bacterial genomes, including gamma- and alphaproteobacterial endosymbionts and Gram-positive bacterial species, using blastn (including “ Candidatus Riesia pediculicola” strain USDA gi295698239 and gi292493920 Sodalis glossinidius strain morsitans gi85057978, gi85060411, gi85060466, and gi85060490 Wigglesworthia glossinidia gi32490749, gi19225058, and gi19225058 Photorhabdus luminescens subsp. Remaining reads were assembled de novo into contigs using ABySS genome assembler (k = 64, paired-end) ( 25). ![]() Reads that had fewer than 75 bp after quality trimming were removed from the library along with their mates. The reads were then soft trimmed from the 3′ end to remove base calls with a phred score of less than 28 using a sliding window of 1 nucleotide. To do this, we trimmed the first five bases from the 5′ end of each read and seven bases from the 3′ end to remove read positions that had elevated AT content. This included removing suspect base calls in the Illumina paired-end read library by quality trimming. We largely followed the symbiont genome assembly methods described by Boyd et al. No obvious masses of the Rickettsia bacterium were observed in louse tissues, nor did we find any evidence of vertical transmission, so the nature of its association remains unclear. From the same lice, we also identified an abundant bacterium belonging to the genus Rickettsia that is closely related to Rickettsia ricketsii, a human pathogen vectored by ticks. These patterns suggest the possibility that this Sodalis endosymbiont might be recently acquired, replacing a now-extinct, ancient endosymbiont. The endosymbiont genome appears to be degrading in symbiosis however, it is considerably larger than the genomes of other mammalian louse endosymbionts. Localization and vertical transmission of this endosymbiont are also more similar to those of bird lice than to those of other mammalian lice. Rather, it is more closely related to endosymbionts of the genus Sodalis associated with spittlebugs and feather-chewing bird lice. One of these is a heritable endosymbiont that is not closely related to endosymbionts of other mammalian lice. Here, we describe two bacterial associates from a louse, Proechinophthirus fluctus, which is an obligate ectoparasite of a marine mammal. The lice parasitizing mammals rely on endosymbionts to provide essential vitamins absent in their blood meals. Roughly 10% to 15% of insect species host heritable symbiotic bacteria known as endosymbionts.
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