The parvorder Rhynchophthirina with a single genus Haematomyzus is a small group of ectoparasites of unclear phylogenetic position, related to sucking and chewing lice. Previous screening based on the 16S rRNA gene indicated that Haematomyzus harbors a symbiotic bacterium whose DNA exhibits a strong shift in nucleotide composition typical of obligate mutualistic symbionts in insects. Within Phthiraptera, the smallest known genomes are found in the symbionts associated with sucking lice, which feed exclusively on mammal blood, compared to the generally larger genomes of the symbionts inhabiting chewing lice, which feed on skin derivatives. In this study, we investigate the genome characteristics of the symbiont associated with Haematomyzus elephantis. We sequenced and assembled the H. elephantis metagenome, extracted a genome draft of its symbiotic bacterium, and showed that the symbiont has a significantly reduced genome, which is with 0.39 Mbp the smallest genome among the symbionts known from Phthiraptera. Multigenic phylogenetic analysis places the symbiont into one of three clusters composed of long-branched symbionts from other insects. More specifically, it clusters together with symbionts from several other sucking lice and also with Wigglesworthia glossinidia, an obligate symbiont of tsetse flies. Consistent with the dramatic reduction of its genome, the H. elephantis symbiont lost many metabolic capacities. However, it retained functional pathways for four B vitamins, a trait typical for symbionts in blood-feeding insects. Considering genomic, metabolic, and phylogenetic characteristics, the new symbiont closely resembles those known from several sucking lice rather than chewing lice.IMPORTANCERhynchophthirina is a unique small group of permanent ectoparasites that is closely related to both sucking and chewing lice. These two groups of lice differ in their morphology, ecology, and feeding strategies. As a consequence of their different dietary sources, i.e., mammals' blood vs vertebrate skin derivatives, they also exhibit distinct patterns of symbiosis with obligate bacterial symbionts. While Rhynchophthirina shares certain traits with sucking and chewing lice, the nature of its obligate symbiotic bacterium and its metabolic role is not known. In this study, we assemble the genome of symbiotic bacterium from Haematomyzus elephantis (Rhynchophthirina), demonstrating its close similarity and phylogenetic proximity to several symbionts of sucking lice. The genome is highly reduced (representing the smallest genome among louse-associated symbionts) and exhibits a significant loss of metabolic pathways. However, similar to other sucking louse symbionts, it retains essential pathways for the synthesis of several B vitamins.

Department of Parasitology Faculty of Science University of South Bohemia České Budějovice Czech Republic

Institute of Parasitology Biology Centre ASCR v v i České Budějovice Czech Republic

The Prague Zoological Garden Prague Czech Republic

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de Moya RS, Yoshizawa K, Walden KKO, Sweet AD, Dietrich CH, Kevin P J. 2021. Phylogenomics of parasitic and nonparasitic lice (Insecta: Psocodea): combining sequence data and exploring compositional bias solutions in next generation data sets. Syst Biol 70:719–738. doi: 10.1093/sysbio/syaa075 PubMed DOI

Boyd BM, Allen JM, Nguyen N-P, Vachaspati P, Quicksall ZS, Warnow T, Mugisha L, Johnson KP, Reed DL. 2017. Primates, lice and bacteria: speciation and genome evolution in the symbionts of hominid lice. Mol Biol Evol 34:1743–1757. doi: 10.1093/molbev/msx117 PubMed DOI PMC

Mahmood S, Nováková E, Martinů J, Sychra O, Hypša V. 2023. Supergroup F Wolbachia with extremely reduced genome: transition to obligate insect symbionts. Microbiome 11:22. doi: 10.1186/s40168-023-01462-9 PubMed DOI PMC

Říhová J, Nováková E, Husník F, Hypša V. 2017. Legionella becoming a mutualist: adaptive processes shaping the genome of symbiont in the louse Polyplax serrata. Genome Biol Evol 9:2946–2957. doi: 10.1093/gbe/evx217 PubMed DOI PMC

McCutcheon JP, Boyd BM, Dale C. 2019. The life of an insect endosymbiont from the cradle to the grave. Curr Biol 29:R485–R495. doi: 10.1016/j.cub.2019.03.032 PubMed DOI

Říhová J, Batani G, Rodríguez-Ruano SM, Martinů J, Vácha F, Nováková E, Hypša V. 2021. A new symbiotic lineage related to Neisseria and Snodgrassella arises from the dynamic and diverse microbiomes in sucking lice. Mol Ecol 30:2178–2196. doi: 10.1111/mec.15866 PubMed DOI

Allen JM, Reed DL, Perotti MA, Braig HR. 2007. Evolutionary relationships of “Candidatus Riesia spp.,” endosymbiotic enterobacteriaceae living within hematophagous primate lice. Appl Environ Microbiol 73:1659–1664. doi: 10.1128/AEM.01877-06 PubMed DOI PMC

Aksoy S. 1995. Wigglesworthia gen. nov. and Wigglesworthia glossinidia sp. nov., taxa consisting of the mycetocyte-associated, primary endosymbionts of tsetse flies. Int J Syst Bacteriol 45:848–851. doi: 10.1099/00207713-45-4-848 PubMed DOI

Šochová E, Husník F, Nováková E, Halajian A, Hypša V. 2017. Arsenophonus and Sodalis replacements shape evolution of symbiosis in louse flies. PeerJ 5:e4099. doi: 10.7717/peerj.4099 PubMed DOI PMC

Balvín O, Roth S, Talbot B, Reinhardt K. 2018. Co-speciation in bedbug Wolbachia parallel the pattern in nematode hosts. Sci Rep 8:8797. doi: 10.1038/s41598-018-25545-y PubMed DOI PMC

Allen JM, Burleigh JG, Light JE, Reed DL. 2016. Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice. PeerJ 4:e2187. doi: 10.7717/peerj.2187 PubMed DOI PMC

Hypša V, Křížek J. 2007. Molecular evidence for polyphyletic origin of the primary symbionts of sucking lice (Phthiraptera, Anoplura). Microb Ecol 54:242–251. doi: 10.1007/s00248-006-9194-x PubMed DOI

Alickovic L, Johnson KP, Boyd BM. 2021. The reduced genome of a heritable symbiont from an ectoparasitic feather feeding louse. BMC Ecol Evol 21:108. doi: 10.1186/s12862-021-01840-7 PubMed DOI PMC

Sweet AD, Browne DR, Hernandez AG, Johnson KP, Cameron SL. 2023. Draft genome assemblies of the avian louse Brueelia nebulosa and its associates using long-read sequencing from an individual specimen. G3 (Bethesda) 13:2160–1836. doi: 10.1093/g3journal/jkad030 PubMed DOI PMC

Price RD, Hellenthal RA, Palma RL, Johnson KP, Clayton DH. 2003. The chewing lice: world checklist and biological overview. Vol. 24.

Buchner P. 1965. Endosymbiosis of animals with plant microorganisms. Interscience Publishers, New York.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403–410. doi: 10.1016/S0022-2836(05)80360-2 PubMed DOI

Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H. 2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895–3903. doi: 10.1128/AAC.02412-14 PubMed DOI PMC

Seemann T. 2014. PROKKA: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi: 10.1093/bioinformatics/btu153 PubMed DOI

Wishart DS, Han S, Saha S, Oler E, Peters H, Grant JR, Stothard P, Gautam V. 2023. PHASTEST: faster than PHASTER, better than PHAST. Nucleic Acids Res 51:W443–W450. doi: 10.1093/nar/gkad382 PubMed DOI PMC

Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212. doi: 10.1093/bioinformatics/btv351 PubMed DOI

Yoon S-H, Ha S, Lim J, Kwon S, Chun J. 2017. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286. doi: 10.1007/s10482-017-0844-4 PubMed DOI

Darling ACE, Mau B, Blattner FR, Perna NT. 2004. MAUVE: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14:1394–1403. doi: 10.1101/gr.2289704 PubMed DOI PMC

Husník F, Chrudimský T, Hypša V. 2011. Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches. BMC Biol 9:87. doi: 10.1186/1741-7007-9-87 PubMed DOI PMC

Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066. doi: 10.1093/nar/gkf436 PubMed DOI PMC

Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649. doi: 10.1093/bioinformatics/bts199 PubMed DOI PMC

Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552. doi: 10.1093/oxfordjournals.molbev.a026334 PubMed DOI

Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321. doi: 10.1093/sysbio/syq010 PubMed DOI

Lefort V, Longueville J-E, Gascuel O. 2017. SMS: smart model selection in PhyML. Mol Biol Evol 34:2422–2424. doi: 10.1093/molbev/msx149 PubMed DOI PMC

Lartillot N, Brinkmann H, Philippe H. 2007. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol 7 Suppl 1:S4. doi: 10.1186/1471-2148-7-S1-S4 PubMed DOI PMC

Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. 2016. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44:D457–62. doi: 10.1093/nar/gkv1070 PubMed DOI PMC

Kanehisa M, Sato Y, Morishima K. 2016. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428:726–731. doi: 10.1016/j.jmb.2015.11.006 PubMed DOI

Fukatsu T, Hosokawa T, Koga R, Nikoh N, Kato T, Hayama S, Takefushi H, Tanaka I. 2009. Intestinal endocellular symbiotic bacterium of the macaque louse Pedicinus obtusus: distinct endosymbiont origins in anthropoid primate lice and the old world monkey louse. Appl Environ Microbiol 75:3796–3799. doi: 10.1128/AEM.00226-09 PubMed DOI PMC

Říhová J, Bell KC, Nováková E, Hypša V. 2022. Lightella neohaematopini: a new lineage of highly reduced endosymbionts coevolving with chipmunk lice of the genus Neohaematopinus. Front Microbiol 13:900312. doi: 10.3389/fmicb.2022.900312 PubMed DOI PMC

Duron O, Gottlieb Y. 2020. Convergence of nutritional symbioses in obligate blood feeders. Trends Parasitol 36:816–825. doi: 10.1016/j.pt.2020.07.007 PubMed DOI

Martin Říhová J, Gupta S, Darby AC, Nováková E, Hypša V. 2023. Arsenophonus symbiosis with louse flies: multiple origins, coevolutionary dynamics, and metabolic significance. mSystems 8:e0070623. doi: 10.1128/msystems.00706-23 PubMed DOI PMC

Scharf A, La‐Rostami F, Illarionov BA, Nemes V, Feldmann AM, Höft LS, Lösel H, Bacher A, Fischer M. 2024. Systematic analysis of the effect of genomic knock-out of non-essential promiscuous HAD-like phosphatases YcsE, YitU and YwtE on flavin and adenylate content in Bacillus subtilis. Chembiochem 25:e202400165. doi: 10.1002/cbic.202400165 PubMed DOI

McCutcheon JP, von Dohlen CD. 2011. An interdependent metabolic patchwork in the nested symbiosis of mealybugs. Curr Biol 21:1366–1372. doi: 10.1016/j.cub.2011.06.051 PubMed DOI PMC