• Simarro PP, Diarra A, Ruiz Postigo JA, Franco JR, Jannin JG. The human African trypanosomiasis control and surveillance programme of the world health organization 2000–2009: the way forward. PLoS Negl Trop Dis. 2011;5:e1007. https://doi.org/10.1371/journal.pntd.0001007.


    Google Scholar
     

  • Franco JR, Cecchi G, Priotto G, Paone M, Diarra A, Grout L, et al. Monitoring the elimination of human African trypanosomiasis at continental and country level: update to 2018. PLoS Negl Trop Dis. 2020;14:e0008261. https://doi.org/10.1371/journal.pntd.0008261.


    Google Scholar
     

  • Holt HR, Selby R, Mumba C, Napier GB, Guitian J. Assessment of animal African trypanosomiasis (AAT) vulnerability in cattle-owning communities of sub-Saharan Africa. Parasit Vectors. 2016;9:53. https://doi.org/10.1186/s13071-016-1336-5.


    Google Scholar
     

  • Vreysen MJB, Seck MT, Sall B, Bouyer J. Tsetse flies: their biology and control using area-wide integrated pest management approaches. J Invertebr Pathol. 2013;112:S15–25. https://doi.org/10.1016/j.jip.2012.07.026.


    Google Scholar
     

  • Wang J, Weiss BL, Aksoy S. Tsetse fly microbiota: form and function. Front Cell Infect Microbiol. 2013. https://doi.org/10.3389/fcimb.2013.00069.


    Google Scholar
     

  • Aksoy S, Weiss BL, Attardo GM. Trypanosome transmission dynamics in Tsetse. Curr Opin Insect Sci. 2014;3:43–9. https://doi.org/10.1016/j.cois.2014.07.003.


    Google Scholar
     

  • Bing X, Attardo GM, Vigneron A, Aksoy E, Scolari F, Malacrida A, et al. Unravelling the relationship between the tsetse fly and its obligate symbiont Wigglesworthia: transcriptomic and metabolomic landscapes reveal highly integrated physiological networks. Proceedings of the Royal Society B: Biological Sciences. 2017;284:20170360. https://doi.org/10.1098/rspb.2017.0360.


    Google Scholar
     

  • Aksoy S, Attardo G. Paratransgenesis applied for control of Tsetse transmitted sleeping sickness. Transgenesis and the management of vector-borne disease. New York, NY: Springer New York; 2008. pp. 35–48. https://doi.org/10.1007/978-0-387-78225-6_3.


    Google Scholar
     

  • Michalkova V, Benoit JB, Weiss BL, Attardo GM, Aksoy S. Vitamin B6 generated by obligate symbionts is critical for maintaining proline homeostasis and fecundity in Tsetse flies. Appl Environ Microbiol. 2014;80:5844–53. https://doi.org/10.1128/AEM.01150-14.


    Google Scholar
     

  • Benoit JB, Vigneron A, Broderick NA, Wu Y, Sun JS, Carlson JR, et al. Symbiont-induced odorant binding proteins mediate insect host hematopoiesis. eLife. 2017. https://doi.org/10.7554/elife.19535.


    Google Scholar
     

  • Weiss BL, Wang J, Aksoy S. Tsetse immune system maturation requires the presence of obligate symbionts in larvae. PLoS Biol. 2011;9:e1000619. https://doi.org/10.1371/journal.pbio.1000619.


    Google Scholar
     

  • Weiss BL, Maltz M, Aksoy S. Obligate symbionts activate immune system development in the Tsetse fly. J Immunol. 2012;188:3395–403. https://doi.org/10.4049/jimmunol.1103691.


    Google Scholar
     

  • Weiss BL, Wang J, Maltz MA, Wu Y, Aksoy S. Trypanosome infection establishment in the Tsetse fly gut is influenced by microbiome-regulated host immune barriers. PLoS Pathog. 2013;9:e1003318. https://doi.org/10.1371/journal.ppat.1003318.


    Google Scholar
     

  • Doudoumis V, Blow F, Saridaki A, Augustinos A, Dyer NA, Goodhead I, et al. Challenging the Wigglesworthia, Sodalis, Wolbachia symbiosis dogma in Tsetse flies: Spiroplasma is present in both laboratory and natural populations. Sci Rep. 2017;7:4699. https://doi.org/10.1038/s41598-017-04740-3.


    Google Scholar
     

  • Dieng MM, Dera KM, Moyaba P, Ouedraogo GMS, Demirbas-Uzel G, Gstöttenmayer F, et al. Prevalence of Trypanosoma and Sodalis in wild populations of Tsetse flies and their impact on sterile insect technique programmes for Tsetse eradication. Sci Rep. 2022;12:3322. https://doi.org/10.1038/s41598-022-06699-2.


    Google Scholar
     

  • Awuoche EO, Smallenberger G, Bruzzese DL, Orfano A, Weiss BL, Aksoy S. Spiroplasma endosymbiont reduction of host lipid synthesis and Stomoxyn-like peptide contribute to trypanosome resistance in the Tsetse fly Glossina fuscipes. PLoS Pathog. 2025;21:e1012692. https://doi.org/10.1371/journal.ppat.1012692.


    Google Scholar
     

  • Son JH, Weiss BL, Schneider DI, Dera KM, Gstöttenmayer F, Opiro R, et al. Infection with endosymbiotic Spiroplasma disrupts Tsetse (Glossina fuscipes fuscipes) metabolic and reproductive homeostasis. PLOS Pathog. 2021;17:e1009539. https://doi.org/10.1371/journal.ppat.1009539.


    Google Scholar
     

  • Schneider DI, Saarman N, Onyango MG, Hyseni C, Opiro R, Echodu R, et al. Spatio-temporal distribution of Spiroplasma infections in the Tsetse fly (Glossina fuscipes fuscipes) in Northern Uganda. PLoS Negl Trop Dis. 2019;13:e0007340. https://doi.org/10.1371/journal.pntd.0007340.


    Google Scholar
     

  • Bové JM, Renaudin J, Saillard C, Foissac X, Garnier M. Spiroplasma citri, a plant pathogenic Mollicute: relationships with its two hosts, the plant and the leafhopper vector. Annu Rev Phytopathol. 2003;41:483–500. https://doi.org/10.1146/annurev.phyto.41.052102.104034.


    Google Scholar
     

  • Whitcomb RF, Tully JG. The Mycoplasmas. United States of America: Academic press; 1979.


    Google Scholar
     

  • Anbutsu H, Fukatsu T. Spiroplasma as a model insect endosymbiont. Environ Microbiol Rep. 2011;3:144–53. https://doi.org/10.1111/j.1758-2229.2010.00240.x.


    Google Scholar
     

  • Fukatsu T, Nikoh N. Endosymbiotic microbiota of the bamboo pseudococcid Antonina crawii (Insecta, Homoptera). Appl Environ Microbiol. 2000;66:643–50. https://doi.org/10.1128/AEM.66.2.643-650.2000.


    Google Scholar
     

  • Lo W-S, Chen L-L, Chung W-C, Gasparich GE, Kuo C-H. Comparative genome analysis of Spiroplasma melliferum IPMB4A, a honeybee-associated bacterium. BMC Genomics. 2013;14:22. https://doi.org/10.1186/1471-2164-14-22.


    Google Scholar
     

  • Markham PG. Spiroplasmas in leafhoppers: a review. Yale J Biol Med. 1983;56:745–51.


    Google Scholar
     

  • Mouches C, Bové JM, Tully JG, Rose DL, McCoy RE, Carle-Junca P, et al. Spiroplasma apis, a new species from the honey-bee Apis mellifera. Ann Inst Pasteur Microbiol. 1983;134:383–97. https://doi.org/10.1016/S0769-2609(83)80063-5.


    Google Scholar
     

  • Tully JG, Rose DL, Yunker CE, Carle P, BOVe JM, Williamson DL, et al. Spiroplasma ixodetis sp. nov., a new species from Ixodes pacificus ticks collected in Oregon. Int J Syst Evol Microbiol. 1995;45:23–8. https://doi.org/10.1099/00207713-45-1-23.


    Google Scholar
     

  • Filee J, Lopez-Villavicencio M, Debat V, Fourdin R, Salazar C, Silva-Brandao K, et al. Genome evolution and between-host transmission of Spiroplasma endosymbiont in wild communities of Morpho butterflies. Preprint. 2024. https://doi.org/10.1101/2024.02.22.581604.


    Google Scholar
     

  • Ballinger MJ, Perlman SJ. Generality of toxins in defensive symbiosis: ribosome-inactivating proteins and defense against parasitic wasps in Drosophila. PLoS Pathog. 2017;13:e1006431. https://doi.org/10.1371/journal.ppat.1006431.


    Google Scholar
     

  • Hamilton PT, Peng F, Boulanger MJ, Perlman SJ. A ribosome-inactivating protein in a Drosophila defensive symbiont. Proc Natl Acad Sci. 2016;113:350–5. https://doi.org/10.1073/pnas.1518648113.


    Google Scholar
     

  • Jaenike J, Unckless R, Cockburn SN, Boelio LM, Perlman SJ. Adaptation via symbiosis: recent spread of a Drosophila defensive symbiont. Science. 2010;329:212–5. https://doi.org/10.1126/science.1188235.


    Google Scholar
     

  • Paredes JC, Herren JK, Schüpfer F, Lemaitre B. The role of lipid competition for endosymbiont-mediated protection against parasitoid wasps in Drosophila. mBio. 2016;7:e01006-16. https://doi.org/10.1128/mBio.01006-16.


    Google Scholar
     

  • Harumoto T, Lemaitre B. Male-killing toxin in a bacterial symbiont of Drosophila. Nature. 2018;557:252–5. https://doi.org/10.1038/s41586-018-0086-2.


    Google Scholar
     

  • Tinsley MC, Majerus MEN. A new male-killing parasitism: Spiroplasma bacteria infect the Ladybird beetle Anisosticta novemdecimpunctata (Coleoptera: Coccinellidae). Parasitology. 2006;132:757–65. https://doi.org/10.1017/S0031182005009789.


    Google Scholar
     

  • Jiggins FM, Hurst GDD, Jiggins CD, Schulenburg JHG, Majerus MEN. The butterfly Danaus chrysippus is infected by a male-killing Spiroplasma bacterium. Parasitology. 2000;120:439–46. https://doi.org/10.1017/S0031182099005867.


    Google Scholar
     

  • Gerth M, Martinez-Montoya H, Ramirez P, Masson F, Griffin JS, Aramayo R, et al. Rapid Mol Evol Spiroplasma Symbionts Drosophila. 2020. https://doi.org/10.1101/2020.06.23.165548.


    Google Scholar
     

  • Paredes JC, Herren JK, Schüpfer F, Marin R, Claverol S, Kuo C-H, et al. Genome sequence of the Drosophila melanogaster male-killing Spiroplasma strain MSRO endosymbiont. mBio. 2015;6:e02437-14. https://doi.org/10.1128/mBio.02437-14.


    Google Scholar
     

  • Dera K-SM, Dieng MM, Moyaba P, Ouedraogo GM, Pagabeleguem S, Njokou F, et al. Prevalence of Spiroplasma and interaction with wild Glossina tachinoides microbiota. Parasite. 2023;30:62. https://doi.org/10.1051/parasite/2023064.


    Google Scholar
     

  • Dera KM, Barro DT, Kaboré BA, Gstöttenmayer F, Dieng MM, Pagabeleguem S, et al. Spiroplasma infection in colonized Glossina fuscipes fuscipes: impact on mass rearing and the sterile insect technique. Insect Sci. 2025;1744–7917. https://doi.org/10.1111/1744-7917.70078.

  • Masson F, Calderon Copete S, Schüpfer F, Garcia-Arraez G, Lemaitre B. In vitro culture of the insect endosymbiont Spiroplasma poulsonii highlights bacterial genes involved in host-symbiont interaction. mBio. 2018;9:e00024-18. https://doi.org/10.1128/mBio.00024-18.


    Google Scholar
     

  • R Core Team. R: A language and environment for statistical computing. 2024.

  • RStudio Team. RStudio: Integrated Development for R. 2022.

  • Heid CA, Stevens J, Livak KJ, Williams PM. Real time quantitative PCR. Genome Res. 1996;6:986–94. https://doi.org/10.1101/gr.6.10.986.


    Google Scholar
     

  • Madigan MT, Bender KS, Buckley DH, Sattley WM, Stahl DA, Brock TD. Brock biology of microorganisms. Sixteenth edition, global edition. Harlow: Pearson Education Limited; 2022.


    Google Scholar
     

  • International Atomic Energy Agency. FAO/IAEA Standard operating procedures for mass-rearing tsetse flies. 2006.

  • Bauer B, Wetzel H. A new membrane for feeding Glossina morsitans Westw. (Diptera: Glossinidae). Bull Entomol Res. 1976;65:563–5. https://doi.org/10.1017/S0007485300006246.


    Google Scholar
     

  • Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001;29:e45. https://doi.org/10.1093/nar/29.9.e45.


    Google Scholar
     

  • Bruzzese DJ, Weiss BL, Echodu R, Mireji PO, Abd-Alla AMM, Aksoy S. New Tsetse (Glossina fuscipes fuscipes) genomes generated from wild and laboratory‐reared specimens. Insect Sci. 2025;1744–7917. https://doi.org/10.1111/1744-7917.70085.

  • Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, et al. Twelve years of samtools and BCFtools. Gigascience. 2021;10:giab008. https://doi.org/10.1093/gigascience/giab008.


    Google Scholar
     

  • Steinig E, Coin L. Nanoq: ultra-fast quality control for nanopore reads. J Open Source Softw. 2022;7:2991. https://doi.org/10.21105/joss.02991.


    Google Scholar
     

  • Kolmogorov M, Bickhart DM, Behsaz B, Gurevich A, Rayko M, Shin SB, et al. MetaFlye: scalable long-read metagenome assembly using repeat graphs. Nat Methods. 2020;17:1103–10. https://doi.org/10.1038/s41592-020-00971-x.


    Google Scholar
     

  • Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017. https://doi.org/10.1101/gr.215087.116. :gr.215087.116.


    Google Scholar
     

  • Li H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics. 2016;32:2103–10. https://doi.org/10.1093/bioinformatics/btw152.


    Google Scholar
     

  • Chen Y, Nie F, Xie S-Q, Zheng Y-F, Dai Q, Bray T, et al. Efficient assembly of nanopore reads via highly accurate and intact error correction. Nat Commun. 2021;12:60. https://doi.org/10.1038/s41467-020-20236-7.


    Google Scholar
     

  • Hu J, Wang Z, Sun Z, Hu B, Ayoola AO, Liang F, et al. NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads. Genome Biol. 2024;25:107. https://doi.org/10.1186/s13059-024-03252-4.


    Google Scholar
     

  • Chen S, Zhou Y, Chen Y, Gu J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90. https://doi.org/10.1093/bioinformatics/bty560.


    Google Scholar
     

  • Wick RR, Holt KE. Polypolish: short-read polishing of long-read bacterial genome assemblies. PLoS Comput Biol. 2022;18:e1009802. https://doi.org/10.1371/journal.pcbi.1009802.


    Google Scholar
     

  • Bouras G, Judd LM, Edwards RA, Vreugde S, Stinear TP, Wick RR. How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies. Microb Genom. 2024;10:001254. https://doi.org/10.1099/mgen.0.001254.


    Google Scholar
     

  • Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34:3094–100. https://doi.org/10.1093/bioinformatics/bty191.


    Google Scholar
     

  • Cheng H, Concepcion GT, Feng X, Zhang H, Li H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021;18:170–5. https://doi.org/10.1038/s41592-020-01056-5.


    Google Scholar
     

  • Bouras G, Grigson SR, Papudeshi B, Mallawaarachchi V, Roach MJ. Dnaapler: a tool to reorient circular microbial genomes. J Open Source Softw. 2024;9:5968. https://doi.org/10.21105/joss.05968.


    Google Scholar
     

  • Formenti G, Abueg L, Brajuka A, Brajuka N, Gallardo-Alba C, Giani A, et al. Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs. Bioinformatics. 2022;38:4214–6. https://doi.org/10.1093/bioinformatics/btac460.


    Google Scholar
     

  • Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210–2. https://doi.org/10.1093/bioinformatics/btv351.


    Google Scholar
     

  • Frolova D, Lima L, Roberts LW, Bohnenkämper L, Wittler R, Stoye J, et al. Applying rearrangement distances to enable plasmid epidemiology with pling. Microb Genom. 2024;10:001300. https://doi.org/10.1099/mgen.0.001300.


    Google Scholar
     

  • Li W, O’Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A, et al. RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation. Nucleic Acids Res. 2020;49:D1020–8. https://doi.org/10.1093/nar/gkaa1105.


    Google Scholar
     

  • Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genomics. 2021;7. https://doi.org/10.1099/mgen.0.000685.

  • Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol. 2021;38:5825–9. https://doi.org/10.1093/molbev/msab293.


    Google Scholar
     

  • Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol. 2016;428:726–31. https://doi.org/10.1016/j.jmb.2015.11.006.


    Google Scholar
     

  • Wishart DS, Han S, Saha S, Oler E, Peters H, Grant JR, et al. PHASTEST: faster than PHASTER, better than PHAST. Nucleic Acids Res. 2023;51:W443–50. https://doi.org/10.1093/nar/gkad382.


    Google Scholar
     

  • Wang M, Liu G, Liu M, Tai C, Deng Z, Song J, et al. ICEberg 3.0: functional categorization and analysis of the integrative and conjugative elements in bacteria. Nucleic Acids Res. 2024;52:D732–7. https://doi.org/10.1093/nar/gkad935.


    Google Scholar
     

  • Xie Z, Tang H. ISEScan: automated identification of insertion sequence elements in prokaryotic genomes. Bioinformatics. 2017;33:3340–7. https://doi.org/10.1093/bioinformatics/btx433.


    Google Scholar
     

  • Teufel F, Almagro Armenteros JJ, Johansen AR, Gíslason MH, Pihl SI, Tsirigos KD, et al. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat Biotechnol. 2022;40:1023–5. https://doi.org/10.1038/s41587-021-01156-3.


    Google Scholar
     

  • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421. https://doi.org/10.1186/1471-2105-10-421.


    Google Scholar
     

  • Blum M, Andreeva A, Florentino LC, Chuguransky SR, Grego T, Hobbs E, et al. InterPro: the protein sequence classification resource in 2025. Nucleic Acids Res. 2025;53:D444–56. https://doi.org/10.1093/nar/gkae1082.


    Google Scholar
     

  • Löytynoja A. Phylogeny-aware alignment with PRANK. In: Russell DJ, editor. Multiple sequence alignment methods. Totowa, NJ: Humana; 2014. pp. 155–70. https://doi.org/10.1007/978-1-62703-646-7_10.


    Google Scholar
     

  • Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics. 2019;35:4453–5. https://doi.org/10.1093/bioinformatics/btz305.


    Google Scholar
     

  • O’Leary NA, Cox E, Holmes JB, Anderson WR, Falk R, Hem V, et al. Exploring and retrieving sequence and metadata for species across the tree of life with NCBI datasets. Sci Data. 2024;11:732. https://doi.org/10.1038/s41597-024-03571-y.


    Google Scholar
     

  • Xu X, Yin Z, Yan L, Zhang H, Xu B, Wei Y, et al. RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches. Genome Biol. 2023;24:121. https://doi.org/10.1186/s13059-023-02961-6.


    Google Scholar
     

  • Gautreau G, Bazin A, Gachet M, Planel R, Burlot L, Dubois M, et al. PPanGGOLiN: depicting microbial diversity via a partitioned pangenome graph. PLoS Comput Biol. 2020;16:e1007732. https://doi.org/10.1371/journal.pcbi.1007732.


    Google Scholar
     

  • Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res. 2002;30:3059–66. https://doi.org/10.1093/nar/gkf436.


    Google Scholar
     

  • Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods. 2015;8:12–24. https://doi.org/10.1039/C5AY02550H.


    Google Scholar
     

  • Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: a fast and versatile genome alignment system. PLoS Comput Biol. 2018;14:e1005944. https://doi.org/10.1371/journal.pcbi.1005944.


    Google Scholar
     

  • Goel M, Sun H, Jiao W-B, Schneeberger K. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 2019;20:277. https://doi.org/10.1186/s13059-019-1911-0.


    Google Scholar
     

  • Goel M, Schneeberger K. Plotsr: visualizing structural similarities and rearrangements between multiple genomes. Bioinformatics. 2022;38:2922–6. https://doi.org/10.1093/bioinformatics/btac196.


    Google Scholar
     

  • Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, et al. Welcome to the Tidyverse. J Open Source Softw. 2019;4:1686. https://doi.org/10.21105/joss.01686.


    Google Scholar
     

  • Chen H, Boutros PC. VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics. 2011;12:35. https://doi.org/10.1186/1471-2105-12-35.


    Google Scholar
     

  • O S, Ma LJ. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genomics. 2021;7. https://doi.org/10.1099/mgen.0.000685.

  • Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32:3047–8. https://doi.org/10.1093/bioinformatics/btw354.


    Google Scholar
     

  • Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14:417–9. https://doi.org/10.1038/nmeth.4197.


    Google Scholar
     

  • Karaji R, Peña-Castillo L, OpDetect. A convolutional and recurrent neural network classifier for precise and sensitive operon detection from RNA-seq data. 2025;:2025.03.24.645056. https://doi.org/10.1101/2025.03.24.645056.

  • Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21. https://doi.org/10.1093/bioinformatics/bts635.


    Google Scholar
     

  • Chen Y, Chen L, Lun ATL, Baldoni PL, Smyth GK. edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets. Nucleic Acids Res. 2025;53:gkaf018. https://doi.org/10.1093/nar/gkaf018.


    Google Scholar
     

  • Lo W-S, Haryono M, Gasparich GE, Kuo C-H. Complete genome sequence of Spiroplasma sp. TU-14. Genome Announc. 2017;5:e01465-16. https://doi.org/10.1128/genomeA.01465-16.


    Google Scholar
     

  • Haryono M, Lo W-S, Gasparich GE, Kuo C-H. Complete genome sequence of Spiroplasma sp. NBRC 100390. Genome Announc. 2017;5:e00008-17. https://doi.org/10.1128/genomeA.00008-17.


    Google Scholar
     

  • Freeman BA, Sissenstein R, McManus TT, Woodward JE, Lee IM, Mudd JB. Lipid composition and lipid metabolism of Spiroplasma citri. J Bacteriol. 1976;125:946–54. https://doi.org/10.1128/jb.125.3.946-954.1976.


    Google Scholar
     

  • Herren JK, Paredes JC, Schüpfer F, Arafah K, Bulet P, Lemaitre B. Insect endosymbiont proliferation is limited by lipid availability. eLife. 2014;3:e02964. https://doi.org/10.7554/eLife.02964.


    Google Scholar
     

  • Wingreen NS, Huang KC. Physics of intracellular organization in bacteria. Annu Rev Microbiol. 2015;69(1):361–79. https://doi.org/10.1146/annurev-micro-091014-104313.


    Google Scholar
     

  • Masson F, Rommelaere S, Schüpfer F, Boquete J-P, Lemaitre B. Disproportionate investment in Spiralin B production limits in-host growth and favors the vertical transmission of Spiroplasma insect endosymbionts. Proc Natl Acad Sci U S A. 2022;119:e2208461119. https://doi.org/10.1073/pnas.2208461119.


    Google Scholar
     

  • Zha G-D, Yang D-H, Wang J-J, Yang B, Yu H-S. Infection function of adhesin-like protein ALP609 from Spiroplasma melliferum CH-1. Curr Microbiol. 2018;75:701–8. https://doi.org/10.1007/s00284-018-1435-y.


    Google Scholar
     

  • Béven L, Duret S, Batailler B, Dubrana M-P, Saillard C, Renaudin J, et al. The repetitive domain of ScARP3d triggers entry of Spiroplasma citri into cultured cells of the vector Circulifer haematoceps. PLoS ONE. 2012;7:e48606. https://doi.org/10.1371/journal.pone.0048606.


    Google Scholar
     

  • Pilo P, Frey J, Vilei EM. Molecular mechanisms of pathogenicity of Mycoplasma mycoides subsp. mycoides SC. Vet J. 2007;174:513–21. https://doi.org/10.1016/j.tvjl.2006.10.016.


    Google Scholar
     

  • Tully JG, Whitcomb RF, Clark HF, Williamson DL. Pathogenic Mycoplasmas: cultivation and vertebrate pathogenicity of a new Spiroplasma. Science. 1977;195:892–4. https://doi.org/10.1126/science.841314.


    Google Scholar
     

  • Bell-Sakyi L, Palomar AM, Kazimirova M. Isolation and propagation of a Spiroplasma sp. from Slovakian Ixodes ricinus ticks in Ixodes spp. cell lines. Ticks Tick-borne Dis. 2015;6:601–6. https://doi.org/10.1016/j.ttbdis.2015.05.002.


    Google Scholar
     

  • Steiner T, McGarrity GJ, Phillips DM. Cultivation and partial characterization of Spiroplasmas in cell cultures. Infect Immun. 1982;35:296–304. https://doi.org/10.1128/iai.35.1.296-304.1982.


    Google Scholar
     

  • Masson F, Lemaitre B. Growing ungrowable bacteria: overview and perspectives on insect symbiont culturability. Microbiol Mol Biol Rev. 2020;84:e00089–20. https://doi.org/10.1128/MMBR.00089-20.


    Google Scholar
     

  • Masson F, Schüpfer F, Jollivet C, Lemaitre B. Transformation of the Drosophila sex-manipulative endosymbiont Spiroplasma poulsonii and persisting hurdles for functional genetic studies. Appl Environ Microbiol. 2020;86:e00835-20. https://doi.org/10.1128/AEM.00835-20.


    Google Scholar
     

  • Catchpowle J, Maynard J, Chang BJ, Payne MS, Beeton ML, Furfaro LL. Miniscule mollicutes: current hurdles to bacteriophage identification. Sustainable Microbiol. 2024;1:qvae019. https://doi.org/10.1093/sumbio/qvae019.


    Google Scholar
     

  • Bébéar C-M, Aullo P, Bové J-M, Renaudin J. Spiroplasma citri virus SpV1: characterization of viral sequences present in the Spiroplasmal host chromosome. Curr Microbiol. 1996;32:134–40. https://doi.org/10.1007/s002849900024.


    Google Scholar
     

  • Krafsur ES, Marquez JG, Ouma JO. Structure of some East African Glossina fuscipes fuscipes populations. Med Vet Entomol. 2008;22:222–7. https://doi.org/10.1111/j.1365-2915.2008.00739.x.


    Google Scholar
     

  • Moore LD, Ballinger MJ. The toxins of vertically transmitted Spiroplasma. Front Microbiol. 2023;14:1148263. https://doi.org/10.3389/fmicb.2023.1148263.


    Google Scholar
     

  • Ballinger MJ, Perlman SJ. The defensive Spiroplasma. Curr Opin Insect Sci. 2019;32:36–41. https://doi.org/10.1016/j.cois.2018.10.004.


    Google Scholar
     

  • Hrdina A, Serra Canales M, Arias-Rojas A, Frahm D, Iatsenko I. The endosymbiont Spiroplasma poulsonii increases Drosophila melanogaster resistance to pathogens by enhancing iron sequestration and melanization. MBio. 2024;15:e0093624. https://doi.org/10.1128/mbio.00936-24.


    Google Scholar
     

  • Rattner R, Thapa SP, Dang T, Osman F, Selvaraj V, Maheshwari Y, et al. Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors. BMC Genomics. 2021;22:373. https://doi.org/10.1186/s12864-021-07637-8.


    Google Scholar
     

  • Wang GH, Sun BF, Xiong TL, Wang YK, Murfin KE, Xiao JH, et al. Bacteriophage WO can mediate horizontal gene transfer in endosymbiotic Wolbachia genomes. Front Microbiol. 2016;7:1867. https://doi.org/10.3389/fmicb.2016.01867.


    Google Scholar
     

  • Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature. 2000;405:299–304. https://doi.org/10.1038/35012500.


    Google Scholar
     

  • Arnold BJ, Huang I-T, Hanage WP. Horizontal gene transfer and adaptive evolution in bacteria. Nat Rev Microbiol. 2022;20:206–18. https://doi.org/10.1038/s41579-021-00650-4.


    Google Scholar
     

  • Fortier L-C, Sekulovic O. Importance of prophages to evolution and virulence of bacterial pathogens. Virulence. 2013;4:354–65. https://doi.org/10.4161/viru.24498.


    Google Scholar
     

  • Tanaka K, Furukawa S, Nikoh N, Sasaki T, Fukatsu T. Complete WO phage sequences reveal their dynamic evolutionary trajectories and putative functional elements required for integration into the Wolbachia genome. Appl Environ Microbiol. 2009;75:5676–86. https://doi.org/10.1128/AEM.01172-09.


    Google Scholar
     

  • Beckmann JF, Ronau JA, Hochstrasser M. A Wolbachia deubiquitylating enzyme induces cytoplasmic incompatibility. Nat Microbiol. 2017;2:17007. https://doi.org/10.1038/nmicrobiol.2017.7.


    Google Scholar
     

  • Perlmutter JI, Bordenstein SR, Unckless RL, LePage DP, Metcalf JA, Hill T, et al. The phage gene Wmk is a candidate for male killing by a bacterial endosymbiont. PLoS Pathog. 2019;15:e1007936. https://doi.org/10.1371/journal.ppat.1007936.


    Google Scholar
     

  • McNamara CJ, Ant TH, Harvey-Samuel T, White-Cooper H, Martinez J, Alphey L, et al. Transgenic expression of Cif genes from Wolbachia strain wAlbB recapitulates cytoplasmic incompatibility in Aedes aegypti. Nat Commun. 2024;15:869. https://doi.org/10.1038/s41467-024-45238-7.


    Google Scholar
     

  • Martinez J, Klasson L, Welch JJ, Jiggins FM. Life and death of selfish genes: comparative genomics reveals the dynamic evolution of cytoplasmic incompatibility. Mol Biol Evol. 2021. https://doi.org/10.1093/molbev/msaa209.


    Google Scholar
     

  • Arai H, Legeai F, Kageyama D, Sugio A, Simon J-C. Genomic insights into Spiroplasma endosymbionts that induce male-killing and protective phenotypes in the pea aphid. FEMS Microbiol Lett. 2024;371:fnae027. https://doi.org/10.1093/femsle/fnae027.


    Google Scholar
     

  • Knoke LR, Abad Herrera S, Götz K, Justesen BH, Günther Pomorski T, Fritz C, et al. Agrobacterium tumefaciens small lipoprotein Atu8019 is involved in selective outer membrane vesicle (OMV) docking to bacterial cells. Front Microbiol. 2020;11:1228. https://doi.org/10.3389/fmicb.2020.01228.


    Google Scholar
     

  • Jin S, Joe A, Lynett J, Hani EK, Sherman P, Chan VL. JlpA, a novel surface-exposed lipoprotein specific to Campylobacter jejuni, mediates adherence to host epithelial cells. Mol Microbiol. 2001;39:1225–36. https://doi.org/10.1111/j.1365-2958.2001.02294.x.


    Google Scholar
     

  • Speare L, Woo M, Dunn AK, Septer AN. A putative lipoprotein mediates cell-cell contact for type VI secretion system-dependent killing of specific competitors. mBio. 2022;13:e0308521. https://doi.org/10.1128/mbio.03085-21.


    Google Scholar
     

  • Duarte EH, Carvalho A, López-Madrigal S, Costa J, Teixeira L. Forward genetics in Wolbachia: regulation of Wolbachia proliferation by the amplification and deletion of an addictive genomic island. PLoS Genet. 2021;17:e1009612. https://doi.org/10.1371/journal.pgen.1009612.


    Google Scholar
     

  • Mills S, Shanahan F, Stanton C, Hill C, Coffey A, Ross RP. Movers and shakers: influence of bacteriophages in shaping the mammalian gut microbiota. Gut Microbes. 2013;4:4–16. https://doi.org/10.4161/gmic.22371.


    Google Scholar
     

  • Ofir G, Sorek R. Contemporary phage biology: from classic models to new insights. Cell. 2018;172:1260–70. https://doi.org/10.1016/j.cell.2017.10.045.


    Google Scholar
     

  • Silpe JE, Bassler BL. A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Cell. 2019;176:268–80. https://doi.org/10.1016/j.cell.2018.10.059. .e13.


    Google Scholar
     

  • Laganenka L, Sander T, Lagonenko A, Chen Y, Link H, Sourjik V. Quorum sensing and metabolic state of the host control lysogeny-lysis switch of bacteriophage T1. mBio. 2019. https://doi.org/10.1128/mbio.01884-19.


    Google Scholar
     

  • Li D, Liang W, Hu Q, Ren J, Xue F, Liu Q, et al. The effect of a spontaneous induction prophage, phi458, on biofilm formation and virulence in avian pathogenic Escherichia coli. Front Microbiol. 2022. https://doi.org/10.3389/fmicb.2022.1049341.


    Google Scholar
     

  • de Sablet T, Chassard C, Bernalier-Donadille A, Vareille M, Gobert AP, Martin C. Human microbiota-secreted factors inhibit shiga toxin synthesis by enterohemorrhagic Escherichia coli O157:H7. Infect Immun. 2009;77:783–90. https://doi.org/10.1128/IAI.01048-08.


    Google Scholar
     

  • Loś JM, Loś M, Wegrzyn A, Wegrzyn G. Hydrogen peroxide-mediated induction of the Shiga toxin-converting lambdoid prophage ST2-8624 in Escherichia coli O157:H7. FEMS Immunol Med Microbiol. 2010;58:322–9. https://doi.org/10.1111/j.1574-695X.2009.00644.x.


    Google Scholar
     

  • Ramirez P, Martinez Montoya H, Aramayo R, Mateos M. Diverse toxin repertoire but limited metabolic capacities inferred from the draft genome assemblies of three Spiroplasma (Citri clade) strains associated with Drosophila. Microb Genomics. 2025;11. https://doi.org/10.1099/mgen.0.001408.

  • Lo W-S, Ku C, Chen L-L, Chang T-H, Kuo C-H. Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. taiwanense. Genome Biol Evol. 2013;5:1512–23. https://doi.org/10.1093/gbe/evt108.


    Google Scholar
     

  • Geigy R, Huber M, Weinman D, Wyatt GR. Demonstration of trehalose in the vector of African trypanosomiasis: the tsetse fly. Acta Trop. 1959;16:255–62.


    Google Scholar
     

  • Scolari F, Benoit JB, Michalkova V, Aksoy E, Takac P, Abd-Alla AMM, et al. The spermatophore in Glossina morsitans morsitans: insights into male contributions to reproduction. Sci Rep. 2016;6:20334. https://doi.org/10.1038/srep20334.


    Google Scholar
     

  • Naguleswaran A, Fernandes P, Bevkal S, Rehmann R, Nicholson P, Roditi I. Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host. PLoS Negl Trop Dis. 2021;15:e0009504. https://doi.org/10.1371/journal.pntd.0009504.


    Google Scholar
     

  • Welburn SC, Arnold K, Maudlin I, Gooday GW. Rickettsia-like organisms and chitinase production in relation to transmission of trypanosomes by Tsetse flies. Parasitology. 1993;107:141–5. https://doi.org/10.1017/S003118200006724X.


    Google Scholar
     

  • Hennigar SR, McClung JP. Nutritional immunity: starving pathogens of trace minerals. Am J Lifestyle Med. 2016;10:170–3. https://doi.org/10.1177/1559827616629117.


    Google Scholar
     

  • Iatsenko I, Marra A, Boquete J-P, Peña J, Lemaitre B. Iron sequestration by transferrin 1 mediates nutritional immunity in Drosophila melanogaster. Proc Natl Acad Sci USA. 2020;117:7317–25. https://doi.org/10.1073/pnas.1914830117.


    Google Scholar
     

  • Marra A, Masson F, Lemaitre B. The iron transporter Transferrin 1 mediates homeostasis of the endosymbiotic relationship between Drosophila melanogaster and Spiroplasma poulsonii. microLife. 2021;2:uqab008. https://doi.org/10.1093/femsml/uqab008.


    Google Scholar
     

  • Patterson A, Stevens C, Cody RM, Gudauskas RT. Differential amino acid utilization by Spiroplasmas and the effect on growth kinetics. J Gen Appl Microbiol. 1985;31:499–505. https://doi.org/10.2323/jgam.31.499.


    Google Scholar
     

  • de Parreira Aquino G, Mendes Gomes MA, Köpke Salinas R, Laranjeira-Silva MF. Lipid and fatty acid metabolism in trypanosomatids. Microb Cell. 2021;8:262–75. https://doi.org/10.15698/mic2021.11.764.


    Google Scholar
     

  • Atella T, Bittencourt-Cunha PR, Araujo MFC, Silva-Cardoso L, Maya-Monteiro CM, Atella GC. Trypanosoma cruzi modulates lipid metabolism and highjacks phospholipids from the midgut of Rhodnius prolixus. Acta Trop. 2022;233:106552. https://doi.org/10.1016/j.actatropica.2022.106552.


    Google Scholar
     

  • Steverding D, Stierhof YD, Fuchs H, Tauber R, Overath P. Transferrin-binding protein complex is the receptor for transferrin uptake in Trypanosoma brucei. J Cell Biol. 1995;131:1173–82. https://doi.org/10.1083/jcb.131.5.1173.


    Google Scholar
     

  • Pilo P, Vilei EM, Peterhans E, Bonvin-Klotz L, Stoffel MH, Dobbelaere D, et al. A metabolic enzyme as a primary virulence factor of Mycoplasma mycoides subsp. mycoides small colony. J Bacteriol. 2005;187:6824–31. https://doi.org/10.1128/JB.187.19.6824-6831.2005.


    Google Scholar
     

  • MacLEOD ET, Maudlin I, Darby AC, Welburn SC. Antioxidants promote establishment of trypanosome infections in Tsetse. Parasitology. 2007;134:827–31. https://doi.org/10.1017/S0031182007002247.


    Google Scholar
     

  • Stirpe F. Ribosome-inactivating proteins. Toxicon. 2004;44:371–83. https://doi.org/10.1016/j.toxicon.2004.05.004.


    Google Scholar
     

  • Markham RH. Biological control of tsetse: prospects and progress in the use of pupal parasites. Int J Trop Insect Sci. 1986;7:1–4. https://doi.org/10.1017/S1742758400003015.


    Google Scholar
     

  • De Zaeytijd J, Van Damme EJM. Extensive evolution of cereal ribosome-inactivating proteins translates into unique structural features, activation mechanisms, and physiological roles. Toxins. 2017;9:123. https://doi.org/10.3390/toxins9040123.


    Google Scholar