Genome sequence of Candidatus Arsenophonus lipopteni, the exclusive symbiont of a blood sucking fly Lipoptena cervi (Diptera: Hippoboscidae)
© The Author(s). 2016
Received: 26 January 2016
Accepted: 7 September 2016
Published: 17 September 2016
Candidatus Arsenophonus lipopteni (Enterobacteriaceae, Gammaproteobacteria) is an obligate intracellular symbiont of the blood feeding deer ked, Lipoptena cervi (Diptera: Hippoboscidae). The bacteria reside in specialized cells derived from host gut epithelia (bacteriocytes) forming a compact symbiotic organ (bacteriome). Compared to the closely related complex symbiotic system in the sheep ked, involving four bacterial species, Lipoptena cervi appears to maintain its symbiosis exclusively with Ca. Arsenophonus lipopteni. The genome of 836,724 bp and 24.8 % GC content codes for 667 predicted functional genes and bears the common characteristics of sequence economization coupled with obligate host-dependent lifestyle, e.g. reduced number of RNA genes along with the rRNA operon split, and strongly reduced metabolic capacity. Particularly, biosynthetic capacity for B vitamins possibly supplementing the host diet is highly compromised in Ca. Arsenophonus lipopteni. The gene sets are complete only for riboflavin (B2), pyridoxine (B6) and biotin (B7) implying the content of some B vitamins, e.g. thiamin, in the deer blood might be sufficient for the insect metabolic needs. The phylogenetic position within the spectrum of known Arsenophonus genomes and fundamental genomic features of Ca. Arsenophonus lipopteni indicate the obligate character of this symbiosis and its independent origin within Hippoboscidae.
Symbiosis has for long been recognized as one of the crucial drivers of evolution. In insects, numerous symbiotic relationships, mainly with bacteria, enabled the hosts to exploit various environments and/or life strategies, and supposedly started adaptive radiations in some groups. The mechanisms of such evolutionary processes include for example contribution to the host immunity, modification of the reproductive strategy, or provision of essential compounds to the hosts relying on nutritionally compromised resources. Blood feeding (hematophagous) insects provide an illuminating example of a life strategy shift coupled with symbiosis. Since blood meal lacks some of the B vitamins, hematophagous insects rely on their supply by symbiotic bacteria. The relationships between bacteria and hematophagous insect displays considerable degree of variability spanning from less intimate associations with entire gut microbial community, e.g. triatomine bugs [1, 2], to highly specialized interactions with few or single obligate symbiont(s), e.g. lice, bed bugs, tsetse flies, louse flies and bat flies [3–7]. With the recent advancement of genomic approaches and genetic manipulations, symbioses in these insect groups, often important disease vectors, have become of a high interest.
Here we describe fundamental biological characteristics and genome properties of the obligate symbiont of a deer ked, Lipoptena cervi (Hippoboscidae). In comparison to multipartite symbiotic systems of closely related hosts from families Hippoboscidae (i.e. Melophagus ovinus ) and Glossinidae (i.e. Glossina sp. ), Lipoptena cervi harbors a single unaccompanied obligate symbiont from the genus Arsenophonus . The genome of Candidatus Arsenophonus lipopteni has been sequenced for two reasons. The first was to extend our knowledge on occurrence and genomics of the obligate symbionts across the spectrum of hematophagous hosts involved in strictly bilateral symbiosis, e.g. bed bugs , head lice , leaches [8, 9]. This is a necessary prerequisite for the future analysis of the origins and evolution of this kind of symbioses. In addition, we intend to use the sequence in a broader comparative framework focused on evolution of bacterial symbiosis, particularly on its role in B vitamin provision to various ecological types of the hosts.
Classification and features
Ca. Arsenophonus lipopteni has an obligate association with its host, L. cervi , and is therefore uncultivable. In order to localize the bacteria within the host, Fluorescent In Situ Hybridization and Transmission Electron Microscopy was performed on dissected gut tissue as described in detail in . For FISH, the tissue was fixed and hybridized in tubes with eubacterial (EUB338, Flc-GCTGCCTCCCGTAGGA; ) and Ca. Arsenophonus lipopteni specific probes (ArL, Cy3-CTGACTAACGCTTGCACC; this study). The later was designed in a variable region of 16S rRNA gene taking the target sequence accessibility into account .
Classification and general features of Ca. Arsenophpnus lipopteni
Species Ca. Arsenophonus lipopteni
pH range; Optimum
Insect host; bacteriome of L. cervi
Ceske Budejovice, Czech Republic
Sample collection date
Apart from the functional characterization, the genome sequence of Ca. Arsenophonus lipopteni was also utilized to assess the relationship of this bacterium to other Arsenophonus symbionts. Since the sequence compositional shift compromises phylogenetic usage of 16S rDNA, leading to topological artifacts with long branched symbiotic taxa clustering together , we carried out a phylogenetic analysis of a multi-gene matrix and used advanced Bayesian approaches. The matrix was generated for all available Arsenophonus genomes (incl. Ca. Riesia pediculicola ), five other symbionts, eight non-symbiotic members of Enterobacteriaceae , and two outgroups. A set of 70 orthologous genes was determined as an intersection of COGs shared by these bacteria (generated using the MicrobesOnline database; ) with “SICO” gene list . The genes were retrieved from the finished assembly using Blastp searches  and processed as described previously . The resulting matrix contained 22618 unequivocally aligned positions. Phylobayes , a tool specifically developed to overcome the difficulty with heterogeneous composition of sequences, was used for the tree reconstruction. The analysis was run in 2 chains under the GTR + CAT model with amino acids recoded according to the Dayhoff6 option. When the convergence was not reached after 20,000 cycles, the program was stopped and majority rule consensus was calculated after discarding 4,000 cycles burn-in.
Genome sequencing information
Genome project history
2 × 100 bp paired end
Gene calling method
RAST, PGAP, PROKKA
Genbank Date of Release
Source Material Identifier
Evolution of bacterial symbiosis
Growth conditions and genomic DNA preparation
Since the bacterium is uncultivable, the host tissue was used for DNA extraction. The gut tissue containing the symbiotic organs were dissected from 6 flies in 1× phosphate buffered saline, homogenized with a sterile mortar and pestle and extracted using QiaAmp DNA Micro Kit (QIAGEN, United Kingdom). The DNA quality was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies).
Genome sequencing and assembly
The paired end 100 bp long reads were generated on one lane of Illumina HiSeq2000 run at Yale Center for Genome Analysis. A5 assembly pipeline with the default settings was used to assemble the reads . Of the 109,640 resulting contigs, the longest contig (836,730 bp) with 40× fold coverage formed a circular molecule with 99 bp overlap at the ends. This contig corresponds to the Ca. Arsenophonus lipopteni genome. Pilon v1.12  was used to check assembly quality and to improve base calls and small indels.
The finished genome was annotated using a combination of following tools: RAST , PGAP, and Prokka v1.10 . The annotation was then manually curated and checked for the presence of gene remnants. The final annotation is available in GenBank (CP013920). Metabolic pathways were reconstructed in the RAST server  and gene absence was verified using BlastP searches. Proteins were assigned to the clusters of orthologous groups using COGnitor , and the presence of signal peptides was detected using SignalP . Pfam domains were predicted using HMMER  against the Pfam-A database . Transmembrane predictions were done using TMHMM Server v. 2.0. The search for CRISPR repeats was performed in Geneious .
Statistics for finished genome assebly of Ca. Arsenophonus lipopteni
% of Totala
Genome size (bp)
DNA coding (bp)
DNA G + C (bp)
Protein coding genes
Genes assigned to COGs
Genes assigned Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of protein coding genes assigned to the COG categories
Percentage of total
Translation, ribosomal structure and biogenesis
Processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, cell division, chromosome partitioning
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Aminoacid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Assigned to more than one category
Not in COGs
The genome properties described above coupled with 16 pseudogenes identified in the genome suggest rather recent establishment of the obligate symbiosis resulting in significant but recent gene/function loss without removal of presently non-coding regions. Regarding the coding capacity for B vitamins and related cofactors, the genome of Ca. Arsenophonus lipopteni appears to be highly economized. Similar to Ca. Arsenophonus melophagi, the bacteria cannot synthesize thiamine (B1), niacin (B3), panthothenic acid (B5) and folic acid (B9). In addition, the genome does not code for heme biosynthesis. Other basic genome characteristics are summarized in Table 3.
Compared to the closely related complex symbiotic system in the sheep ked, Melophagus ovinus , Lipoptena cervi appears to maintain symbiosis exclusively with Ca. Arsenophonus lipopteni . The growing number of genome sequences available for the symbionts and the hematophagous hosts involved in strictly bilateral symbiosis (e.g. [29, 30]) will help elucidating some common requirements on B vitamins, or possibly highlight diverse needs of insects digesting blood of various vertebrates. Ca. Arsenophonus lipopteni possesses complete gene sets for biosynthesis of three B vitamins, riboflavin (B2), pyridoxine (B6) and biotin (B7). While the metabolic capacity is directly assessed from genomic data, the presence of any vitamin efflux systems cannot be easily elucidated due to yet poorly understood mechanisms for vitamin export . However, based on recent findings from other hematophagous systems, it has become more clear that the nutritional interaction does not rely on biosynthesis of all B vitamins as originally suggested by Puchta . For instance, similar to all the other Arsenophonus genomes, biosynthetic capacity for thiamin is compromised in Ca. Arsenophonus lipopteni . The genome however possesses ABC thiamin transporter genes (thiP, thiQ, tbpA) implying the content of thiamin or thiamin pyrophosphate, compared to e.g. biotin or riboflavin, in the host blood might be sufficient for the insect metabolic needs (Novakova, unpublished data). Within the spectrum of known Arsenophonus genomes ranging from 0.57 Mb of Ca. Riesia pediculicola to 3.5 Mb of A. nasoniae , representing various symbiotic types, the genomic sequence of Ca. Arsenophonus lipopteni clearly reflects characteristics common for obligate mutualists. Furthermore, the phylogenetic reconstruction suggests an independent origin of this obligate association within Hippoboscidae.
This work was supported by grant 13-01878S (Czech Science Foundation) to VH, and the project Postdoc USB (reg.no.CZ.1.07/2.3.00/30.0006) realized through EU Education for Competitiveness Operational Programme. PN was supported by Grant 14-35819P of the Czech Science Foundation.
EN, AD, VH participated in the design of the study and coordination. EN, FH and PN performed the imaging. VH and FH assembled and annotated the genome sequence. All authors participated in editing of the manuscript and read and approved the final version.
The authors declare that they have no involvement in any organization or entity with any financial interest, or non-financial interest in the subject matter or materials discussed in this manuscript.
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
- Beard CB, Cordon-Rosales C, Durvasula RV. Bacterial Symbionts of the Triatominae and their potential use in control of Chagas disease transmission 1. Annu Rev Entomol. 2002;47:123–41.View ArticlePubMedGoogle Scholar
- Gumiel M, da Mota FF, Rizzo Vde S, Sarquis O, de Castro DP, Lima MM, et al. Characterization of the microbiota in the guts of Triatoma brasiliensis and Triatoma pseudomaculata infected by Trypanosoma cruzi in natural conditions using culture independent methods. Parasit Vectors. 2015;8:245.View ArticlePubMedPubMed CentralGoogle Scholar
- Hypša V, Křížek J. Molecular evidence for polyphyletic origin of the primary symbionts of sucking lice (Phthiraptera, Anoplura). Microbial Ecol. 2007;54:242–51.View ArticleGoogle Scholar
- Sasaki-Fukatsu K, Koga R, Nikoh N, Yoshizawa K, Kasai S, Mihara M, et al. Symbiotic bacteria associated with stomach discs of human lice. Appl Environ Microbiol. 2006;72:7349–52.View ArticlePubMedPubMed CentralGoogle Scholar
- Hosokawa T, Koga R, Kikuchi Y, Meng XY, Fukatsu T. Wolbachia as a bacteriocyte-associated nutritional mutualist. Proc Natl Acad Sci U S A. 2010;107:769–74.View ArticlePubMedGoogle Scholar
- Aksoy S, Chen X, Hypsa V. Phylogeny and potential transmission routes of midgut-associated endosymbionts of tsetse (Diptera: Glossinidae). Insect Mol Biol. 1997;6:183–90.View ArticlePubMedGoogle Scholar
- Nováková E, Husník F, Šochová E, Hypša V. Arsenophonus and Sodalis symbionts in louse flies: an analogy to the Wigglesworthia and Sodalis system in tsetse flies. Appl Environ Microbiol. 2015;81:6189–99.View ArticlePubMedPubMed CentralGoogle Scholar
- Nelson M, Graf J. Bacterial symbioses of the medicinal leech Hirudo verbana. Gut Microbes. 2012;3:322–31.View ArticlePubMedPubMed CentralGoogle Scholar
- Manzano-Marín A, Oceguera-Figueroa A, Latorre A, Jiménez-García LF, Moya A. Solving a bloody mess: B-vitamin independent metabolic convergence among gammaproteobacterial obligate endosymbionts from blood-feeding arthropods and the leech Haementeria officinalis. Gen Biol Evol. 2015;7:2871–84.View ArticleGoogle Scholar
- Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol. 1990;56:1919–25.PubMedPubMed CentralGoogle Scholar
- Behrens S, Rühland C, Inácio J, Huber H, Fonseca A, Spencer-Martins I, et al. In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes. App Environ Microbiol. 2003;69:1748–58.View ArticleGoogle Scholar
- Charles H, Heddi A, Rahbe Y. A putative insect intracellular endosymbiont stem clade, within the Enterobacteriaceae, inferred from phylogenetic analysis based on a heterogeneous model of DNA evolution. C R Acad Sci Ser III Sci Vie. 2001;324:489–94.View ArticleGoogle Scholar
- Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, et al. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res. 2010;38:D396–400.View ArticlePubMedGoogle Scholar
- Lerat E, Daubin V, Moran NA. From gene trees to organismal phylogeny in prokaryotes: the case of the γ-proteobacteria. PLoS Biol. 2003;1:e19.View ArticlePubMedPubMed CentralGoogle Scholar
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.View ArticlePubMedGoogle Scholar
- Lartillot N, Lepage T, Blanquart S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics. 2009;25:2286–8.View ArticlePubMedGoogle Scholar
- Nováková E, Hypša V, Moran NA. Arsenophonus, an emerging clade of intracellular symbionts with a broad host distribution. BMC Microbiol. 2009;9:1–14.View ArticleGoogle Scholar
- Tritt A, Eisen JA, Facciotti MT, Darling AE. An integrated pipeline for de novo assembly of microbial genomes. PLoS One. 2012;7:e42304.View ArticlePubMedPubMed CentralGoogle Scholar
- Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014;9:e112963.View ArticlePubMedPubMed CentralGoogle Scholar
- Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75.View ArticlePubMedPubMed CentralGoogle Scholar
- Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.View ArticlePubMedGoogle Scholar
- Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000;28:33–6.View ArticlePubMedPubMed CentralGoogle Scholar
- Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;8:785–6.View ArticlePubMedGoogle Scholar
- Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011;7:e1002195.View ArticlePubMedPubMed CentralGoogle Scholar
- Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, et al. The Pfam protein families database. Nucleic Acids Res. 2002;30:276–80.View ArticlePubMedPubMed CentralGoogle Scholar
- Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28:1647–9.View ArticlePubMedPubMed CentralGoogle Scholar
- McCutcheon JP, Moran NA. Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol. 2012;10:13–26.Google Scholar
- Merhej V, Royer-Carenzi M, Pontarotti P, Raoult D. Massive comparative genomic analysis reveals convergent evolution of specialized bacteria. Biol Direct. 2009;4:13.View ArticlePubMedPubMed CentralGoogle Scholar
- Kirkness EF, Haas BJ, Sun W, Braig HR, Perotti MA, Clark JM, et al. Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. Proc Natl Acad Sci U S A. 2010;107:12168–73.View ArticlePubMedPubMed CentralGoogle Scholar
- Attardo GM, Abila PP, Auma JE, Baumann AA, Benoit JB, Brelsfoard CL, et al. Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis. Science. 2014;344:380–6.View ArticleGoogle Scholar
- Jaehme M, Slotboom DJ. Diversity of membrane transport proteins for vitamins in bacteria and archaea. Biochimica et Biophysica Acta (BBA)-General Subjects. 2015;1850:565–76.View ArticleGoogle Scholar
- Puchta O. Experimentelle Untersuchungen über die Bedeutung der Symbiose der Kleiderlaus Pediculus vestimenti Burm. Z Parasitenkd. 1955;17:1–40.View ArticlePubMedGoogle Scholar
- Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990;87:4576–9.View ArticlePubMedPubMed CentralGoogle Scholar
- Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey’s Manual of Systematic Bacteriology, vol. Volume 2, Part B. 2nd ed. New York: Springer; 2005. p. 1.View ArticleGoogle Scholar
- Garrity GM, Bell JA, Lilburn T. Class III. Gammaproteobacteria class. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey’s Manual of Systematic Bacteriology, vol. Volume 2, Part B. 2nd ed. New York: Springer; 2005. p. 1.View ArticleGoogle Scholar
- Garrity GM, Holt JG. Taxonomic Outline of the Archaea and Bacteria. In: Garrity GM, Boone DR, Castenholz RW, editors. Bergey’s Manual of Systematic Bacteriology, vol. Volume 1. 2nd ed. New York: Springer; 2001. p. 155–66.Google Scholar
- Judicial Commission Conservation of the family name Enterobacteriaceae, of the name of the type genus, and designation of the type species OPINION NO. 15. Int Bull Bacteriol Nomencl Taxon. 1958;8:73–4.Google Scholar
- Werren JH. Arsenophonus. Bergey’s Manual of Systematic Bacteriology (Vol. 2), G.M. Garrity (ed), New York: Springer-Verlag; 2004:1–4Google Scholar
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–9.View ArticlePubMedPubMed CentralGoogle Scholar