Poulin R. Evolutionary ecology of parasites. Princeton: Princeton University Press; 2007.
Google Scholar
Poulin R, Randhawa HS. Evolution of parasitism along convergent lines: from ecology to genomics. Parasitology. 2015;142:S6–15.
Article
PubMed
Google Scholar
Heinz E, Williams TA, Nakjang S, Noel CJ, Swan DC, Goldberg AV, et al. The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution. PLoS Pathog. 2012;8:e1002979.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rohmer L, Hocquet D, Miller SI. Are pathogenic bacteria just looking for food? Metabolism and microbial pathogenesis. Trends Microbiol. 2011;19:341–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jackson A, Otto T, Aslett M, Armstrong S, Bringaud F, Schlacht A, et al. Kinetoplastid phylogenomics reveals the evolutionary innovations associated with the origins of parasitism. Curr Biol. 2016;26:161–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Woo YH, Ansari H, Otto TD, Klinger CM, Kolisko M, Michálek J, et al. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. eLife. 2015;4:e06974.
Article
PubMed
PubMed Central
Google Scholar
Gould SJ. Dollo on Dollo’s law: irreversibility and the status of evolutionary laws. J Hist Biol. 1970;3:189–212.
Article
CAS
PubMed
Google Scholar
Cruickshank RH, Paterson AM. The great escape: do parasites break Dollo’s law? Trends Parasitol. 2006;22:509–15.
Article
PubMed
Google Scholar
Dorris M, Viney ME, Blaxter ML. Molecular phylogenetic analysis of the genus Strongyloides and related nematodes. Int J Parasitol. 2002;32:1507–17.
Article
CAS
PubMed
Google Scholar
Klimov PB, OConnor B. Is permanent parasitism reversible? – critical evidence from early evolution of house dust mites. Syst Biol. 2013;62:411–23.
Article
PubMed
Google Scholar
Siddall ME, Brooks DR, Desser SS. Phylogeny and the reversibility of parasitism. Evolution. 1993;47:308–13.
Article
Google Scholar
Brugerolle G, Lee JJ. Order Diplomonadida. In: Lee JJ, Leedale GF, Bradbury P, editors. An Illustrated Guide to the Protozoa. 2nd ed. Lawrence: Society of Protozoologists; 2002. p. 1125–35.
Adl SM, Simpson AG, Lane CE, Lukes J, Bass D, Bowser SS, et al. The revised classification of eukaryotes. J Eukaryot Microbiol. 2012;59:429–514.
Article
PubMed
PubMed Central
Google Scholar
Monis PT, Caccio SM, Thompson RC. Variation in Giardia: towards a taxonomic revision of the genus. Trends Parasitol. 2009;25:93–100.
Article
PubMed
Google Scholar
Caccio SM, Ryan U. Molecular epidemiology of giardiasis. Mol Biochem Parasitol. 2008;160:75–80.
Article
CAS
PubMed
Google Scholar
Jørgensen A, Sterud E. The marine pathogenic genotype of Spironucleus barkhanus from farmed salmonids redescribed as Spironucleus salmonicida n. sp. J Eukaryot Microbiol. 2006;53:531–41.
Article
PubMed
Google Scholar
Sterud E, Mo TA, Poppe TT. Systemic spironucleosis in sea-farmed Atlantic Salmon Salmo salar, caused by Spironucleus barkhanus transmitted from feral Arctic Char Salvelinus alpinus? Dis Aquat Organ. 1998;33:63–6.
Article
CAS
PubMed
Google Scholar
Sterud E, Poppe TT, Bornø G. Intracellular infection with Spironucleus barkhanus (Diplomonadida, Hexamitidae) in farmed Arctic char Salvelinus alpinus. Dis Aquat Org. 2003;56:155–61.
Article
PubMed
Google Scholar
Morrison HG, McArthur AG, Gillin FD, Aley SB, Adam RD, Olsen GJ, et al. Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science. 2007;317:1921–6.
Article
CAS
PubMed
Google Scholar
Xu F, Jerlström-Hultqvist J, Einarsson E, Astvaldsson A, Svärd SG, Andersson JO. The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments. PLoS Genet. 2014;10:e1004053.
Article
PubMed
PubMed Central
Google Scholar
Lundin D, Torrents E, Poole AM, Sjoberg BM. RNRdb, a curated database of the universal enzyme family ribonucleotide reductase, reveals a high level of misannotation in sequences deposited to Genbank. BMC Genomics. 2009;10:589.
Article
PubMed
PubMed Central
Google Scholar
Kolisko M, Silberman JD, Cepicka I, Yubuki N, Takishita K, Yabuki A, et al. A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitats. Environ Microbiol. 2010;12:2700–10.
CAS
PubMed
Google Scholar
Takishita K, Kolisko M, Komatsuzaki H, Yabuki A, Inagaki Y, Cepicka I, et al. Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of ‘amitochondriate’ diplomonads and retortamonads. Protist. 2012;163:344–55.
Article
PubMed
Google Scholar
Adam RD. Biology of Giardia lamblia. Clin Microbiol Rev. 2001;14:447–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ankarklev J, Jerlström-Hultqvist J, Ringqvist E, Troell K, Svärd SG. Behind the smile: cell biology and disease mechanisms of Giardia species. Nat Rev Microbiol. 2010;8:413–22.
CAS
PubMed
Google Scholar
Williams CF, Lloyd D, Poynton SL, Jorgensen A, Millet COM, Cable J. Spironucleus species: economically-important fish pathogens and enigmatic single-celled eukaryotes. J Aquac Res Devel. 2011;S2:002. http://www.omicsonline.org/spironucleus-species-economically-important-fish-pathogens-and-enigmatic-single-celled-eukaryotes-2155-9546.S2-002.php?aid=2762.
Poynton SL, Fraser W, Francis-Floyd R, Rutledge P, Reed P, Nerad TA. Spironucleus vortens n. sp. from fresh-water angel fish Pterophyllum scalare. Morphology and culture. J Eukaryot Microbiol. 1995;42:731–42.
Article
Google Scholar
Paull GC, Matthews RA. Spironucleus vortens, a possible cause of hole-in-the-head disease in cichlids. Dis Aquat Organ. 2001;45:197–202.
Article
CAS
PubMed
Google Scholar
Sterud E, Mo TA, Poppe TT. Ultrastructure of Spironucleus barkhanus n. sp. (Diplomonadida: Hexamitidae) from grayling Thymallus thymallus (L.) (Salmonidae) and Atlantic salmon Salmo salar L (Salmonidae). J Eukaryot Microbiol. 1997;44:399–407.
Article
Google Scholar
Poynton SL, Fard MRS, Jenkins J, Ferguson HW. Ultrastructure of Spironucleus salmonis n. comb. (formerly Octomitus salmonis sensu Moore 1922, Davis 1926, and Hexamita salmonis sensu Ferguson 1979), with a guide to Spironucleus species. Dis Aquat Organ. 2004;60:49–64.
Article
PubMed
Google Scholar
Fard MRS, Jorgensen A, Sterud E, Bleiss W, Poynton SL. Ultrastructure and molecular diagnosis of Spironucleus salmonis (Diplomonadida) from rainbow trout Oncorhynchus mykiss in Germany. Dis Aquat Organ. 2007;75:37–50.
Article
PubMed
Google Scholar
Poynton SL, Morrison CM. Morphology of diplomonad flagellates: Spironucleus torosa n. sp. from Atlantic cod Gadus morhua L., and haddock Melanogrammus aeglefinus (L.) and Hexamita salmonis Moore from brook trout Salvelinus fontinalis (Mitchill). J Protozool. 1990;37:369–83.
Article
CAS
PubMed
Google Scholar
Brett SJ, Cox FEG. Immunological aspects of Giardia muris and Spironucleus muris infections in inbred and outbred strains of laboratory mice: a comparative study. Parasitology. 1982;85:85–99.
Article
PubMed
Google Scholar
Siddall ME, Hong H, Desser SS. Phylogenetic analysis of the Diplomonadida (Wenyon, 1926) Brugerolle, 1975: evidence for heterochrony in protozoa and against Giardia lamblia as a “missing link”. J Protozool. 1992;39:361–7.
Article
CAS
PubMed
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Keeling PJ, Doolittle WF. A non-canonical genetic code in an early diverging eukaryotic lineage. EMBO J. 1996;15:2285–90.
CAS
PubMed
PubMed Central
Google Scholar
Kolisko M, Cepicka I, Hampl V, Leigh J, Roger AJ, Kulda J, et al. Molecular phylogeny of diplomonads and enteromonads based on SSU rRNA, alpha-tubulin and HSP90 genes: implications for the evolutionary history of the double karyomastigont of diplomonads. BMC Evol Biol. 2008;8:205.
Article
PubMed
PubMed Central
Google Scholar
Lozupone CA, Knight RD, Landweber LF. The molecular basis of nuclear genetic code change in ciliates. Curr Biol. 2001;11:65–74.
Article
CAS
PubMed
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.
Article
PubMed
Google Scholar
Andersson JO. Gene transfer and diversification of microbial eukaryotes. Annu Rev Microbiol. 2009;63:177–93.
Article
CAS
PubMed
Google Scholar
Hirt RP, Alsmark C, Embley TM. Lateral gene transfers and the origins of the eukaryote proteome: a view from microbial parasites. Curr Opin Microbiol. 2014;23C:155–62.
Google Scholar
Soucy SM, Huang J, Gogarten JP. Horizontal gene transfer: building the web of life. Nat Rev Genet. 2015;16:472–82.
Article
CAS
PubMed
Google Scholar
Yue J, Hu X, Sun H, Yang Y, Huang J. Widespread impact of horizontal gene transfer on plant colonization of land. Nat Commun. 2012;3:1152.
Article
PubMed
PubMed Central
Google Scholar
Ropars J, Rodríguez dela Vega Ricardo C, López-Villavicencio M, Gouzy J, Sallet E, Dumas É, et al. Adaptive horizontal gene transfers between multiple cheese-associated fungi. Curr Biol. 2015;25:2562–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Andersson JO, Sjögren ÅM, Horner DS, Murphy CA, Dyal PL, Svärd SG, et al. A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. BMC Genomics. 2007;8:51.
Article
PubMed
PubMed Central
Google Scholar
Franzén O, Jerlström-Hultqvist J, Castro E, Sherwood E, Ankarklev J, Reiner D, et al. Draft genome sequencing of Giardia intestinalis assemblage B isolate GS: are human giardiasis caused by two different species? PLoS Pathog. 2009;5(8):e1000560.
Article
PubMed
PubMed Central
Google Scholar
Frickey T, Lupas AN. PhyloGenie: automated phylome generation and analysis. Nucleic Acids Res. 2004;32:5231–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Podell S, Gaasterland T. DarkHorse: a method for genome-wide prediction of horizontal gene transfer. Genome Biol. 2007;8:R16.
Article
PubMed
PubMed Central
Google Scholar
Elsbach P, Weiss J. Role of the bactericidal/permeability-increasing protein in host defence. Curr Opin Immunol. 1998;10:45–9.
Article
CAS
PubMed
Google Scholar
Balakrishnan A, Marathe SA, Joglekar M, Chakravortty D. Bactericidal/permeability increasing protein: A multifaceted protein with functions beyond LPS neutralization. Innate Immun. 2013;19:339–47.
Article
PubMed
Google Scholar
Makarova KS, Aravind L, Koonin EV. A superfamily of archaeal, bacterial, and eukaryotic proteins homologous to animal transglutaminases. Protein Sci. 1999;8:1714–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Z, Wilhelmsson C, Hyrsl P, Loof TG, Dobes P, Klupp M, et al. Pathogen entrapment by transglutaminase—a conserved early innate immune mechanism. PLoS Pathog. 2010;6:e1000763.
Article
PubMed
PubMed Central
Google Scholar
Anantharaman V, Aravind L. Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes. Genome Biol. 2003;4:R11.
Article
PubMed
PubMed Central
Google Scholar
Firczuk M, Bochtler M. Folds and activities of peptidoglycan amidases. FEMS Microbiol Rev. 2007;31:676–91.
Article
CAS
PubMed
Google Scholar
Vollmer W, Joris B, Charlier P, Foster S. Bacterial peptidoglycan (murein) hydrolases. FEMS Microbiol Rev. 2008;32:259–86.
Article
CAS
PubMed
Google Scholar
Sobhanifar S, King DT, Strynadka NC. Fortifying the wall: synthesis, regulation and degradation of bacterial peptidoglycan. Curr Opin Struct Biol. 2013;23:695–703.
Article
CAS
PubMed
Google Scholar
Kashyap DR, Wang M, Liu L-H, Boons G-J, Gupta D, Dziarski R. Peptidoglycan recognition proteins kill bacteria by activating protein-sensing two-component systems. Nat Med. 2011;17:676–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Baum KF, Berens RL, Marr JJ, Harrington JA, Spector T. Purine deoxynucleoside salvage in Giardia lamblia. J Biol Chem. 1989;264:21087–90.
CAS
PubMed
Google Scholar
Dwivedi B, Xue B, Lundin D, Edwards R, Breitbart M. A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes. BMC Evol Biol. 2013;13:33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sillo A, Bloomfield G, Balest A, Balbo A, Pergolizzi B, Peracino B, et al. Genome-wide transcriptional changes induced by phagocytosis or growth on bacteria in Dictyostelium. BMC Genomics. 2008;9:291.
Article
PubMed
PubMed Central
Google Scholar
Castoreno AB, Wang Y, Stockinger W, Jarzylo LA, Du H, Pagnon JC, et al. Transcriptional regulation of phagocytosis-induced membrane biogenesis by sterol regulatory element binding proteins. Proc Natl Acad Sci U S A. 2005;102:13129–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Summons RE, Bradley AS, Jahnke LL, Waldbauer JR. Steroids, triterpenoids and molecular oxygen. Philos Trans R Soc B. 2006;361:951–68.
Article
CAS
Google Scholar
Mallory FB, Gordon JT, Conner RL. The isolation of a pentacyclic triterpenoid alcohol from a protozoan. J Am Chem Soc. 1963;85:1362–3.
Article
CAS
Google Scholar
Takishita K, Chikaraishi Y, Leger MM, Kim E, Yabuki A, Ohkouchi N, et al. Lateral transfer of tetrahymanol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen. Biol Direct. 2012;7:5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.
Article
CAS
PubMed
Google Scholar
Alsmark C, Foster PG, Sicheritz-Ponten T, Nakjang S, Martin Embley T, Hirt RP. Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes. Genome Biol. 2013;14:R19.
Article
PubMed
PubMed Central
Google Scholar
Paganini J, Campan-Fournier A, Da Rocha M, Gouret P, Pontarotti P, Wajnberg E, et al. Contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes. PLoS One. 2012;7:e50875.
Article
CAS
PubMed
PubMed Central
Google Scholar
Boto L. Horizontal gene transfer in the acquisition of novel traits by metazoans. Proc R Soc B. 2014;281:20132450.
Article
PubMed
PubMed Central
Google Scholar
Wijayawardena BK, Minchella DJ, DeWoody JA. Hosts, parasites, and horizontal gene transfer. Trends Parasitol. 2013;29:329–38.
Article
CAS
PubMed
Google Scholar
Stensvold CR, Lebbad M, Victory EL, Verweij JJ, Tannich E, Alfellani M, et al. Increased sampling reveals novel lineages of Entamoeba: consequences of genetic diversity and host specificity for taxonomy and molecular detection. Protist. 2011;162:525–41.
Article
PubMed
Google Scholar
Clark CG, Diamond LS. Intraspecific variation and phylogenetic relationships in the genus Entamoeba as revealed by riboprinting. J Eukaryot Microbiol. 1997;44:142–54.
Article
CAS
PubMed
Google Scholar
Yubuki N, Ceza V, Cepicka I, Yabuki A, Inagaki Y, Nakayama T, et al. Cryptic diversity of free-living parabasalids, Pseudotrichomonas keilini and Lacusteria cypriaca n. g., n. sp., as inferred from small subunit rDNA sequences. J Eukaryot Microbiol. 2010;57:554–61.
Article
CAS
PubMed
Google Scholar
Blaxter M, Koutsovoulos G. The evolution of parasitism in Nematoda. Parasitology. 2015;142:S26–39.
Article
PubMed
Google Scholar
Wu B, Novelli J, Jiang D, Dailey HA, Landmann F, Ford L, et al. Interdomain lateral gene transfer of an essential ferrochelatase gene in human parasitic nematodes. Proc Natl Acad Sci U S A. 2013;110:7748–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998;8:175–85.
Article
CAS
PubMed
Google Scholar
Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res. 1998;8:195–202.
Article
CAS
PubMed
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10–2.
Article
Google Scholar
Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011;27:863–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
UniProt C. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012;40:D71–5.
Article
Google Scholar
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2013;42:D222–30.
Article
PubMed
PubMed Central
Google Scholar
Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011;7:e1002195.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li L, Stoeckert Jr CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13:2178–89.
Article
CAS
PubMed
PubMed Central
Google Scholar
Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007;35:W182–5.
Article
PubMed
PubMed Central
Google Scholar
HMMER: biosequence analysis using profile hidden Markov models. 2016. http://hmmer.org/. Accessed 3 Feb 2016.
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Criscuolo A, Gribaldo S. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol. 2010;10:210.
Article
PubMed
PubMed Central
Google Scholar