Price PW. General concepts on the evolutionary biology of parasites. Evolution. 1977;31:405–20.

Article  PubMed  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 

Katinka MD, Duprat S, Cornillot E, Méténier G, Thomarat F, Prensier G, et al. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature. 2001;414:450–3.

Article  CAS  PubMed  Google Scholar 

Keeling PJ, Fast NM. Microsporidia: biology and evolution of highly reduced intracellular parasites. Annu Rev Microbiol. 2002;56:93–116.

Article  CAS  PubMed  Google Scholar 

Keeling PJ, Slamovits CH. Causes and effects of nuclear genome reduction. Curr Opin Genet Dev. 2005;15:601–8.

Article  CAS  PubMed  Google Scholar 

Hikosaka K, Kita K, Tanabe K. Diversity of mitochondrial genome structure in the phylum Apicomplexa. Mol Biochem Parasitol. 2013;188:26–33.

Article  CAS  PubMed  Google Scholar 

Jackson AP, Otto TD, Aslett M, Armstrong SD, 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 

Pombert J-F, Blouin NA, Lane C, Boucias D, Keeling PJ. A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium. PLoS Genet. 2014;10:e1004355.

Article  PubMed  PubMed Central  Google Scholar 

Janouškovec J, Tikhonenkov Denis V, Burki F, Howe AT, Kolísko M, Mylnikov AP, et al. Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives. Proc Natl Acad Sci. 2015;112:10200–7.

Article  PubMed  PubMed Central  Google Scholar 

M’Gonigle LK, Shen JJ, Otto SP. Mutating away from your enemies: the evolution of mutation rate in a host–parasite system. Theor Popul Biol. 2009;75:301–11.

Article  PubMed  Google Scholar 

Papkou A, Gokhale CS, Traulsen A, Schulenburg H. Host–parasite coevolution: why changing population size matters. Zoology. 2016;119:330–8.

Article  PubMed  Google Scholar 

Bass D, Ward GM, Burki F. Ascetosporea. Curr Biol. 2019;29:R7-8.

Article  CAS  PubMed  Google Scholar 

Hartikainen H, Ashford OS, Berney C, Okamura B, Feist SW, Baker-Austin C, et al. Lineage-specific molecular probing reveals novel diversity and ecological partitioning of haplosporidians. ISME J. 2014;8:177–86.

Article  CAS  PubMed  Google Scholar 

Winters AD, Faisal M. Molecular and ultrastructural characterization of Haplosporidium diporeiae n. sp., a parasite of Diporeia sp. (Amphipoda, Gammaridea) in the Laurentian Great Lakes (USA). Parasit Vect. 2014;7:343.

Article  Google Scholar 

Laing I, Dunn P, Peeler E, Feist S, Longshaw M. Epidemiology of Bonamia in the UK, 1982 to 2012. Dis Aquat Organ. 2014;110:101–11.

Article  CAS  PubMed  Google Scholar 

Alderman DJ. Epizootiology of Marteilia refringens in Europe. Mar Fish Rev. 1979;41:67–9.

Google Scholar 

Ward GM, Bennett M, Bateman K, Stentiford GD, Kerr R, Feist SW, et al. A new phylogeny and environmental DNA insight into paramyxids: an increasingly important but enigmatic clade of protistan parasites of marine invertebrates. Int J Parasitol. 2016;46:605–19.

Article  PubMed  Google Scholar 

Hartikainen H, Stentiford GD, Bateman KS, Berney C, Feist SW, Longshaw M, et al. Mikrocytids are a broadly distributed and divergent radiation of parasites in aquatic invertebrates. Curr Biol. 2014;24:807–12.

Article  CAS  PubMed  Google Scholar 

Lynch SA, Lepée-Rivero S, Kelly R, Quinn E, Coghlan A, Bookelaar B, et al. Detection of haplosporidian protistan parasites supports an increase to their known diversity, geographic range and bivalve host specificity. Parasitology. 2020;147:584–92.

Article  CAS  PubMed  Google Scholar 

Collins E, Ward GM, Bateman KS, Cheslett DL, Hooper C, Feist SW, et al. High prevalence of Paramarteilia canceri infecting velvet swimming crabs Necora puber in Ireland. Dis Aquat Organ. 2022;148:167–81.

Article  PubMed  Google Scholar 

Skujina I, Hooper C, Bass D, Feist SW, Bateman KS, Villalba A, et al. Discovery of the parasite Marteilia cocosarum sp. nov. in common cockle (Cerastoderma edule) fisheries in Wales, UK and its comparison with Marteilia cochillia. J Invertebr Pathol. 2022;192:107786.

Article  PubMed  Google Scholar 

Stentiford G, Bateman K, Stokes N, Carnegie R. Haplosporidium littoralis sp. nov.: a crustacean pathogen within the Haplosporida (Cercozoa, Ascetosporea). Dis Aquat Organ. 2013;105:243–52.

Article  CAS  PubMed  Google Scholar 

Cavalier-Smith T, Chao EE-Y. Phylogeny and classification of phylum cercozoa (Protozoa). Protist. 2003;154:341–58.

Article  PubMed  Google Scholar 

Bass D, Chao EE-Y, Nikolaev S, Yabuki A, Ishida K, Berney C, et al. Phylogeny of novel naked filose and reticulose cercozoa: granofilosea cl. n. and proteomyxidea revised. Protist. 2009;160:75–109.

Article  PubMed  Google Scholar 

Sierra R, Cañas-Duarte SJ, Burki F, Schwelm A, Fogelqvist J, Dixelius C, et al. Evolutionary origins of Rhizarian parasites. Mol Biol Evol. 2016;33:980–3.

Article  CAS  PubMed  Google Scholar 

Burki F, Corradi N, Sierra R, Pawlowski J, Meyer GR, Abbott CL, et al. Phylogenomics of the intracellular parasite Mikrocytos mackini reveals evidence for a mitosome in Rhizaria. Curr Biol. 2013;23:1541–7.

Article  CAS  PubMed  Google Scholar 

Onuț-Brännström I, Stairs CW, Campos KIA, Thorén MH, Ettema TJG, Keeling PJ, et al. A mitosome with distinct metabolism in the uncultured protist parasite Paramikrocytos canceri (Rhizaria, Ascetosporea). Genome Biol Evol. 2023;15:evad022.

Article  PubMed  PubMed Central  Google Scholar 

Žárský V, Karnkowska A, Boscaro V, Trznadel M, Whelan TA, Hiltunen-Thorén M, et al. Contrasting outcomes of genome reduction in mikrocytids and microsporidians. BMC Biol. 2023;21:137.

Article  PubMed  PubMed Central  Google Scholar 

Carrasco N, Green T, Itoh N. Marteilia spp. parasites in bivalves: a revision of recent studies. J Invertebr Pathol. 2015;131:43–57.

Article  PubMed  Google Scholar 

Astashyn A, Tvedte ES, Sweeney D, Sapojnikov V, Bouk N, Joukov V, et al. Rapid and sensitive detection of genome contamination at scale with FCS-GX. Genome Biol. 2024;25:60.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Waterhouse RM, Seppey M, Simão FA, Manni M, Ioannidis P, Klioutchnikov G, et al. BUSCO Applications from quality assessments to gene prediction and phylogenomics. Mol Biol Evol. 2018;35:543–8.

Article  CAS  PubMed  Google Scholar 

Salas-Leiva DE, Tromer EC, Curtis BA, Jerlström-Hultqvist J, Kolisko M, Yi Z, et al. Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist. Nat Commun. 2021;12:6003.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chevignon G, Dotto-Maurel A, Serpin D, Chollet B, Arzul I. De novo transcriptome assembly and analysis of the flat oyster pathogenic protozoa Bonamia ostreae. Front Cell Infect Microbiol. 2022;12:921136.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Keeling PJ, Corradi N. Shrink it or lose it: balancing loss of function with shrinking genomes in the Microsporidia. Virulence. 2011;2:67–70.

Article  PubMed  Google Scholar 

Lopes FR, Silva JC, Benchimol M, Costa GG, Pereira GA, Carareto CM. The protist Trichomonas vaginalis harbors multiple lineages of transcriptionally active Mutator-like elements. BMC Genomics. 2009;10:330.

Article  PubMed  PubMed Central  Google Scholar 

Hirakawa Y, Watanabe A. Organellar DNA polymerases in complex plastid-bearing algae. Biomolecules. 2019;9:140.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Villalba A, Mourelle S, López M, Carballal M, Azevedo C. Marteiliasis affecting cultured mussels Mytilus galloprovincialis of Galioa (NW Span). I. Etiology, chases of the infection, and temporal and spatial variability in prevalence. Dis Aquat Organ. 1993;16:61–72.

Article  Google Scholar 

Perkins FO. Ultrastructure of sporulation in the European flat oyster pathogen, Marteilia refringens—taxonomic implications. J Protozool. 1976;23:64–74.

Article  Google Scholar 

Ward GM, Neuhauser S, Groben R, Ciaghi S, Berney C, Romac S, et al. Envi