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Bigyra

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Bigyra
Aplanochytrium, SEM showing one vegetative cell and extended ectoplasmic network.
Aplanochytrium,SEMshowing onevegetative celland extendedectoplasmicnetwork.
Scientific classificationEdit this classification
Domain: Eukaryota
Clade: Diaphoretickes
Clade: SAR
Clade: Stramenopiles
Phylum: Bigyra
Cavalier-Smith1998,[1]emend. 2006[2]emend. 2013[3]
Clades[4]

Bigyra(fromLatinbi-'twice', andgyrus'circle')[1]is aphylumof microscopiceukaryotesthat are found at the base of theStramenopilesclade.It includes three well-knownheterotrophicgroupsBicosoecida,OpalinataandLabyrinthulomycetes,as well as several smallcladesinitially discovered throughenvironmental DNAsamples:Nanomonadea,Placididea,OpalomonadeaandEogyrea.The classification of Bigyra has changed several times since its origin, and itsmonophylyremains unresolved.

Ecological diversity

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Bigyra is a diverse group ofheterotrophic,mainlyphagotrophicstramenopilesthat lackcell walls.[4]It contains three well-known important groups with widely different ecological functions and morphologies:labyrinthulomycetes,opalinesandbicosoecids.[5]

Labyrinthulomycetesis a group ofprotiststhat absorb nutrients in anosmotrophicorphagotrophicmanner. They can behave either as free-livingamoebaeor asmycelium-like networks ofcytoplasmicthreads. Some of them aresaprotrophicdecomposersof thedetritalfood web;as such, they play a role in making organic matter more accessible to other organisms. Others areparasitic,and others are predators ofbacteria.They arecosmopolitan,ubiquitousinmarine,freshwaterandestuarineenvironments. They live in association withalgae,marineplantsanddetritus.[5]

Opalinatais a diverse assemblage of modifiedparasiticprotists known as 'opalines'. They inhabit theintestinesof variousanimals,primarilyamphibians.They are found on everycontinent.Among them, theopalinidsare highly unusual protists: their large cells have numerous flagella and from two to hundreds ofnuclei.Theircell surfaceis delicately folded, giving it aniridescentappearance (hence their name, a reference to the iridescentopal). Another important group of opalines isBlastocystis,a prevalent parasite of humans and other animals.[5]

Bicosoecidais a small group that contains free-livingmarineandfreshwaternanoflagellatesthat feed onbacteria.They are present in every ecosystem, including extreme environments such as the deep sea or salt flats. They play a crucial role in themicrobialfood web by composing the link between bacteria and highertrophic levels.They are also important in biogeochemical cycles by remineralizing the nutrients. Their classification has changed multiple times over the years,[6]and is still an unresolved issue.[7]

Opalinid
Blastocystisfromprimateintestines
Labyrinthulidwith cytoplasmic network
Bicosoecidwith twoheterokontflagella

Evolution and systematics

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External

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Bigyra contains many of the earliest-divergingcladesof theStramenopiles.[8]The Stramenopiles are asupergroupofeukaryoticorganisms (protists) characterized by the presence of an anteriorflagellumwith tripartite hairs, calledmastigonemes.Together withRhizariaandAlveolata,the Stramenopiles compose theSAR supergroup.[4]

All of Bigyra areheterotrophicmicroorganisms evolved from the last common ancestor of Stramenopiles, which is thought to have been phototrophic. Following this hypothesis, the bigyran ancestor would havesecondarily losttheir photosyntheticplastids.Some characteristics of bigyran groups can be explained by their origin from ancestral plastids. For example,labyrinthulomycetescan produceomega-3 poly-unsaturated fatty acidsthrough adesaturaseusually present inchloroplasts.[9]

Internal

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Bigyra is composed of twosubphyla:OpalozoaandSagenista.Opalozoa is further subdivided into two groups:Placidozoa,which contains theopalinesand three clades discovered through the detection ofenvironmental DNA(Nanomonadea,OpalomonadeaandPlacididea), and thebicosoecidflagellates. Sagenista contains thelabyrinthulomycetesand two environmental clades grouped under the nameEogyrea.[10][11]

Themonophylyof Bigyra remains uncertain. The positions of the two bigyranclades(Opalozoa and Sagenista) are not consistent between the published studies, because theydivergedfrom each other very early after the separation from the ancestor of allstramenopiles.This 'deep branching' makes it difficult to find the exact branching order of bigyran clades.[2]Additionally, not all clades are well-represented by molecular data in these studies.[10]Several studies support themonophylyof Bigyra.[10][11]Other studies support itsparaphyly.[12][13]

Monophyletic Bigyra[10] Paraphyletic Bigyra[13]
Stramenopiles
Stramenopiles
Bigyra

History

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Initial phylogeny of Bigyra (1997)[14]
Heterokonta

Bigyra was first described in 1997 by theprotozoologistThomas Cavalier-Smithas aphylumwithinHeterokonta(synonymof Stramenopiles). Bigyra was defined as organisms with thesynapomorphyof aciliary transition region(i.e. a structure that controls protein transport at the base of the flagellum) with structures in the shape of two helices or rings, hence the name 'bigyra' meaning 'double helix'. It contained three subgroups:[1]

  1. Pseudofungi,saprotrophicprotists withcell walls.
  2. Opalinata,non-phagotrophicgut-symbiotesfound inanimals.
  3. Bigyromonada,phagotrophiczooflagellates.

Their common ancestor was thought to have evolved fromphotosyntheticheterokonts, but would havesecondarily lostitsplastids,as opposed to the photosyntheticOchrophytawhich retain them. Bigyra was, at the time, postulated as amonophyleticgroup (orclade), evolved from aparaphyleticgradeofochrophyteclasses.[1][14]

Posterior analyses completely changed the phylogeny of Stramenopiles. They revealedPseudofungiandBigyromonadeawere more closely related to a monophyleticOchrophytathan they were toOpalinata,meaning that thesynapomorphyof a double helix could have been present in the common ancestor of all heterokonts. This rendered Bigyraparaphyletic.Consequently, Bigyra was revised andmodifiedin 2006 to comprise a different set of three subphyla:

  1. Opalozoa,a previouslypolyphyleticdiverse phylum that was modified to only includeOpalinataandNucleohelea;
  2. Bicoecea,containing thebicosoecids;
  3. Sagenista,containing theosmotrophicLabyrinthulea.

Bigyra was modified again in 2013 after the discovery of severalenvironmentalclades called MAST ('MArineSTramenopiles’). The subphylumOpalozoaassimilated thebicosoecidsand an array of new clades:Placididea,Nanomonadea(MAST-3) andOpalomonadea(MAST-12). The subphylumSagenista,on the other hand, received a new classEogyreathat was composed of several MAST lineages not yet described.[3]Later, one of the MAST clades withinEogyreawould be described asPseudophyllomitus(MAST-6).[15]

References

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  1. ^abcdCavalier-Smith T (1998). "A revised six-kingdom system of life".Biol Rev Camb Philos Soc.73(3): 203–66.doi:10.1111/j.1469-185X.1998.tb00030.x.PMID9809012.S2CID6557779.
  2. ^abCavalier-Smith T, Chao EE (April 2006). "Phylogeny and megasystematics of phagotrophic heterokonts (kingdom Chromista)".J. Mol. Evol.62(4): 388–420.Bibcode:2006JMolE..62..388C.doi:10.1007/s00239-004-0353-8.PMID16557340.S2CID29567514.
  3. ^abCavalier-Smith, Thomas; Scoble, Josephine Margaret (2013)."Phylogeny of Heterokonta:Incisomonas marina,a uniciliate gliding opalozoan related toSolenicola(Nanomonadea), and evidence that Actinophryida evolved from raphidophytes ".European Journal of Protistology.49(3): 328–353.doi:10.1016/j.ejop.2012.09.002.PMID23219323.
  4. ^abcAdl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A, Agatha S, Berney C, Brown MW, Burki F, Cárdenas P, Čepička I, Chistyakova L, del Campo J, Dunthorn M, Edvardsen B, Eglit Y, Guillou L, Hampl V, Heiss AA, Hoppenrath M, James TY, Karnkowska A, Karpov S, Kim E, Kolisko M, Kudryavtsev A, Lahr DJG, Lara E, Le Gall L, Lynn DH, Mann DG, Massana R, Mitchell EAD, Morrow C, Park JS, Pawlowski JW, Powell MJ, Richter DJ, Rueckert S, Shadwick L, Shimano S, Spiegel FW, Torruella G, Youssef N, Zlatogursky V, Zhang Q (2019)."Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes".Journal of Eukaryotic Microbiology.66(1): 4–119.doi:10.1111/jeu.12691.PMC6492006.PMID30257078.
  5. ^abcBennett, Reuel M.; Honda, D.; Beakes, Gordon W.; Thines, Marco (2017). "Chapter 14. Labyrinthulomycota". In Archibald, John M.; Simpson, Alastair G.B.; Slamovits, Claudio H. (eds.).Handbook of the Protists.Springer. pp. 507–542.doi:10.1007/978-3-319-28149-0_25.ISBN978-3-319-28147-6.
  6. ^Karpov SA, Sogin ML, Silberman JD (2001). "Rootlet homology, taxonomy, and phylogeny of bicosoecids based on 18S rRNA gene sequences".Protistology.2(1): 34–47.
  7. ^Schoenle A, Hohlfeld M, Rybarski A, Sachs M, Freches E, Wiechmann K, Nitsche F, Arndt H (2022). "Cafeteria in extreme environments: Investigations on C. burkhardae and three new species from the Atacama Desert and the deep ocean".European Journal of Protistology.85:125905.doi:10.1016/j.ejop.2022.125905.PMID35868212.S2CID249935619.
  8. ^Riisberg I, Orr RJ, Kluge R, et al. (May 2009). "Seven gene phylogeny of heterokonts".Protist.160(2): 191–204.doi:10.1016/j.protis.2008.11.004.PMID19213601.
  9. ^Tsui, Clement K M; Marshall, Wyth; Yokoyama, Rinka; Honda, Daiske; Lippmeier, J Casey; Craven, Kelly D; Peterson, Paul D; Berbee, Mary L (January 2009). "Labyrinthulomycetes phylogeny and its implications for the evolutionary loss of chloroplasts and gain of ectoplasmic gliding".Molecular Phylogenetics and Evolution.50(1): 129–40.doi:10.1016/j.ympev.2008.09.027.PMID18977305.
  10. ^abcdThakur, Rabindra; Shiratori, Takashi; Ishida, Ken-ichiro (2019)."Taxon-rich Multigene Phylogenetic Analyses Resolve the Phylogenetic Relationship Among Deep-branching Stramenopiles".Protist.170(5): 125682.doi:10.1016/j.protis.2019.125682.ISSN1434-4610.PMID31568885.S2CID202865459.
  11. ^abCavalier-Smith, Thomas (2017)."Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences".Protoplasma.255(1): 297–357.doi:10.1007/s00709-017-1147-3.PMC5756292.PMID28875267.
  12. ^Tan MH, Loke S, Croft LJ, Gleason FH, Lange L, Pilgaard B, Trevathan-Tackett SM (2021). "First Genome ofLabyrinthulasp., an Opportunistic Seagrass Pathogen, Reveals Novel Insight into Marine Protist Phylogeny, Ecology and CAZyme Cell-Wall Degradation ".Microbial Ecology.82(2): 498–511.doi:10.1007/s00248-020-01647-x.PMID33410934.S2CID230819360.
  13. ^abCho A, Tikhonenkov DV, Hehenberger E, Karnkowska A, Mylnikov AP, Keeling PJ (2022)."Monophyly of diverse Bigyromonadea and their impact on phylogenomic relationships within stramenopiles"(PDF).Molecular Phylogenetics and Evolution.171(107468): 107468.doi:10.1016/j.ympev.2022.107468.ISSN1055-7903.PMID35358688.S2CID247815732.
  14. ^abCavalier-Smith T (1998). "Sagenista and Bigyra, two phyla of heterotrophic heterokont chromists".Archiv für Protistenkunde.148(3): 253–267.doi:10.1016/S0003-9365(97)80006-1.
  15. ^Shiratori, Takashi; Thakur, Rabindra; Ishida, Ken-ichiro (2017)."Pseudophyllomitus vesiculosus (Larsen and Patterson 1990) Lee, 2002, a Poorly Studied Phagotrophic Biflagellate is the First Characterized Member of Stramenopile Environmental Clade MAST-6".Protist.168(4): 439–451.doi:10.1016/j.protis.2017.06.004.ISSN1434-4610.PMID28822908.
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