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Diplomova Prace Pavla Smejkalova Univerzita Karlova v Praze Přírodov ědecká fakulta Katedra parazitologie Evoluce skupiny Retortamonadida (Eukaryota: Excavata: Fornicata) Bc. Pavla Smejkalová Diplomová práce Praha 2010 Vedoucí diplomové práce: RNDr. Ivan Čepi čka, Ph.D. Konzultant: Prof. RNDr. Jaroslav Kulda, CSc. Prohlašuji, že jsem tuto práci vypracovala samostatn ě a uvedla citace všech použitých pramen ů. V Praze, 3. 5. 2010 Pavla Smejkalová 2 Na tomto místě bych cht ěla vyjád řit velké pod ěkování svému školiteli RNDr. Ivanu Čepi čkovi, Ph.D. za vedení b ěhem práce v laborato ři a za mnoho podn ětných p řipomínek při sepisování diplomové práce. D ěkuju Ivane, bez tvé pomoci bych tuto práci nikdy nedopsala. Také bych cht ěla pod ěkovat prof. RNDr. Jaroslavu Kuldovi, CSc. za poskytnuté výsledky ultrastrukturní studie a odborné rady. Děkuji všem lidem z našeho týmu za pomoc a za p říjemn ě strávený čas nejen v laborato ři, ale i mimo ni. V neposlední řad ě bych cht ěla poděkovat svým rodi čů m za podporu b ěhem studia. 3 1. ABSTRAKT .........................................................................................................................6 2. ABSTRAKT .........................................................................................................................7 3. CÍLE......................................................................................................................................8 4. LITERÁRNÍ P ŘEHLED ......................................................................................................9 4.1. Vývoj taxonomie od skupiny Metamonadida k Fornicata........................................... 9 4.1.1. Metamonadida a p ůvodní Metamonada............................................................... 9 4.1.2. Teorie Archezoa................................................................................................. 10 4.1.3. Exkavátní hypotéza............................................................................................ 12 4.1.4. Moderní Metamonada........................................................................................ 14 4.1.5. Fornicata ............................................................................................................ 14 4.2. Fornicata z hlediska morfologie................................................................................. 18 4.2.1. Řád Retortamonadida......................................................................................... 18 4.2.2. Řád Diplomonadida ........................................................................................... 25 4.2.3. Bazální Fornicata ............................................................................................... 26 5. MATERIÁL A METODY..................................................................................................27 5.1. Kultivace a izolace nových izolát ů ............................................................................ 27 5.1.1. Složení a p říprava používaných médií............................................................... 27 5.1.2. Získávání nových izolát ů ................................................................................... 29 5.1.3. Kultivace retortamonád...................................................................................... 30 5.2. Příprava a zpracování trvalých preparát ů .................................................................. 31 5.2.1. Barvení protargolem podle Bodiana.................................................................. 31 5.2.2. Mikroskopické pozorování a zpracovávání preparát ů ....................................... 33 5.3. Izolace DNA .............................................................................................................. 33 5.4. Amplifikace DNA a sekvenace.................................................................................. 33 5.4.1. Amplifikace DNA pomocí specifických primer ů .............................................. 34 5.4.2. Elektroforéza amplifikované DNA.................................................................... 36 5.4.3. Přečišt ění PCR produktu.................................................................................... 37 5.4.4. Klonování........................................................................................................... 37 5.4.5. Colony PCR....................................................................................................... 38 5.4.6. Izolace plasmid ů ................................................................................................ 39 5.4.7. Sekvena ční reakce.............................................................................................. 39 5.5. Vyhodnocování sekvencí a fylogenetická analýza .................................................... 40 5.5.1. Tvorba a úprava alignmentu .............................................................................. 40 5.5.2. Tvorba fylogenetických strom ů ......................................................................... 41 6. VÝSLEDKY.......................................................................................................................42 6.1. Izoláty ........................................................................................................................ 42 6.1.1. Vyšet ření hostitelé ............................................................................................. 42 6.1.2. Kultury............................................................................................................... 43 6.2. Fylogenetická analýza................................................................................................ 44 6.3. Porovnání délek a hypervariabilních oblastí u blízce p říbuzných druh ů retortamonád ........ 47 6.4. Morfologie ................................................................................................................. 48 4 7. DISKUZE ...........................................................................................................................52 7.1. Získávání nových izolát ů a sekvence:........................................................................ 52 7.2. Molekulárn ě-fylogenetická analýza........................................................................... 54 7.3. Rod Retortamonas...................................................................................................... 55 7.4. Rod Chilomastix ........................................................................................................ 56 7.5. Řád Retortamonadida................................................................................................. 57 8. ZÁV ĚRE ČNÉ SHRNUTÍ ..................................................................................................59 9. SEZNAM POUŽITÉ LITERATURY ................................................................................60 10. SEZNAM ZKRATEK ........................................................................................................72 5 1. ABSTRAKT Řád Retortamonadida je malou skupinou heterotrofních bi číkovc ů, kte ří se d ělí do dvou rod ů (Chilomastix , Retortamonas ). Zástupci obou rod ů žijí zejména jako st řevní komenzálové obratlovc ů a bezobralých. V nedávné dob ě byl popsán také jeden voln ě žijící druh rodu Chilomastix . Poté, co molekulárn ě-fylogenetické studie prokázaly p říbuznost mezi řádem Retortamonadida, Diplomonadida a voln ě žijícím rodem Carpediemonas , byl vytvo řen taxon Fornicata. V sou časné dob ě tento taxon zahrnuje také voln ě žijící rody Dysnectes , Hicanonectes , Kipferlia a dva doposud nepopsané rody voln ě žijících bi číkovc ů. Řád Retortamonadida byl dlouhou dobu považován za monofyletický taxon. První molekulárn ě-fylogenetická studie, která zahrnovala sekven ční data obou rod ů, ale ukázala, že retortamonády vytvá ří parafyletický taxon, jehož vnit řní skupinou jsou diplomonády. I přesto retortamonády z ůstaly velmi málo prostudovaným taxonem a dodnes mnoho nevíme o příbuzenských vztazích uvnit ř řádu Retortamonadida. Hlavním cílem naší práce bylo získat co nejvíce nových sekven čních dat rodu Retortamonas i Chilomastix . Poda řilo se nám získat nové sekvence 14 kmen ů řádu Retortamonadida (4 kme- ny rodu Chilomastix , 10 kmen ů rodu Retortamonas ) a jednoho doposud nepopsaného rodu enteromonád. Rod Retortamonas vytvo řil v naší analýze, s vysokou statistickou podporou, sesterskou linii řádu Diplomonadida a rozpadl se na t ři samostatné skupiny A, B a C. Pozice rodu Chilomastix z ůstala nejasná, ale díky nov ě získaným sekvencím se v ětev rodu Chilomastix rozpadla na p ět samostatných linií. Naše studie odhalila u rodu Chilomastix obrovskou mezidruhovou i vnitrodruhovou variabilitu sekvencí genu pro SSU rRNA. Klí čová slova: Fornicata, fylogeneze, Chilomastix, Retortamonas , Retortamonadida, SSU rDNA 6 2. ABSTRAKT Retortamonads (Retortamonadida; genera Chilomastix and Retortamonas ) are a small group of protists comprising intestinal commensals of both vertebrates and invertebrates and one free-living species of the genus Chilomastix . Molecular phylogenetic studies showed that retortamonads are closely related to diplomonads, Carpediemonas , Dysnectes , Hicanonectes , Kipferlia and two undescribed lineages of free-living Carpediemonas -like organisms, together forming the monophyletic excavate group Fornicata. For a long time Retortamonadida have been assumed to be a monophyletic group. However, first molecular phylogenetic study including sequence data from both Retortamonas and
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