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Lenka Kočková

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Lenka Kočková MASARYKOVA UNIVERZITA PŘÍRODOVĚDECKÁ FAKULTA ÚSTAV BOTANIKY A ZOOLOGIE Velikost genomu a poměr bazí v genomu v čeledi Ranunculaceae Diplomová práce Lenka Kočková Vedoucí práce: Doc. RNDr. Petr Bureš, Ph. D. Brno 2012 Bibliografický záznam Autor: Bc. Lenka Kočková Přírodovědecká fakulta, Masarykova univerzita, Ústav botaniky a zoologie Název práce: Velikost genomu a poměr bazí v genomu v čeledi Ranunculaceae Studijní program: Biologie Studijní obor: Systematická biologie a ekologie (Botanika) Vedoucí práce: Doc. RNDr. Petr Bureš, Ph. D. Akademický rok: 2011/2012 Počet stran: 104 Klíčová slova: Ranunculaceae, průtoková cytometrie, PI/DAPI, DNA obsah, velikost genomu, GC obsah, zastoupení bazí, velikost průduchů, Pignattiho indikační hodnoty Bibliographic Entry Author: Bc. Lenka Kočková Faculty of Science, Masaryk University, Department of Botany and Zoology Title of Thesis: Genome size and genomic base composition in Ranunculaceae Programme: Biology Field of Study: Systematic Biology and Ecology (Botany) Supervisor: Doc. RNDr. Petr Bureš, Ph. D. Academic Year: 2011/2012 Number of Pages: 104 Keywords: Ranunculaceae, flow cytometry, PI/DAPI, DNA content, genome size, GC content, base composition, stomatal size, Pignatti‘s indicator values Abstrakt Pomocí průtokové cytometrie byla změřena velikost genomu a AT/GC genomový poměr u 135 druhů z čeledi Ranunculaceae. U druhů byla naměřena délka a šířka průduchů a z literatury byly získány údaje o počtu chromozomů a ekologii druhů. Velikost genomu se v rámci čeledi liší 63-krát. Nejmenší genom byl naměřen u Aquilegia canadensis (2C = 0,75 pg), největší u Ranunculus lingua (2C = 47,93 pg). Mezi dvěma hlavními podčeleděmi Ranunculoideae a Thalictroideae je ve velikosti genomu markantní rozdíl (2C = 2,48 – 47,94 pg a 0,75 – 4,04 pg). Velikost genomu u méně zastoupených podčeledí Glaucidioideae, Hydrastioideae a Coptidoideae je malá (2C = 2,73 pg, 2,69 pg or 1,37 pg); stejně tak sesterské čeledi Papaveraceae, Eupteleaceae, Berberidaceae, Menispermaceae a Lardizabalaceae mají velikost genomu malou, což svědčí o zvětšování genomu v rámci čeledi. Předpokládaný vztah mezi genomovými parametry (velikostí genomu a zastoupení GC bazí) se za použití fylogenetických kontrastů nepotvrdil. Naopak vztah mezi velikostí genomu a velikostí průduchu potvrzen byl. Nejtěsnější korelace je mezi velikostí genomu a délkou průduchu, při použití délky na třetí nebo délky krát šířky na druhou není korelace tak těsná. Geofyty mají signifikantně větší genom než negeofytní druhy. Genom negativně koreluje s dobou kvetení. Z vlastností prostředí genom negativně ovlivňuje vlhkost. Tento vliv může být zprostředkovaný negativní korelací velikostí průduchů s vlhkostí. Na genomové vlastnosti mají také nemalý vliv klimatické podmínky. Velikost genomu je podmíněna pozitivně teplotou. GC obsah negativně koreluje s teplotou a srážkami. Abstract The overall genomic parameters, somatic DNA content and base composition were analyzed in 135 taxa of Ranunculaceae by use flow cytometry method. The variation in DNA amount across the family is 63,9-fold. The smallest genome has been foun in Aquilegia canadensis (2C = 0,75 pg) while the largest in Ranunculus lingua (2C = 47,93 pg). Within the family there are two main most evolved clades represented by large subfamilies Ranunculoideae and Thalictroideae which exhibited strongly contrasting variation in genome size (2C = 2,48 – 47,94 pg a 0,75 – 4,04 pg, respectivelly). The DNA content in small sister subfamilies Glaucidioideae, Hydrastioideae and Coptidoideae was small (2C = 2,73 pg, 2,69 pg or 1,37 pg); similarly in outgroups of sister families Papaveraceae, Eupteleaceae, Berberidaceae, Menispermaceae and Lardizabalaceae the DNA content was lower, therefore that’s suggesting increasing trend in evolution of genome size in the family. Expected correlation between genomic parameters (genome size and GC content) was not confirmed if tested by independent phylogenetic contrasts. The correlation between DNA amount and stomatal size was confirmed. The better predictor of genome size was shown to be length while other tested variables width x width x width and width x width x length exhibited less closser correlation. Geophyts have significantly larger genomes than no-geophyts species. Genome negatively correlated with flowering time. Moisture negatively affects genome size from the properties of the environment genome. This effect may be mediated by a negative correlation between stomatal size and moisture. Climatic conditions also have significant influence on genomic parameters. Genome size is positively affected by temp. GC content correlates negatively with temperature and precipitation. Poděkování V první řadě bych chtěla poděkovat doc. RNDr. Petru Burešovi Ph.D. za trpělivost, kterou se mnou měl během doby, kdy vznikala tato diplomová práce. Dále mu děkuji za pomoc při sběru materiálu, časté odborné konzultace a za všechno, co mě naučil. Za cenné rady děkuji především Mgr. Petru Šmardovi Ph.D., doc. RNDr. Vítu Grulichovi CSc., Mgr. Pavlovi Veselému a Mgr. Ivaně Hralové. Za pomoc při cytometrickém měření děkuji Mgr. Lucii Horové a Ing. Alexandře Březinové. Dále děkuji Mgr. Ondřeji Hájkovi za poskytnutí klimatických dat. Také všem, kteří mi ze svých cest přivezli cytometrický materiál a botanickým zahradám, které mi daly své rostliny k dispozici, za to děkuji. Děkuji přátelům a rodině za pomoc, podporu, zázemí a lásku. Prohlášení Prohlašuji, že jsem svoji diplomovou práci vypracovala samostatně s využitím informačních zdrojů, které jsou v práci citovány. Brno 7. května 2012 . Lenka Kočková Obsah 1. Význam velikosti genomu a zastoupení GC bazí…………………………………… 1 1.1 Velikost genomu………………………………………………………………. 1 1.2 Variabilita velikosti genomu……………………………………………….…. 1 1.3 Adaptivita velikosti genomu………………………………………………….. 2 1.4 AT/GC genomový poměr……………………………………………………... 4 1.5 Chromozomy………………………………………………………………….. 5 2. Materiál a metodika…………………………………………………………………. 6 2.1 Sběr materiálu…………………………………………………………………. 6 2.2 Měření velikosti genomu……………………………………………………… 8 2.3 Stanovení chromozomových počtů a průměrné velikosti chromozomů……… 10 2.4 Měření velikosti průduchových buněk………………………………………... 13 2.5 Stanovení fenotypových a ekologických vlastností druhu……………………. 14 2.6 Sestavení fylogenetického stromu…………………………………………….. 15 2.7 Statistické zpracování dat……………………………………………………... 16 3. Čeleď Ranunculaceae jako model pro studium velikosti genomu …………………. 18 4. Cíle práce……………………………………………………………………………. 22 5. Výsledky…………………………………………………………………………….. 23 5.1 Fylogenetická analýza genomických znaků…………………………………... 23 5.2 Vztah genomických parametrů k fenotypu…………………………………… 32 5.3 Vztah ekologických parametrů ke genomovým vlastnostem………………..... 38 6. Diskuse……………………………………………………………………………… 41 6.1 Fylogenetická analýza genomických znaků…………………………………... 41 6.2 Vztah genomických parametrů k fenotypu…………………………………… 43 6.3 Vztah ekologických parametrů ke genomovým vlastnostem…………………. 45 7. Závěr………………………………………………………………………………… 48 8. Literatura……………………………………………………………………………. 49 9. Přílohy 1. Význam velikosti genomu a zastoupení AT/GC bazí 1.1 Velikost genomu Genom je veškerá genetická informace uložená v DNA buněčného jádra konkrétního organismu (druhu). V užším slova smyslu je to kompletní sekvence DNA obsažená v jedné gametě daného druhu. Termín genom poprvé použil Hans Winkler v roce 1920. Jaderný obsah DNA se dá popsat dvěma termíny a to „velikost genomu“ a „C-value“. Termín „velikost genomu“ začal používat pro množství DNA odpovídající monoploidnímu genomu (monoploidní velikost genomu = somatický obsah DNA / stupeň ploidie) pravděpodobně v 70. letech Ralph Hinegardner (1976). Pojem „C-value“ znamená poloviční somatický obsah DNA, bez ohledu na stupeň ploidie, tj. množství DNA odpovídající holoploidnímu genomu (holoploidní velikost genomu = somatický obsah DNA / 2 = gametický obsah DNA). Tuto zkratku zavedl v roce 1950 H. Swift. Z jeho práce ale nebylo zřejmé, co přesně písmeno „C“ vyjadřuje. To objasnil až v roce 1975 v dopise M. D. Bennettovi, v kterém stálo, že „C“ znamená „constant“ (Bennett & Leitch 2005). C-value se však běžně využívá a využívalo jako ekvivalent "velikosti genomu". Tím mohlo docházet ke konfúzi, kdy se pod stejným pojmem mohly chápat různé věci. Proto Greilhuber et al. (2005) nabízejí novou terminologii. Pro monoploidní obsah DNA doporučují termín „Cx-value“ (kde x je základní chromozomové číslo) a pro obsah DNA charakteristický pro konkrétní organismus termín „C-value“. Velikost genomu je vyjádřena v počtu párů bází, nebo jako její hmotnost v pikogramech. Pro přepočet se používají různé hodnoty – například 1 pg = 978 Mbp (Doležel et al. 2003). První měření velikosti genomu byla uskutečněna v 50. letech 20. století. Od roku 1976 se M. D. Bennett se svými kolegy snažili změřit co největší množství druhů (Gregory 2007). Současný počet zjištěných velikostí rostlinných genomů je přes 7000 (Bennett & Leitch 2010). Tento počet zahrnuje všech pět částí Plant DNA C-values database (krytosemenné, nahosemenné, kapraďorosty, mechorosty a řasy). Zdaleka největší rozsah dat je přitom znám v případě krytosemenných, jichž bylo dosud analyzováno 6287 druhů (Bennett & Leitch 2010). 1.2 Variabilita velikosti genomu Rozdíly mezi velikostmi genomu jsou obrovské, často i mezi poměrně blízce příbuznými druhy, aniž by to souviselo s rozdíly ve složitosti jejich organismální struktury (Thomas 1971). -1- Rozsah velikosti genomu se u kvetoucích rostlin pohybuje mezi 2C = 0,13 pg, což je hmotnost zjištěná u Genlisea
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