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Přírodovědecká Fakulta Ústav Botaniky a Zoologie Obsah DNA a AT/GC

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Přírodovědecká Fakulta Ústav Botaniky a Zoologie Obsah DNA a AT/GC MASARYKOVA UNIVERZITA Přírodovědecká fakulta Ústav botaniky a zoologie Obsah DNA a AT/GC genomový poměr u druhů rodu Carex Diplomová práce Bc. Ivana Hralová Brno2010 Školitel: doc. RNDr. Petr Bureš, Ph.D. Prohlášení Souhlasím s uložením této diplomové práce v knihovně Ústavu botaniky a zoologie PřF MU v Brně, případně v jiné knihovně MU, s jejím veřejným půjčováním a využitím pro vědecké, vzdělávací nebo jiné veřejně prospěšné účely, a to za předpokladu, že převzaté informace budou řádně citovány a nebudou využívány komerčně. V Brně dne ............. Poděkování Na tomto místě bych chtěla poděkovat lidem, kteří se na této práci podíleli a bez jejichž pomoci by tato práce nikdy nevznikla. Poděkování za patří doc. RNDr. Petru Burešovi Ph.D. za vedení, nápady a konzultace, jakožto i za organizování rozsáhlých sběrů a měření ostřic. Dále Mgr. Olze Rotreklové, Ph.D. a Mgr. Františku Zedkovi za napočítání spousty malých chromozomů. Mgr. Lucce Horové a dalším za cytometrické změření většiny ostřic, Mgr. Petru Šmardovi, Ph.D. pak za obětavé konzultace nad problémy phylocomu a sekvencí obecně. Ing. Radomíru Řepkovi, Ph.D. a doc. RNDr. Vítku Grulichovi, CSc. patří dík za determinaci druhů. Poděkování patří všem, kteří se podíleli na sběru a dovážení ostřic ze všech koutů Evropy a Ruska, kromě výše jmenovaných také Ph.D., Ing. Jiřímu Danihelkovi, Ph.D., doc. Michalu Hájkovi, Ph.D., Mgr. Karlu Fajmonovi, Mgr. Kláře Helánové, Mgr. Janu Rolečkovi, Ph.D., Mgr. Danu Dvořákovi, RNDr. Zdeně Lososové, Ph.D., Ph.D., Ing. Tomáši Kouteckému, Mgr. Pavlu Veselému a mnoha dalším. Děkuji také všem svým přátelům, kteří mi poskytli neocenitelné rady a trpělivě snášeli všechny možné i nemožné výkyvy nálad. Jmenovitě patří dík Bc. DAniele Bártové a Mgr. Pavlu Veselému za dlouhé noční konzultace statistických a jiných problémů, Bc. Janě "šnečkovi" Dvořákové za nezřízený optimismus a Bc. Tomáši Lipnerovi a Bc. Hance Buchtové za zdravou míru realismu a kibicování. Poděkování patří také mým nejbližším, mé rodině, bratříčkovi a Tasmince. Abstrakt Tato práce se zabývala vztahy genomických znaků, jako je velikost genomu, AT/GC genomový poměr a počet chromozomů, k evoluci rodu, k faktorům prostředí a k morfologickým znakům. Byla změřena velikost genomu a AT/GC genomový poměr pro 159 druhů rodu Carex a 55 dalších zástupců čeledi Cyperaceae, pro část druhů byly spočítány počty chromozomů. Byly změřeny délky průduchů, z literatury byly převzaty informace o ekologických nárocích druhů (Ellenbergovy indikační hodnoty) a rozměry mošniček a nažek. K určení vztahů mezi získanými hodnotami byly použity neparametrické korelace a analýzy fylogenetických kontrastů. Rod Carex má jedny z nejmenších genomů mezi vyššími rostlinami, AT/GC genomový poměr je pak v rozmezí běžném mezi rostlinami. Velká variabilita v chromozomových počtech je ve shodě s obecně přijímanými názory na evoluci karyotypu v rodu. Ekologické parametry prostředí, vyjádřené pomocí Ellenbergových indikačních skupin, hrály v evoluci rodu určitou roli a podílejí se na dnešní variabilitě rodu, nicméně jejich vliv není jednoznačný. Závislosti velikosti genomu a AT/GC genomového poměru mezi sebou a na teplotě prostředí naznačují možnost proliferace transpozonů jako jedné z hybných sil evoluce genomických znaků rodu. Soustředění velké části zamokření tolerujících druhů do jedné větve fylogenetického stromu naznačuje možnost evoluci tohoto znaku v modu konzervativnosti niky spíš než adaptivní radiací. Délka průduchů u ostřic není ve vztahu k velikosti genomu, což je v protikladu k obecně přijímaným názorům a důkazům plynoucím z několika rozsáhlých studií na těsnou závislost těchto dvou znaků. Možné důvody a důsledky tohoto stavu jsou diskutovány. Klíčová slova: průtoková cytometrie, ostřice, Cyperaceae, velikost genomu, zastoupení AT bazí, Ellenbergovy indikační hodnoty, délka průduchů, adaptabilita velikosti genomu Abstract This study was focused on determining relationship among genetical, morphological and ecological characters of species of genus Carex. Its aim was to find out whether the environmental effect on the evolution of species resulted in changes of genome size (studied on closely related species); if AT/GC genomic ratio was shifted during phylogeny, e. g., by transposone proliferation, and if there is correlation between DNA composition and genome size. Its aim was also to find whether the changes in genome are correlated with changes in stomatal length or length of peryginia or achenes. We measured DNA content, AT/GC genomic ratio, and average chromosomal size for 159 species of the genus Carex and 55 other species of the Cyperaceae family growing mainly in Central Europe and for some other Russian or North American taxa. Stomatal length was measured for 110 species of Carex and 17 other species of family Cyperaceae. The genus Carex has one of the smallest genome size among angiosperms. We found high chromosomal count variability as expected. Environmental effects, aproximated by Ellenberg's indicator values, played siginificant role in evolution of genus, although the way of interaction with genomic characters is not clear. The relationship between genome size and AT/GC genomic ratio and among these characters and temperature suggest shift of these characters due to transposone proliferation. The clustering of main part of wetland species within one particular clade sugests a niche conservatism as a mode of evolution in traits related to waterlooging tolerance. Stomatal length is not correlated with genome size. Such absence of realtionship was not observed before. Reasons and conclusions of genome size unrelated variation in stomatal length is discussed. Key words: flow cytometry, sedges, Cyperaceae, genome size, A+T content, Ellenberg's indicator value, stomatal length, genome size adaptability 1 OBSAH 1. Úvod....................................................................................................................................1 1.1. Rod Carex....................................................................................................................1 1.1.1. Taxonomické pojetí založené na morfologických znacích...........................1 1.1.2. Taxonomické pojetí založené na molekulárních znacích.............................2 1.1.3. Taxonomické pojetí použité v této práci........................................................6 1.2. Velikost genomu.........................................................................................................6 1.2.1. Variabilita velikosti genomu...........................................................................6 1.2.2. Mechanismy změn velikosti genomu.............................................................9 1.2.3. Selekční vlivy na velikost genomu...............................................................10 1.3. AT/GC genomový poměr.........................................................................................13 1.4. Chromozomy.............................................................................................................13 1.5. ITS sekvence.............................................................................................................15 1.6. Fylogenetické kontrasty...........................................................................................17 1.6.1. Úvod do fylogenetických kontrastů .............................................................17 1.6.2. Předpoklady analýzy.....................................................................................17 1.6.3. Phylocom.......................................................................................................19 1.6.4. Fylogenetické kontrasty................................................................................19 1.6.5. Fylogenetický signál.....................................................................................20 1.6.6. Kontribuční index..........................................................................................21 2. Cíle práce..........................................................................................................................23 3. Materiál a metodika.........................................................................................................24 3.1. Materiál.....................................................................................................................24 3.2. Průtoková cytometrie................................................................................................24 3.3. Stanovení počtu chromozomů..................................................................................25 3.4. Morfologické znaky..................................................................................................25 3.5. Ellenbergovy indikační hodnoty..............................................................................26 3.6. Nomenklatura............................................................................................................26 3.7. Analýza ITS sekvencí...............................................................................................27 3.8. Analýza fylogenetických kontrastů .........................................................................28 3.9. Zpracování výsledků ................................................................................................28 2 4. Výsledky...........................................................................................................................31 4.1. Sekvence a fylogenetické analýzy...........................................................................31
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