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Obsah DNA a AT/GC Genomový Poměr V Čeledi Apiaceae

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Obsah DNA a AT/GC Genomový Poměr V Čeledi Apiaceae MASARYKOVA UNIVERZITA Přírodovědecká fakulta Ústav botaniky a zoologie Obsah DNA a AT/GC genomový poměr v čeledi Apiaceae Diplomová práce Brno 2012 Bc. Jana Schwarzová Vedoucí diplomové práce: doc. RNDr. Petr Bureš, Ph.D. PROHLÁŠENÍ Prohlašuji, ţe jsem tuto práci vypracovala samostatně, pod vedením doc. RNDr. Petra Bureše, Ph.D. na základě uvedených pramenů a odborné literatury. Souhlasím s uloţením této diplomové práce v knihovně Ústavu botaniky a zoologie PřF MU v Brně, případně jiné knihovně Masarykovy univerzity, s jejím veřejným půjčováním a vyuţitím pro vědecké, vzdělávací nebo jiné veřejně prospěšné účely, a to za předpokladu, ţe převzaté informace budou řádně citovány a nebudou vyuţívány komerčně. V Brně, 11. ledna 2012 …………………………… podpis PODĚKOVÁNÍ Děkuji hlavně svému školiteli doc. RNDr. Petru Burešovi, Ph.D. Dále bych chtěla poděkovat Mgr. Lucii Horové, která mi byla oporou při měření na cytometrech, a Ing. Jakubovi Šmerdovi, Ph.D. za jeho dobré rady. Srdečný dík patří doc. RNDr. Vítu Grulichovi, CSc. za pomoc při hledání vhodných lokalit a determinaci rostlin, Ing. Jiřímu Danihelkovi, Ph.D. děkuji za pomoc s herbářem. Za pomoc při sběru rostlin a zvládání počítačových záludností děkuji kamarádům Marku Schwarzovi, Karlu Fajmonovi, DAniele Bártové, Viky Hralové, Pavlu Veselému, Boţce a Marťasovi Jirouškovým. Za rostlinný materiál vděčím také Mgr. Věře Hroudové z botanické zahrady PřF UK, Mgr. Magdaléně Chytré, Ing. Marii Tupé a celému kolektivu botanické zahrady PřF MU. Mnoha dalším lidem, hlavně rodině, děkuji za veškerou hmotnou i nehmotnou podporu. „Ostrouhej a pokrájej mrkev na drobné nudličky.“ Magdalena Dobromila Rettigová POUŢITÉ ZKRATKY AT dusíkaté báze adenin a thymin AFLP polymorfismus délek amplifikovaných fragmentů CV koeficient variance DNA deoxyribonukleová kyselina cpDNA chloroplastová DNA nrDNA jaderná ribozomální DNA DAPI barvivo 4’,6-diamidino-2-fenylindol EIH Ellenbergovy indikační hodnoty GC dusíkaté báze guanin a cytosin ITS vnitřní přepisované mezerníky LMA mnoţství listové sušiny na jednotku plochy PCR polymerázová řetězová reakce PI barvivo propidium jodid SLA specifická listová plocha 1C haploidní obsah DNA v jádře 1Cx monoploidní obsah DNA, často synonymum k termínu velikost genomu 2n počet chromozomů v nereplikované somatické buňce ABSTRAKT V průběhu evoluce druhů dochází neustále k plynulým či skokovým změnám v jaderných genomech. Výsledkem je dnešní vysoká variabilita v obsahu DNA i jejím sloţení u krytosemenných rostlin. V předkládané práci byly cytometrickým měřením stanoveny absolutní obsah DNA (2C-value), monoploidní velikost genomu (Cx-value), průměrná velikost chromozomů a poměr AT/GC bazí pro 79 taxonů čeledi Apiaceae a 2 druhy čeledi Araliaceae. Z čeledi Apiaceae jsou zastoupeny všechny běţné rody rostoucí v České republice. Celkově se stanovené hodnoty pro obsah DNA v čeledi Apiaceae liší téměř třináctkrát, rozdíl v obsahu GC bazí činí necelá čtyři procenta. Dále byl sledován vztah těchto genomických parametrů vůči sobě navzájem a vůči vybraným ekologickým a fenotypovým znakům. K tomu byla pouţita neparametrická statistika a analýza fylogeneticky nezávislých kontrastů. Zjištěná pozitivní korelace mezi obsahem DNA (1Cx i 1C), průměrnou velikostí chromozomů a obsahem GC bazí vypovídá o pravděpodobném namnoţení GC bohatých retrotranspozonů. Obsah DNA má přitom silnou vazbu k evoluci testovaných druhů. Čeleď Apiaceae se zřejmě vyvíjela pod vlivem proměnných prostředí (zjištěn signifikantní fylogenetický signál u Ellenbergových indikačních hodnot pro světlo, teplo, vlhkost a úţivnost půdy), ale přímý vztah těchto faktorů ke genomickým parametrům nebyl zaznamenán. Z fenotypových znaků jsou ve vztahu s velikostí genomu výška rostlin, délka ţivotního cyklu (ţivotní strategie) a počet okolíčků v okolíku (ten navíc pozitivně koreluje s obsahem GC bazí). Vztah velikosti semen s jakýmkoliv genomickým parametrem nebyl potvrzen. Klíčová slova: Apiaceae (čeleď miříkovité), průtoková cytometrie, velikost genomu, obsah GC bazí, průměrná velikost chromozomů, Ellenbergovy indikační hodnoty, fylogeneticky nezávislé kontrasty. ABSTRACT DNA content and AT/GC genomic ratio in the family Apiaceae During the evolution of the species continuous or jump changes in nuclear genomes constantly occure. These processes lead to high nowaday variability in DNA content and its composition in angiosperms. In this study, absolute DNA content (2C-value), monoploid genome size (Cx-value), average chromosome size and AT/GC genomic ratio was measured using flow cytometry for 79 Apiaceae family taxa and 2 Araliaceae family species. All common Apiaceae genera growing in the Czech Republic are included. Overall the estimations for DNA content in the Apiaceae family vary about 13-fold, the difference in GC content is almost four percent. Consequently, the relationship of these genomic parameters against each other and against the chosen environmental and phenotypic characteristics was observed. For this purpose nonparametric statistics and the phylogenetically independent contrasts analysis were used. A detected positive correlation between DNA content (both 1Cx and 1C), average chromosome size and GC bases content suggests GC-rich retrotransposon proliferation. Furthermore, DNA content shows strong relationship to the evolution of the tested species. The Apiaceae family evolution was evidently influenced by the environmental variables (there was found a significant phylogenetic signal for the Ellenberg's indicator values for light, temperature, moisture and soil nutrients), but a direct relationship of these factors to genomic parameters was not detected. From phenotypic traits growth size, life cycle length (life history strategy) and a number of umbellets in an umbel (which also positively correlates with GC content) corresponded positively with genome size. Relationship between seed size and any genomic parameter was not confirmed. Key words: Apiaceae (the celery family), flow cytometry, genome size, GC content, average chromosome size, Ellenberg’s indicator values, phylogenetically independent contrasts. OBSAH 1. ÚVOD ...................................................................................................................................... 1 1.1. Modelový taxon – čeleď Apiaceae ............................................................................................................. 2 1.1.1. Taxonomie a fylogeneze ...................................................................................................................... 3 1.1.2. Morfologie a biologie .......................................................................................................................... 5 1.2. Obsah DNA ................................................................................................................................................ 6 1.2.1. Terminologie ........................................................................................................................................ 6 1.2.2. Obsah DNA a proč ho měřit ................................................................................................................ 7 1.2.3. Hlavní mechanismy změn velikosti genomu ....................................................................................... 8 1.2.4. Velikost genomu a jeho vztah k fenotypovým vlastnostem ............................................................... 11 1.2.5. Velikost genomu a jeho vztah k faktorům prostředí .......................................................................... 14 1.3. AT/GC genomový poměr ........................................................................................................................ 16 1.4. Cíle diplomové práce ............................................................................................................................... 17 2. MATERIÁL A METODIKA ...................................................................................................... 18 2.1. Rostlinný materiál ................................................................................................................................... 18 2.2. Průtoková cytometrie .............................................................................................................................. 19 2.2.1. Historie............................................................................................................................................... 19 2.2.2. Stavba a princip průtokového cytometru ........................................................................................... 20 2.3. Měření materiálu ..................................................................................................................................... 21 2.4. Stanovení velikosti genomu, chromozomů a AT/GC genomového poměru ........................................ 23 2.5. Sestavení fylogenetického stromu ........................................................................................................... 24 2.6. Znaky pouţité v analýzách ...................................................................................................................... 26 2.7. Statistické zpracování dat ....................................................................................................................... 26 2.7.1. Phylocom ........................................................................................................................................... 26 2.7.2. Další pouţité programy .....................................................................................................................
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