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Databáze Živočišné Rdna MASARYKOVA UNIVERZITA Přírodovědecká fakulta Biofyzikální ústav AVČR, v.v.i. Databáze živočišné rDNA Disertační práce Jana Sochorová Školitel: RNDr. Aleš Kovařík, CSc. Brno, 2019 Bibliografický záznam Jméno a příjmení autora: Ing. Jana Sochorová Biofyzikální ústav AVČR, v.v.i. Název disertační práce: Databáze živočišné rDNA Studijní program: Biochemie Studijní obor: Genomika a proteomika Školitel: RNDr. Aleš Kovařík, CSc. Biofyzikální ústav AVČR, v.v.i. Akademický rok: 2018/2019 Počet stran: 92 Klíčová slova: 5S rDNA, 45S rDNA, databáze, hybridizace in situ, karyotyp Bibliographic entry Author: Ing. Jana Sochorová Institute of Biophysics of the CAS, v.v.i. Title of Dissertation: Animal rDNA database Degree Programme: Biochemistry Field of Study: Genomics and proteomics Supervisor: RNDr. Aleš Kovařík, CSc. Institute of Biophysics of the CAS, v.v.i. Akademic Year: 2018/2019 Number of Pages: 92 Keywords: 5S rDNA, 45S rDNA, database, in situ hybridization, karyotyp Abstrakt Ribozomální DNA (rDNA), která kóduje 5S a 45S (18S-5.8S-26S) rRNA, je důležitou součástí eukaryotických chromozomů, počet a pozice lokusů rDNA se však liší. V důsledku nárůstu počtu publikací o živočišné rDNA (více než 600 publikací do roku 2017) vyvstala potřeba data zpřehlednit, zpřístupnit a statisticky je vyhodnotit. Proto jsme vytvořili Databázi živočišné rDNA, která udává informace o počtech a poloze lokusů rDNA na chromozomech. Shromážděná data z hybridizací in situ (s radioaktivním i fluorescenčním značením) metafázních chromozomů (mitotických i meiotických) zahrnují informace o karyotypech obratlovců (ryby, plazi, ptáci, obojživelníci a savci) a bezobratlých (hmyz a měkkýši). Další skupiny jsou zastoupené pouze několika druhy. Databáze živočišné rDNA je přístupná na internetové stránce http://www.animalrdnadatabase.com/. V databázi se nachází informace o počtu a pozici 5S a 45S rDNA ve více než 1 700 karyotypech (>300 čeledích). rDNA může být lokalizována na kterémkoliv typu chromozomu, včetně pohlavních chromozomů (X, Y, Z a W), B chromozomů a mikrochromozomů. Medián počtu lokusů rDNA má hodnotu kolem dvou lokusů na diploidní počet chromozomů, navzdory velké variabilitě počtu lokusů. Největší variabilitu v počtu lokusů 45S vykazují ryby (1 až 27 45S/ 1C), nejvíce variabilní v počtu lokusů 5S rDNA jsou plazi (1 až 37 5S/ 1C). Počet lokusů a velikost genomu nevykazují žádnou korelaci, stejně tak i počet lokusů 5S a 45S. V každé skupině živočichů se vyskytují všechny základní pozice rDNA na chromozomech. Pozice lokusu 45S rDNA je většinou terminální (>60% karyotypů) kromě druhů z kmene členovců, které vykazují většinou pericentromerickou pozici, a to především v řádu Orthoptera. Pozice 5S rDNA je více variabilní než 45S. Internetová stránka Databáze živočišné rDNA zaznamenala od roku 2017 více než 2200 přístupů. Aktualizace databáze, která je plánovaná na rok 2019, jistě přinese ohlas vědecké veřejnosti. Abstract Ribosomal DNA (rDNA) loci encoding 5S and 45S (18S-5.8S-26S) rRNA are important components of eukaryotic chromosomes varying both in numbers and locations. Accumulation of cytogenetic information on animal rDNA loci (more than 600 papers published until 2017) resulted in an increased demand for its archiving, public accessibility and the robust statistical analysis. We therefore took effort and constructed the Animal rDNA database containing information about the number and position of rDNA loci on animal chromosomes. The collected data are based on in situ hybridisation studies (both radioactive and fluorescent) of metaphase chromosomes (both mitotic and meiotic) carried out in major groups of vertebrates (fish, reptiles, birds, amphibians and mammals) and invertebrates (insects and mollusks). Other groups of animals (such as the worms) are only minor represented. The Animal rDNA database is publicly accessible via a web-based interphase at http://www.animalrdnadatabase.com/. The database contains cytogenetic information about 5S and 45S rDNA loci in more than 1 700 animal karyotypes (species coming from >300 families). rDNA loci can occur on any chromosome type including autosomes, sex chromosomes (X, Y, Z and W), supernumerary B chromosomes and microchromosomes. Statistical evaluation indicates that the median number of rDNA sites per diploid genome is close to two despite large interspecies variation. Fishes have the greatest variability in the number of 45S rDNA loci (2 to 54 sites/2C). Among the 5S loci the highest variability was recorded in reptiles (2 to 74 sites/2C). There is no significant correlation between the number of rDNA loci and genome size and also between the number of 5S and 45S rDNA loci in karyotypes. Each group contained rDNA sites at any chromosome location. The most prevalent position of 45S rDNA loci is terminal (>60% karyotypes) with the exception of arthropods, where the pericentromeric location is more frequent, particularly in the Orthoptera order. The position of 5S rDNA loci is generally more variable than the position of 45S rDNA loci. We observed that the internet page of the Animal rDNA database is viable and has been contacted for more 2200 times since its establishment in 2017. We are optimistic in that its next update scheduled to 2019 will receive attention from the scientific community. © Jana Sochorová, Masarykova univerzita, 2019 Obsah 1 Literární úvod ............................................................................................................9 1.1 Ribozomální DNA ...............................................................................................9 1.2 Názvosloví rDNA a rRNA ................................................................................. 10 1.3 Struktura rDNA ................................................................................................. 10 1.4 5S rDNA............................................................................................................ 12 1.5 45S rDNA .......................................................................................................... 13 1.6 Pseudogeny a orphony ....................................................................................... 15 1.7 Metody detekce rDNA. ...................................................................................... 15 1.8 Eukaryotický chromozom .................................................................................. 16 1.9 Lokalizace rDNA na chromozomech ................................................................. 17 1.10 Využití rDNA................................................................................................. 18 1.11 Modely evoluce rDNA ................................................................................... 18 1.11.1 Model birth-and-death ................................................................................ 18 1.11.2 Model koncertované evoluce ...................................................................... 19 1.12 rDNA prokaryot ............................................................................................. 20 1.13 Struktura lokusů 45S a 5S rDNA u eukaryot................................................... 21 1.14 rDNA kvasinek .............................................................................................. 21 1.15 Rostlinná rDNA ............................................................................................. 22 1.16 Živočišná rDNA ............................................................................................. 23 1.17 Biologické databáze ....................................................................................... 24 1.17.1 Databáze nukleových kyselin ...................................................................... 26 1.17.2 Sekundární databáze ................................................................................... 27 1.17.3 Genomové databáze .................................................................................... 27 1.17.4 Databáze velikosti genomů a počtu chromozomů ........................................ 28 1.17.5 Databáze, zabývající se rDNA a rRNA ....................................................... 29 1.17.6 Další databáze............................................................................................. 30 1.17.7 Meta Databáze ............................................................................................ 30 2 Cíle disertační práce ................................................................................................. 31 3 Materiál a metody .................................................................................................... 32 3.1 Vyhledávání informací ....................................................................................... 32 7 3.2 Tvorba a statistická analýza databáze ................................................................. 33 3.3 Konstrukce webové stránky ............................................................................... 33 4 Výsledky .................................................................................................................. 34 4.1 Internetová podoba databáze živočišné rDNA .................................................... 34 4.2 Statistické vyhodnocení výsledků databáze ........................................................ 36 4.2.1 Druhové složení databáze ........................................................................... 36 4.2.2 Analýza počtu lokusů rDNA ....................................................................... 37 4.2.3 Pozice rDNA
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