20.500.12556/RUL-150022 Povezava med sorodnostjo in ekologijo različnih sevov rodu Bacillus z uporabo podatkovne baze PATRIC Association between the relatedness and ecology of Bacillus subtilis, Bacillus pumilus, Bacillus cereus and Bacillus megaterium strains using the PATRIC database Vrste, ki sestavljajo rod Bacillus združuje sposobnost tvorbe dormantnih endospor. Sicer so to izredno raznolike vrste, ki so prisotne v praktično vseh ekoloških nišah po celotnem svetu. Ravno zaradi široke ekologije in obče prisotnosti vrst smo se odločili v nalogi preveriti vpliv okolja in geografije na sorodnost sevov. Iz podatkovne baze PATRIC smo pridobili celotne genome in metapodatke sevov iz klad subtilis, cereus, pumilus in megaterium rodu Bacillus. Najprej smo naredili pregled metapodatkov. Nato smo izvedli analizo FastANI genomov in dobili distančne matrike, ki so odražale količino nukleotidnih razlik med sevi. Matrike smo uvozili v program MEGA11 in z uporabo slednjega izrisali različna filogenetska drevesa, na podlagi katerih smo opazovali sorodnost sevov znotraj posameznih ter kako na sorodnost sevov znotraj iste vrste vplivata okolje in geografija. Filogenetska drevesa klad na podlagi rezultatov FastANI so omogočala dobro razlikovanje med vrstami, razen pri kladah pumilus, ki je imela kar nekaj napačno determiniranih sevov, ter cereus. Slednjo sestavljajo genetsko zelo sorodne vrste, a se ločujejo zaradi pomembnih razlik v fenotipu. Na podlagi filogenetskih dreves posameznih vrst, z ločevanjem sevov glede na metapodatke o njihovi ekologiji in geografiji, smo opazili nekatere ponavljajoče vzorce, ki so kazali vpliv okolja in geografije na sorodnost sevov znotraj vrst, a ti niso bili dovolj očitni, da bi lahko naredili zanesljive zaključke. A common feature of the genus Bacillus is the ability to form dormant endospores. It is comprised of very diverse species which are present in almost any environment and every part of the world. Based on the diverse ecology and ubiquitous nature of these species, we have decided to assess the effect of environment and geography on strain relatedness. We retrieved the complete genomes and metadata of strains from the clades subtilis, cereus, pumilus and megaterium of the Bacillus genus. First, we made an overview of the metadata. We then analysed the genomes using FastANI to get distance matrices which showed the amount of nucleotide discrepancies. The matrices were imported into the MEGA11 software, which we used to construct several different phylogenetic trees. We used them to observe the inter species relatedness within clades and how the environment and geography of strains affects the intra species relatedness. The clades’ phylogenetic trees based on the FastANI results provided good differentiation between species. Except for the clades pumilus (because of several incorrectly determined species) and cereus. The latter is comprised of genetically very closely related species, that are separated based on important phenotypic properties. Based on phylogenetic trees of single species and separating strains based on metadata about their ecology and geography, some patterns showing the influence of the environment and geography on the intra species relatedness of strain. However, this was not enough to make any definite conclusions. rod Bacillus sorodnost ekologija biogeografija genus Bacillus relatedness ecology biogeography true false false Slovenski jezik Angleški jezik Diplomsko delo/naloga 2023-09-13 08:15:53 2023-09-13 08:15:56 2023-10-23 13:44:34 0000-00-00 00:00:00 2023 0 0 0000-00-00 NiDoloceno NiDoloceno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 229177 164585987 35383.pdf 35383.pdf 1 A9BE1A504FAD9B7F1DCF2FB7D9E27FCD fcc5940a860fc559af875319235a5eca72bbd3c6560c8c6eaf92b9aa0a708baa 003b6135-51fd-11ee-916e-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=174555 Biotehniška fakulteta 0 0 0