Bioinformacijska analiza evolviranih genomov bakterije Bacillus subtilis

Kralj, Jernej (author), Štefanič, Polonca (mentor)

Na Katedri za mikrobno ekologijo in fiziologijo, Oddelka za mikrobiologijo Biotehniške fakultete so izvedli ekperiment eksperimentalne evolucije, pri katerem so testirali vpliv sorodstvenega razlikovanja na evolucijo seva PS-216. V procesu eksperimentalne evolucije so starševski sev PS-216 periodično izpostavili stičnim sevom PS-216, PS-218 in PS-13 in po dvajsetih ciklih testirali spremembe fenotipa razlikovanja sorodnosti, torej ali roji evolviranih sevov z rojem starševskega seva PS-216 tvorijo linijo. Prav tako pa so preverili, ali je prišlo do sprememb fenotipa rojenja. Na sekvenciranje so poslali 21 sevov, med katerimi so bili sevi s spremenjenim fenotipom rojenja in razlikovanja sorodnosti, prav tako pa tudi sevi, ki niso spremenili fenotipov razlikovanja sorodnosti ali rojenja. Namen magistrske naloge je bila identifikacija mutacij in potencialnega HGT (ang. Horizontal Gene Transfer). Genom starševskega seva PS-216 in stičnega seva PS-13 smo sestavili tako s kratkimi odčitki Illumina kot z dolgimi odčitki PacBio. Genome evolviranih sevov ter stičnega seva PS-218 smo sestavili s kratkimi odčitki Illumina. Mutacije, kot so SNP-ji in večje delecije, smo identificirali z bioinformacijskim orodjem Breseq, medtem ko smo insercije, ki bi nakazovale na potencialen HGT, identificirali s skripto MUMandCo. Mutacije smo odkrili v genih, vpletenih v sintezo ekstracelularnega matriksa, sporulacijo, transport peptidov in stresne odgovore. Prav tako smo identificirali mutacije v šestih genih, katerih produkti in funkcije še niso poznani. Potencialnega dogodka HGT nismo zaznali.

• Language: Slovenian
• Keywords: Bacillus subtilis, eksperimentalna evolucija, sorodstveno razlikovanje, bioinformatika
• Work type: Master's thesis/paper
• Typology: 2.09 - Master's Thesis
• Organization: BF - Biotechnical Faculty
• Year: 2023
• PID: 20.500.12556/RUL-145381
• COBISS.SI-ID: 149849091
• Publication date in RUL: 20.04.2023

Secondary language

• Language: English
• Title: Bioinformatical analysis of evolved B. subtilis genomes

Abstract

At the chair of Microbial Ecology and Physiology, Department of Microbiology of the Biotechnical Faculty, an experimental evolution was conducted in which they tested the effect of kin discrimination on the evolution of the PS-216 strain. Parental strain PS-216 was cyclically exposed to contact strains PS-13, PS-216 and PS-218 during experimental evolution. After 20 cycles they tested evolved strains for changes in kin discrimination and swarming phenotypes. They observed if swarms of evolved strains merged with swarm of parental strain PS-216 or if they form a line. They picked 21 strains for sequencing. Among sequenced strains were strains that changed kin discrimination or swarming phenotypes and also strains that did not change phenotypes. The goals of this master's thesis disertation were the identification of mutations and detection of the potential horizontal gene transfer (HGT). The genomes of parental strain PS-216 and contact strain PS-13 were assembled with long PacBio and short Illumina reads, while the genomes of sequenced evolved and contact strain PS-218 were assembled with short Illumina reads only. For the identification of SNPs and indels we used Breseq pipeline while for the identification of potential HGT we used MUMandCo script. We identified mutations in genes that are involved in the synthesis of extracellular matrix, peptide transport, sporulation and stress response. We also identifed mutations in six genes whose products and functions are currently unknown. We did not detect a potential HGT event.

• Keywords: Bacillus subtilis, experimental evolution, bioinformatics, kin discrimination