magistrsko delo
Povzetek
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.
Ključne besede
Bacillus subtilis;eksperimentalna evolucija;sorodstveno razlikovanje;bioinformatika;
Podatki
Jezik: |
Slovenski jezik |
Leto izida: |
2023 |
Tipologija: |
2.09 - Magistrsko delo |
Organizacija: |
UL BF - Biotehniška fakulteta |
Založnik: |
[J. Kralj] |
UDK: |
602.3:579.852.11:579.25:575.112:004(043.2) |
COBISS: |
149849091
|
Št. ogledov: |
220 |
Št. prenosov: |
59 |
Ocena: |
0 (0 glasov) |
Metapodatki: |
|
Ostali podatki
Sekundarni jezik: |
Angleški jezik |
Sekundarni naslov: |
Bioinformatical analysis of evolved Bacillus subtilis genomes |
Sekundarni povzetek: |
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. |
Sekundarne ključne besede: |
Bacillus subtilis;experimental evolution;bioinformatics;kin discrimination; |
Vrsta dela (COBISS): |
Magistrsko delo/naloga |
Študijski program: |
0 |
Komentar na gradivo: |
Univ. v Ljubljani, Biotehniška fak., Študij biotehnologije |
Strani: |
1 spletni vir (1 datoteka PDF (XII, 80 str., [19] str. pril.)) |
ID: |
18659456 |