Bioinformacijska analiza genomov talnih izolatov Bacillus subtilis

magistrsko delo

Urška Murovec (Author), Cene Gostinčar (Reviewer), Ines Mandić-Mulec (Mentor), Polonca Štefanič (Co-mentor)

Abstract

Bacillus subtilis so paličaste po Gramu pozitivne bakterije, ki so sposobne razlikovanja med visokosorodnimi (»kin«) in manj sorodnimi sevi (»non-kin«) iste vrste. Fenotip prepoznavanja se odraža v nastanku mejne linije ob srečanju dveh rojev različnih sevov. V mehanizem prepoznavanja so vključeni različni sistemi: antibiotiki in toksini, proteini CDI, molekule na celični površini in mobilni elementi (npr. fagi). Namen magistrske naloge je bil analizirati genome in gene, ki so vključeni v sorodstveno razlikovanje (geni KD) pri 21 sevih Bacillus subtilis subsp. subtilis ter na osnovi 8 hišnih genov določiti njihovo filogenijo. Predvidevali smo, da bodo filogenetsko bolj sorodni sevi pokazali večjo podobnost tudi na nivoju genov KD tako na nivoju nukleotidne identitete kot na nivoju prisotnosti/odsotnosti teh genov. Fasta datoteke 21-ih genomov B. subtilis smo z algoritmom BWA-SW prilegali na referenčni genom B. subtilis 168 in iskali potencialne gene KD v programu IGV, izolirali zaporedja teh genov in tudi hišnih genov ter skonstruirali dendrograme podobnosti v MEGAX in R. Pokazali smo, da je analiza genov KD na podlagi sekvenčne podobnosti sovpadala s filogenijo, ki smo jo pridobili na podlagi 8-ih hišnih genov. Prav tako smo ugotovili, da dendrogram narejen na podlagi odsotnosti/prisotnosti genov v sevih korelira s KD-fenotipi sevov pri rojenju.

Keywords

Bacillus subtilis;sorodstvena diskriminacija;genomika;bioinformacijska analiza genomov;

Data

Language:	Slovenian
Year of publishing:	2020
Typology:	2.09 - Master's Thesis
Organization:	UL BF - Biotechnical Faculty
Publisher:	[U. Murovec]
UDC:	579.22/.26:579.852.11:575.111
COBISS:	32529411
Views:	533
Downloads:	248
Average score:	0 (0 votes)
Metadata:

Other data

Secondary language:	English
Secondary title:	Bioinformatic analysis of B. subtilis genomes obtained from soil isolates
Secondary abstract:	Bacillus subtilis are Gram-positive bacteria that are able to distinguish between highly related ("kin") and less related strains ("non-kin") of the same species. The discrimination phenotype is reflected in the formation of a visible boundary line at the meeting point of two swarms, which is absent between kin swarms. Various systems are involved in the recognition mechanism, such as: antibiotics and toxins, CDI proteins, cell surface molecules and mobile elements. The purpose of the master's thesis was to analyse the genomes and genes involved in kin discrimination (KD genes) in 21 strains of Bacillus subtilis subsp. subtilis. We also aimed to reconstruct their phylogeny based on 8 housekeeping genes. We hypothesized that more related strains would show greater similarity at the level of KD genes both in percent of nucleotide identity and in their presence. Fasta files of 21 of B. subtilis genomes were aligned to the reference genome of B. subtilis 168 using the BWA-SW algorithm. Then we searched KD genes using the IGV program, isolated sequences of KD genes and housekeeping genes, and constructed similarity dendrograms in MEGAX and R. We showed that analysis of KD genes based on sequence similarity coincided with phylogeny obtained on the basis of 8 housekeeping genes. We also found that a dendrogram prepared based on the absence/presence of genes correlated with strain interactions during swarming.
Secondary keywords:	Bacillus subtilis;kin discrimination;genomics;bioinformatic analysis;
Type (COBISS):	Master's thesis/paper
Study programme:	0
Embargo end date (OpenAIRE):	1970-01-01
Thesis comment:	Univ. v Ljubljani, Biotehniška fak., Študij mikrobiologije
Pages:	X, 47 f., [8] f. pril.
ID:	12035089