Draft genomes annotation of Staphylococcus chromogenes and Staphylococcus simulans

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School of Science | Master's thesis
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Date

2013

Department

Perustieteiden korkeakoulu

Major/Subject

Informaatiotekniikka

Mcode

T-61

Degree programme

Language

en

Pages

(7) + 65 s. + liitt. 14

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Abstract

Staphylococcus chromogenes and Staphylococcus simulans, the target organisms in this study are known to be causative agents in 'subclinical mastitis', this disease manifests itself mainly in dairy cattle. Mastitis is defined as the inflammation of the udder. Characterizing the genomic and proteomic features of these organisms is essential to better understand their fitness, virulence potential and phylogenetic relationship to other bacterial species. The objective of this study was to characterize and determine the genetic makeup of both the organisms. Characterizing the genome is referred to as 'Genome Annotation', a multi-layered process that involves determining information with biological relevance or Significance from the raw sequence data generated from sequencing projects. In this work we present the 'draft genome' sequences of both these organisms, as well as the underlying gene/protein set and their annotations. Apart from genome characterization or annotation, we performed comparative proteomic analysis with 28 completely sequenced bacterial genomes, which included bacterial species under three categories; pathogenic bacteria causing mastitis in cows, milk pathogens harmful to humans and mastitis associated bacteria or those living in milk environment. This thesis consists of three principal parts. Firstly, nucleotide level annotation: this mainly comprises of the gene finding task; prediction of potential gene or CDS sequences in the targets genomes, predicting transfer-RNA and ribosomal-RNA genes in the genome. Secondly, protein level annotation: this part includes adding additional layers of information to the predicted proteins(Le translated CDS or genes). Finally, comparative proteomic analysis: this involves the comparison of the target genomes with other bacterial species. Future directions of this project would involve additional sequencing for 'gap closure' in order to generate complete 'circular chromosomes' for both bacterial species.

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Supervisor

Lähdesmäki, Harri

Thesis advisor

Iivanainen, Antti

Keywords

draft genome, genome annotation, Staphylococcus chromogenes and simulans

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Citation

Permanent link to this item

https://urn.fi/URN:NBN:fi:aalto-2020122859911

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[dipl] Perustieteiden korkeakoulu / SCI