A Study on the Relationship of the Core and Accessory Genome in S. aureus Restricted; Files Only

Abstract

With the advent of next-generation sequencing (NGS), thousands of Staphylococcus aureus genomes have been sequenced. In this study, a large sample of 83,383 public S. aureus genomes were sampled down to a representative set of 5,784. Leveraging this extensive dataset, it was discovered that there exists a close correlation between the core and accessory genome of S. aureus. Furthermore, besides typical multi-locus sequence typing (MLST) classification, absence-presence of a few high Fst genes in the accessory genome can be used to delineate samples. These results show that the diversity and structure of the S. aureus genome can be best understood as between clonal complexes.

Table of Contents

1 Introduction 1

2 Methods 4

2.1 Data Curation............................. .. 4

2.2 FST Calculation............................ .. 4

3 Results 6

3.1 Clustering strains by accessory genome content gives similar results to clustering by core genome alleles................... .. 6

3.2 Accessory genes have a bimodal distribution of FST . . . . . . . . .. 10

3.3 A small number of accessory genes are sufficient to predict MLST .. 11

4 Discussion 16

5 References 18

About this Honors Thesis

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School	Emory College
Department	Quantitative Science
Degree	B.S.
Submission	Honors Thesis
Language	English
Research Field	Biology, Biostatistics Biology, Bioinformatics Biology, Genetics
Stichwort	Clonal Complex MLST biology Machine Learning
Committee Chair / Thesis Advisor	Michal Arbilly, Emory University
Committee Members	Daniel Weissman, Emory University Timothy Read, Emory University

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