PanPhlAn Strain Detection and Characterization

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What is the genome size range of Escherichia Coli?

4.5-4.7M b (correct)

6.0-6.5M b

3.5-4.0M b

5.0-5.5M b

How many genes does the genome of Escherichia Coli typically contain?

4000-5000 genes (correct)

1000-2000 genes

5000-6000 genes

2000-3000 genes

Where was the original E.coli strain K-12 obtained from?

A diphtheria patient in Palo Alto, California in 1922 (correct)

A tuberculosis patient in India in 1935

An influenza patient in Spain in 1945

A patient with cholera in Brazil in 1900

How many ribosomal RNA operons are present in the genome of Escherichia Coli?

Seven operons Signup and view all the answers

What percentage of the genes of E.coli strain K-12 were experimentally identified?

38% Signup and view all the answers

In the E.coli long-term evolution experiment, how often are samples saved for tracking evolutionary changes?

Every 500 generations Signup and view all the answers

What is PanPhlAn primarily used for?

Detecting and characterizing individual strains in metagenomic samples Signup and view all the answers

Which component of the E. coli genome consists of genes shared by all members of the species?

Core genome Signup and view all the answers

How many genes approximately are included in the core genome of E. coli strains?

1000-3000 genes Signup and view all the answers

Which term refers to the set of genes present in some but not all genomes within the same bacterial species?

Accessory genome Signup and view all the answers

What is the pangenome of a bacterial species?

The union of the core genome and the accessory genome Signup and view all the answers

What was a specific strain identified using PanPhlAn during an outbreak in Germany in 2011?

Shiga-toxigenic Escherichia coli (STEC) Signup and view all the answers

What is the main difference between a closed pangenome and an open pangenome?

Closed pangenome size keeps increasing as new genomes are added, while open pangenome size tends to a maximum. Signup and view all the answers

What is the significance of the core genome in a species like E. coli?

Core genome genes are responsible for basic cellular functionalities and survival in the environment. Signup and view all the answers

How does sequencing more organisms of the same species affect the core genome and pangenome?

Sequencing more organisms decreases the size of the core genome and increases the pangenome. Signup and view all the answers

What are some characteristics of elements in the pangenome of E. coli?

Pangenome elements are specific to a single strain, like antibiotic resistance, and may not be well characterized functionally. Signup and view all the answers

What can be inferred from Figure 2.1 regarding E. coli's gene distribution among different strains?

51% of E. coli genes are strain-specific, while the rest are shared between 2 to 20 strains. Signup and view all the answers

Why do different pan-genome gene numbers exist in E. coli strains according to Chapter 2?

Due to different gene thresholds that define what is considered enough similarity to be the same gene. Signup and view all the answers