Lecture 2 Flashcards
How can regions of low GC content been acquired
By horizontal transfer
What did analysis of K-12 genome in regards to HGT lead to
Concluded that 755 of the 4288 genes were likely derived from HGT. These were acquired in at least 234 separate events
What is E.coli O157:H7 strain of e.coli
Is an emergent human pathogen which was first identified in 1982. It’s an enterohaemorrhagic E.coli which produces shiga toxin and is associated with maemorrhagic colitis and haemolytic uraemic syndrome (can lead to kidney failure)
Whats the size of E.coli OH157:H7 strain
The genome is 5.5Mb - 1Mb bigger than K-12
It’s colinear
It was the second genome to be sequenced
What was the extra DNA in the o157 strainb
It was clustered into genomic islands.
There were also some K-islands with regions unique to E.coli K-12.
The O and K islands were located at the same position in the genome. The genome has a patchwork structure with a shared co-linear backbone interrupted by strain-specific islands
What are genomic islands
An extension of the previously used term “pathogenicity islands”
What’s the CFT073 strain of E.coli
It’s a strain of uropathogenic E.coli (UPEC) and was the third E.coli genome to be sequenced in 2002. It’s an example of extraintestinal E.coli (ExPEC) and is associated with UTIs
What is ExPEC and UPEC
Can be harmless when in intestines but become pathogens when they invade the urinary tract, blood or CSF.
UPEC strains are responsible for 70-90% of the 7 million cases of acute cystitis and 250,000 cases of pyelonephritis
Whats the CFT073 genome like
Is 5.2Mb so similar size to O157:H7 genome, the extra sequences relative to K-12 are not the same.
What did the 3 way analysis of the 3 e.coli strains find
Of the total non- redundant set of proteins encoded by any of the 3 genomes, only 2996 are encoded by all 3 genomes.
The total gene set in all 3 strains is 7638, only 2996 are found in all 3 so less than 40% is conserved
What does core genome mean
Genes conserved across all strains of a species
What does dispensible/ accessory genome mean
Genes from a genome which are not conserved in at least one other member of the species
What does pan genome mean
The total set of (non-redundant) genes present in any strain of the species
How big was the S. agalactiae core genome
Estimated at 1800 genes representing 80% of each individual genome
How big is the E.coli core genome and how do we estimate
2200 genes
Estimate the size of the core genome by randomising the order of the genomes and looking at how the size of the core genome reduces as additional genomes are added. This is done lots and the median size of the core genome is calculated