Bacterial Genomics Flashcards
(22 cards)
Which microorganism was first to have its whole genome attempted to be sequenced?
E.coli K12
What microorganisms were actually the first to get their genomes sequenced?
H.influenza and Mycoplasma genitalium
What technique was used that lead to the first successful bacterial whole genome sequencing?
Whole genome shotgun approach
Who initiated the whole genome shotgun approach on H.influenza?
Craig venter
What sequencing technique was used in the first, unsuccessful whole bacterial genome sequencing project?
Clone by clone approach
In brief, what are the steps for whole genome shotgun sequencing?
- whole bacterial chromosome is randomly sheared using sonication or enzymes
- segments are selected for size
- clone fragments into a vector plasmid
- pick colonies to create a shotgun library
- prep library for sanger sequencing
- sequence using 2 primers that are in the insert
What type of sequence data does shotgun sequencing produce?
contigs
How can the gaps produced in shotgun sequencing be filled?
PCR
What three strains of E.coli were used in the initial studies of E.coli genome comparison?
K12 as reference genome (lab strain)
E.coli O157:H7
E.coli UPEC CFT073
how many base pairs in E.coli K12 genome?
4,639,221 bp
How many base pairs in E.coli O157:H7 genome?
roughly 5.5mb (roughly 1mb more than K12)
What pathogenic tendency separates E.coli UPEC from E.coli O157:H7?
UPEC strain is extraintestinal - is a uropathogenic strain (urinary tract infections)
What key genomic differences were found in the comparison of the 3 genome strains?
Islands corresponding to each different strain which were not found in the others = O islands and K islands (and islands in UPEC strain not in either)
How much of the genome was conserved across all three strains of E.coli?
roughly 40%
Define E.coli pangenome
Total set of genes found across all strains of E.coli
Define E.coli core genome
Conserved genes found in every strain of E.coli
What sequencing technology has dramatically increased the number of bacterial genomes publicly available?
Illumina
What is the problem with most of the bacterial genomes now readily available?
They are unfinished and sometimes no annotated as these parts remain very laborious despite current sequencing technologies
What is PROKKA used for?
Automated annotation pipeline used to help speed up annotation of newly sequenced bacterial genomes.
What gene of interest was discovered when comparing different strains of Campylobacter?
Genes used in Vitamin B5 synthesis were found in cattle strains but not chicken strains
Was any strict evolutionary lineage seen across different Campylobacter strains
Nope
What technology will probably be used to sequence bacterial genomes in the future?
MinION and PacBioSequel
