Module Five Flashcards
what is a genome?
the total complement of genetic information of a cell or a virus
what are the features of the bacterial genome?
- Double stranded DNA
- Usually cirular
- Usually one chromosome
- Size ranges from 0.112 Mb to 14.7 Mb
- Can contain plasmids
what is genomics?
the discipline involving the mapping sequence and analysis of genomes
what are the steps in bacterial genomics and comparative genomics?
- Determine genome sequence of bacterium
- Identify genes/features in bacterial genome
- Biological interpretation of genome content
- Comparison of genome content of two or more bacteria
what are the methods for genome sequencing?
Sanger sequencing
Next-generation sequencing
What are the features of next-generation sequencing?
- no cloning step required (no problem with toxic genes)
- Massively parallel sequence data
- Short read technology (and long read technology)
- More sequence reads for time/cost
what are the stages of next-generation sequencing?
- gDNA
- Parallel Sequencing
- Alignment
- Sequence
how is genomic DNA prepared in Illumina sequencing?
random fragments of genomic DNA and ligate adapters to both ends of the fragmentsq
how does the DNA attach to the surface in Illumina sequencing?
Binds single-stranded fragments randomly to the inside surface of the flow cell channels
what is bridge amplification in Illumina sequencing?
Add unlabeled nucleotides and enzyme to initiate solid-phase bridge amplification
what is the first chemistry cycle in Illumina sequencing?
Determine first base
-to initiate the first sequencing cycle, add all four labeled reversible terminators, primers, and DNA polymerase enzyme to the flow cell.
what is the image of the first chemistry cycle in Illumina sequencing?
after laser excitation, capture the image of emitted fluorescence from each cluster on the flow cell. Record the identity of the first base for each cluster
what happens before initiating the next chemistry cycle in Illumina sequencing?
The blocked 3’ terminus and the fluorophore and each incorporated base are removed
what are the steps of Illumina sequencing?
- Prepare genomic DNA sample
- Attach DNA to surface
- Bridge amplification
- Denature the double stranded molecules
- First chemistry cycle: determine the first base
- Image of first chemistry cycle
- Before initiating the next chemistry cycle
- sequence read over multiple chemistry cycles
what is genome annotation?
Just a selection of automated annotation tools
what are some examples of automated annotation tools?
RAST Prokka PGAP BEACON BASyS ....
What is NCBI?
Prokaryotic Genome Annotation Process
What is PGAP?
Automated annotation
what is automated annotation?
Automated genome annotation is fast/consistent
human (manual) annotation can add value
what can the genes present in the genome do?
can determine the biology of that organism
what can determine the genome content?
The biology or niche inhabited by a bacterium can determine genome content
what is metabolic modeling?
sets of metabolic genes can be analyzed and used to determine what metabolism a bacterium has
what is part of the accessory (pan) genome?
Transposons Insertion sequences (IS) Genomic islands Prophages Plasmids
what are the features of the accessory genome?
- These can be active/inactive
- Highly ‘flexible’ part of the bacterial genome that drives rapid evolution
what is comparative genomics?
Comparative genomics is the comparison of genome structure and function across different biological species or strains
what is the purpose of the comparison of genomes?
- comparison can aid in identifying differences
- The regions of difference can help identify genes involved in particular process
- close comparisons
- distant comparisons
