Lecute 19 Flashcards
Genetics
Study of genes
Genomics
The study of genomes
Metagenomics
The study of all the genomes in a sample
What is a genome?
The total complement of genetic information of a cell or virus
Difference between Sanger sequencing and NGS
Sanger technology sequences one DNA fragment as a time using capillary electrophoresis
NGS allows massive parable sequencing using solid surface teachnology
Microbial genomic features of viruses
- can be single or double stranded
- non segmented or segmented
- range from 1000nt to 250000000 nt
- can contain envelopes
- high mutation rates
Microbial genomic feature of bacteira
- double stranded DNA
- usually circular
- usually one chromosome
- size range form 1-14 minion nt
- can contain plasmids
- slow mutation rates
What is genomics
The discipline involving the mapping sequencing and analysis of genomics
Microbial and comparative genomics - 4 steps to get from determining the genome sequence to understanding what it means
Two types of DNA sequencing
Sanger sequencing
Next generation sequencing
- short read technology (illumina)
- long read technology (oxford)
Next generation sequencing - iliumiina sequencing
Long vs short reads - oxford nanopore and illumina
Main difference is that long generates long reads and short generates short read
Main downfall of short rads in next gen sequencing
You may miss gaps - sequence gaps in short reads
Main downfall of short rads in next gen sequencing
You may miss gaps - sequence gaps in short reads
What kind of next gen sequencing are used for viscoses
Short reads as their RNA is rapidly degradable
Once all the short reads are sequenced what must happen?
Assembly to make a long sequence
How do u do gene annotation - like knowing what part of the genome belongs to each gene or protein
- using a selection of automated tools
Automated genome annotation vs manual genome annotation
- automated genome annotation is fast/consitant
- manual annotation can add value as wont miss anything
Are people needed to interpret the genome data?
Yes
genome data interpretation
- people are needed to interpret the data and compare this to the biology of the organism
- genes present in genome can determine the biology of that organism
- conversely the biology or niche inhabited by an organism can determine its genome content
- host genetics play a huge role in a virus’ ability to adapt to a new host
Genome data interpretation - SARS-CoV-2 spike example
- the genome of SARS-CoV-2 includes a gene that encodes the spike protein
- changes in the RNA sequence of that spike protein results in changes in the shape of the spikes structure
- its spike changes all the time to invades to immunity we have from past infections and vaccines
= it changes at a fast rate in order to survive
What two things can sequencing genome data tell us?
- what is there
- how much of it there is
What does interpreting the genome data amount show us?
- can estimate the relative abundance of sequence reads
- this corresponds to an organisms abundance or gene expression
- read abundance can tell us a lot about genetic function
- how many reads per contig?
What is comparative genomics
Comparative genomics is the comparison of genome strucuture and function across different biological species or strains
