Lecture 22 Flashcards
What is a genome?
A genome is the total complement of genetic information of a cell or a virus.
What are some key facts about bacterial genomes?
Bacterial genomes can vary from really small to really large. Endosymbionts only live inside other cells and tend to have the smallest genomes, parasites tend to be slightly larger as they siphon off host cells. Free living cells tend to be largest.
Bacterial genome features are double stranded DNA which are usually circular, usually there is only one chromosome but there can be more and size ranges from 0.112 Mb to 14.7 Mb. They can also contain plasmids (which could be big enough to appear to be a chromosome, a megaplasmid), these will not be essential to survival.
What are the steps in bacterial genomics and comparitive genomics?
Bacterial genomics and comparitive genomics steps are:
- Determine genome sequence of bacterium (sequencing).
- Identify genes/features in bacterial genome(automated annotation).
- Biological interpretation of genome content (relationship to biology of organism).
- Comparison of genome content of two or more bacteria.
What does illumina sequencing involve?
illumina sequencing needs no cloning step, it allows for massively parallel sequence data and generally shorter reads, hence more sequence reads for time/cost. Steps involve prepping the DNA by adding sequences to the end of the DNA, clustering is then done, where the fragments attach to oligos via the added sequences, these will then be copied by polymerase (tethering to the base at the same time) which can then in turn be copied to nearby oligos. Marked nucleotides are then added one at a time, lighting up clusters of same DNA fragments with each colour representing one base.
What does genome annotation involve?
Genome annotation involves putting in sequence to fasta, this will predict the genes. Then for each gene we compare to reference genome /uniprot, if there is a homologue take reference annotation, if not label as hypothetical protein, we then predict protein domains and add annotation. Once this has been done for each gene we can predict other features. When annotating off of previous work we must be careful that the previous work wasn’t wrong.
What is important for gene analysis?
Genes present in genome can determine the biology of that organism, conversely the biology or niche inhabited by a bacterium can determine its genome content. It can be nice to give crude groupings to help determine trends in gene content and function. Also metabolic modelling can be done to give predictions of the metabolism of the bacterium or allow for creation of special growth mediums.
What is comparitive genomics and what is it good for?
Comparitive genomics is the comparison of genome structure and function across different biological species or strains, this can aid in identifying differences, with the regions of difference being able to help identify genes involved in particular processes. Comparitive genomics can be very good for studying slow growing organisms.
