topic 6 comparative genomics

Pan genome

entire set of genome in the experiment even including multiple organisms

variable genome

genes not shared by everyone and maybe only 1 or 2 organisms

Core genome

Genes shared by everyone

how to visualize gene sets

by using a Venn diagram Seeing that proteins that air closer to each other or are core genes will be together and in the middle of the Venn diagram but genes that are variable will be in the outskirts and outside of the circle.

genes that are closer to each other which are core genomes Is essential to the Organism

genes that are in the outside circles are not that essential to the Organism such as antibiotic resistance It is not a conserved region in the genome

Orthology

genes that are the same but are found in different species

paralogs

genes that are from the same gene family but have duplicated in the same genome

novel genes

they arise from either mutations or donovo but theyre insertions

what programs to use to do orthology mapping

1. eggnog

2. ENSMBL compare

3. all by all BLAST

what is all by all B BLAST

blast genome one with genome 2 and then last genome two with genome one to see what gene areas match up to each other Which showcases a one to one ratio and shows an orthology relationship

what is the most used command

Outfit 6 which means out format 6

one too many and many too one relationship in orthology mapping

one too many: shows that a gene from Genome One when blasted showcases that it's connected to one gene from genome 2 However when genome two is blasted with genome one it shows two genes connected to 1 This indicates that there was paralogue gene loss in genome one Or a paralogue duplication event in genome two

what if there is no hit in Orthology mapping

it means that there was a gene loss or deletion event or an addition of a new gene happened in the gene that is being blasted

tree mapping versus Blast

tree mapping is more efficient than BLAST for doing comparative genome studies This is because sometimes BLAST makes errors when looking at homology patterns between genes of two different species

how many genomes do we need for tree mapping

more than two for sure to build a high confidence and make orthology sets of different organisms That with confidence if there is a gene present in that location or not

functional comparison of genome sets

after we do a orthology mapping We can then how frequently those functions are occurring in the genome To do this we can use KEGG And GO terms And we can tally up the frequencies we see in each genome and then compare the functional frequencies of each genome to another To see how different they are in their function

this has been done before to see the get microbes constructing a heat map Where red indicates a hot spot of functional similarities between different bacteria And green indicates almost no similarity in function inmate in two different bacterias

how to do structural comparison of whole genomes

we compare chromosomes Or do whole genome alignment to see if there are any syntenic blocks

syntenic blocks

synteny is used to describe how much of the genome is matching with the other and it can also show what regions don't match up It can also tell us. when synteny lines up it means that there are orthologs

it can also tell us what kind of chromosomal rearrangement

happened such as inversion which would end up looking like an X

types of chromosomal rearrangements

things that result in change in gene content: duplication and deletion

things that result in no change in gene content: inversion, translocation, insertion

Arabdipopsis synteny

is a result of ancestor whole genome duplication and that is why we see some shifted areas where the genes match up

Syntenic relationships with Time

as organisms move farther away from each other with time their syntony changes and they loose synteny.

parasitic organisms and synteny

they lose a lot of genetic information so that they can rely more on the host's genetic information

artemis /ACT

this is a synteny visualization software Where they look at different genomes but they are all the same colour and sometimes the orientation has flipped

we have to make sure we're looking had both genomes in the same direction And if we are looking at prokaryotes with circular genomes we have to make sure that the start sites line up with each other If not we see an X pattern which resembles different start sites

mauve

this is another synteny software which colour codes different orthologs based on BLAST And you can see them in the same strands forward or reverse You don't have to do it yourself

BRIG analysis

another way to look at syntony which is more relevant for genomic prokaryotes with circular DNA

in the middle there is a circular genome of a reference Organism

it builds out with more circles that have different organisms in each circle

the genes are colour coded to match the reference genome and see if it is in that same position with the reference genome

if there are gaps then that means that there was an insertion event in the genome that has a gene at that spot

the gap can also mean that that gene is just not present in the reference genome And that is why we can't see if any insertion events happened