7. Duplicated genomes Flashcards
What are gene families?
Gene families - set of several similar genes, formed by single original gene duplication and having similar biochemical function
Many genes in eukaryotes occur in multiple copies
What are homolous genes?
Homologs - genes which share common ancestry - homology
What are the three types of homology?
Types of homology:
- paralogy - homologs after duplication
- orthology - homologs after speciation
- ohnology - homologs after whole genome duplication
Explain globin gene family in human genome
Globin gene family - genes on:
- chrom 16: α-like -> blood
- chrom 11: β-like -> blood
- chrom 22: myoglobin -> muscle
-> these genes diverged 600-800 Mil ya - calculated using mutation rate as a time unit
How can genes be duplicated?
New gene copies rise:
- local gene duplication - single gene duplicated
- segmental duplication - large region / entire chrom duplicated
- whole genome duplication (WGD)
What are the types of whole genome duplication?
Type of WGD:
- autotetraploidy: duplication of diploid genome
- allotetraploidy: merging of two diploid genomes
What leads to gene families?
Gene duplication leads to gene family formation - different types of duplications
What is a well studied example of mammalian gene family?
Hox gene family - arranged in clusters in different locations - based on gene repeats - what genome arrangements have occurred - based on Hox genes - humans underwent 2 WGD - because 1 Hox copy -> 4 Hox copies
How is segmental duplication differentiated from WGD?
In segmental duplication vs WGD: ???????????
What is the timeline of human gene families’ emergence?
749 gene families in humans emerged in 3 main waves
Why was it first thought that 2 rounds of WGD occurred in chordate evolution?
Because first overestimated the human genome - though x4 more genes than other
Why does S. cerevisiae have reduced number of genes if it is thought that there was WGD?
After WGD underwent gene loss ~90% of duplicates? - when compared to an outgroup Kluyveromyces lactis - saw how differently genes arranged - double synteny => concluded that WGD, not segmental gene duplication
Explain patterns of gene loss in yeast
After WGD different strains underwent differential gene loss - reciprocal gene loss: one species loses one gene, the other loses another gene
How severe was the gene loss in yeast in evolution?
After 10% of time after WGD alread half of duplicated genes were lost
What are the consequences of reciprocal gene loss in yeast?
Reciprocal gene loss can lead to:
- speciation
- reproductive isolation
- 25% of inviable spores due to random assortment after hybridization
Yeats genome conclusion
What is an outgroup for chordate WGD
Chordate WGD outgroup - sea squirt
How were 2 rounds of WGD inferred from comparign human genome to amphioxus?
Compared human genoem to amphioxus - syntenic blocks observed but quadruple synteny
Why are ohnologs common in plants?
Genome duplication is common in plants
What are the possible fates of duplicated genes?
Fates of duplicated genes in genomes:
- loss
- concerted evolution
- divergence
- further rearrangements
Explain loss as a potential fate of duplicated genes
A duplicated gene can be lost:
- KO mutations / degeneration / deletion
- pseudogenisation: base mutataion / deletion / insertion -> disrupt regulation or splicing / premature STOP codon / frameshift mutation / TE
What is a pseudogene?
Pseudogene - DNA segment that structurally resembles a gene but is not capable of coding for a protein
Ex: >900 olfactory genes but ~63% pseudogenes - non-functional
Explain concerted evolution as a potential fate of duplicated genes
Concerted evolution - genes become more familiar in same species than their paralogs - homogenisation within a gene family:
- recombination
- unequal crossing-over
- gene conversion
What is concerted evolution?
Concerted evolution - phenomenon where paralogous genes within one species are more closely related to one another than to members of the same gene family in closely related species - due to recombination
Explain how recombination leads to concerted evolution
Genes of the same family in same organism recombine - tandem repeats match -> unequal crossing-over because not whole sequence matches -> gene conversion - homogenisation
Explain divergence as a potential fate of duplicated genes
Divergence of duplicated genes within a genome - specialisation of one / both duplicates to new role - subfunctionalisation
Give an example of a subfunctionalisation of genes in a gene family
Globin gene family - different globin expressed at different developmental stages - better O2 affinity
Explain how subfunctionalisation of gene duplicates can occur
Subfunctionalisation - divergence + specialisation of the copies - gene regulatory regions affected - environmental control which duplicate will be turned on + changes in coding region - different protein products - ex globin duplicates have different O2 affinities
How can gene duplicate subfunctionalisation turn into pseudogenisation?
When all necessary regulatory regions are mutated to a point of KO - non-functional gene left - gene exists but no protein expression due to disruoted
Case study of gene duplication -> subfunctionalisation -> pseudogenisation
Explain further rearrangements as a potential fate of duplicated genes
See next lectures on introns:
- internal duplications
- exon suffling in modular genes / proteins
Lecture summary
