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
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
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
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
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
Lecture summary
