evolution of duplicated genomes
DESCRIPTION
Evolution of Duplicated Genomes. Talline Martins 4.24.07. Null hypothesis. Interlocus gene conversion. Loss of homoeologue. Possible Consequences of Polyploidization. Wendel, 2000. Genomic changes. Many genome-level changes may occur as a result of genomic ‘shock’ - PowerPoint PPT PresentationTRANSCRIPT
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Evolution of Duplicated Genomes
Talline Martins4.24.07
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Possible Consequences of Polyploidization
Null hypothesis Interlocus gene conversion
Loss of homoeologue
Wendel, 2000
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Genomic changes
• Many genome-level changes may occur as a result of genomic ‘shock’– Increased transposable element activity– Elevated levels of DNA methylation
• Homoeologous recombination• Inter-genomic concerted evolution• Non- and reciprocal translocations
Processes involved in diploidization
What happens to the duplicate genes that remain???
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Persistence of Duplicate Genes
• Classical model:– The most common fate of duplicated genes is to become
null through deleterious mutations. The only mechanism for preservation of duplicate genes is through fixation of beneficial mutations (neofunctionalization).
• Problems with the classical model:– Fraction of genes preserved is higher than predicted– Evidence for purifying selection can be found in both loci– Relative lack of null alleles segregating in extant
populations
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The Duplication-Degeneration-Complementation (DDC) Model
• Degenerative mutations facilitate rather than hinder the preservation of duplicate functional genes.– Duplicate genes lose different regulatory
subfunctions– They must complement each other to retain all
ancestral functions
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Possible Fates of Duplicate Genes
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Probability of Subfunctionalization
• The probability of maintenance of duplicate genes increases with number of number of regulatory elements
zPS = Σ PS,i
i=2
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Complex Regulatory Regions
Why are some duplicates expressed in some tissues together but not in others?
Embedded and overlapping regulatory regions may reduce the number of subfunctions
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Relaxed Selection Among Duplicate Regulatory Genes in Lamiales
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LFY/FLO & AP3/DEF
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Why are the duplicates still around?
• Role of selection
– Non-synonymous/synonymous substitution Dn/ds ()
– If < 1; purifying selection = 1; no selection (neutral) > 1; positive selection
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Codon Substitution Models
• Branch and fixed-sites models• Sites and branch-site models
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Branch and Fixed-Sites Models
• Branch models: Models R1-R4
• Fixed-sites model: compare ’s between paralogs– Model C (single )– Model E (allows
separate ’s for paralogs)
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Results
LFY/FLO = paralogs diverging more quickly relative to single-copy lineages (R2) , and significantly different from each other (model E).AP3/DEF = paralogs diverging more quickly relative to single-copy lineages (R2), but not significantly different from each other (models C and E).
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Sites and Branch-Sites Models(more powerful way to test for positive selection)
• Sites models: “hold constant among all branches while allowing to take on multiple values among site classes”– Models: M1a, M2a, M7, M8
• Branch-sites models: 1 set as foreground branches, allowing for different ’s over different branches and sites.– Reflects initial positive selection on duplicates
followed by purifying selection on ancestral lineages
– Model A and Model Anull. (2 is fixed at 1)
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Results
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Is different among functional domains of LFY/FLO & AP3/DEF?
• DEF: MADS (DNA-binding site), I, K, and C-terminus
• FLO: N- and C-terminus (putative DNA-binding site)
• How: used sites, fixed-sites, and branch models in addition to Bayes
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Results 1. DNA-binding domain in FLO and MADS domain in DEF are under stronger purifying selection than other domains.
3. DEF’s increase in is due to I, K, and C-terminus domains
2. FLOB has higher than FLOA in both domains
FLO
DEF
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Conclusions….• Continuous purifying selection on both
paralogs for both genes, although relaxed in comparison to single-copy taxa (supports the DDC model).
• Relaxed constraint in some domains may be an indication of subfunctionalization.– Subfunctionalization rather than adaptive
evolution contributes to preservation of duplicate genes
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Alternative explanations
• Gene Dosage– Unlikely, because duplicates have diverged
and because of partial functional redundancy
• Transcriptional regulatory interactions– FLO and DEF paralogs may have co-
evolved (concerted divergence)– Still needs to be tested
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References• Chen, ZF and Z Ni. 2006. Mechanisms of genomic
rearrangements and gene expression changes in plant polyploids. BioEssays 28:240-252.
• Adams, KL and JF Wendel. 2005. Polyploidy and genome evolution in plants. Curr. Op. Plant Bio. 8:135-141
• Wendel JF. 2000. Genome evolution in polyploids. Plant Mol. Bio. 42:225-249.
• Force et al. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545.
• Aagard JE, Willis JH, and PC Phillips. 2006. Relaxed selection among duplicate floral regulatory genes in Lamiales. J Mol. Evol. 63:493-503.
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Time to Subfunctionalization
Fates of duplicated genes are determined shortly after polyploidization
Ratio of mutation rate in regulatory and coding regions is a weak factor in expected degree of resolution
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