Genomic gigantism in plant mitochondria Andy Alverson.
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Transcript of Genomic gigantism in plant mitochondria Andy Alverson.
Genomic gigantism in plant mitochondria
Andy Alverson
Outline
1. Mitochondrial genome size evolution
• Cucurbitaceae
• Silene
2. Horizontal gene transfer (HGT) in the mitochondrial genome of
Amborella
The three plant genomes
The disparate trajectories of organelle genomes
The disparate trajectories of organelle genomes
1kb = 1000 base pairs
The disparate trajectories of organelle genomes
1kb = 1000 base pairs
The disparate trajectories of organelle genomes
Mutation pressure hypothesis (Lynch et al. 2006. Science)
1kb = 1000 base pairs
Ward et al. 1981
Estimated mitochondrial genome sizes in Cucurbitaceae
Ward et al. 1981
Estimated mitochondrial genome sizes in Cucurbitaceae
Prediction: Larger genomes have lower mutation rates
Actual mitochondrial genome sizes in Cucurbitaceae
Alverson et al. 2010. Mol. Biol. Evol.
Estimating the mutation rate of a genome
CUA
CUC
CUG
CUU
Leu
CCA
CCC
CCG
CCU
Pro
GGA
GGC
GGG
GGU
Gly
• Multiple codons for the same amino acid
• Synonymous mutations
– do not change the amino acid
– invisible to natural selection ≈ neutral
– rate of neutral change ≈ mutation rate
Do large genomes have lower mutation rates?
(dS)
Do large genomes have lower mutation rates?
Total coding: 17% 7% 19% 5% 4%
Coding sequences in cucurbit mitochondrial genomes
Large genomes integrate massive amounts of new sequence
Traffic patterns of plant DNA
Traffic patterns of plant DNA
Chloroplast sequences in the mitochondrial genome
Chloroplast-derived sequences turn over rapidly
Chloroplast-derived sequences turn over rapidly
Chloroplast-derived sequences turn over rapidly
Traffic patterns of plant DNA
Nuclear–mitochondrial sequence exchange
Huang et al. 2009
The cucumber mitochondrial and nuclear genomes
share a lot of DNA
33% of the mitochondrial genome
Alverson et al. 2011. Plant Cell.
The cucumber mitochondrial and nuclear genomes
share a lot of DNA
33% of the mitochondrial genome
Alverson et al. 2011. Plant Cell.
Outline
1. Mitochondrial genome size evolution
• Cucurbitaceae
• Silene
2. Horizontal gene transfer (HGT) in the mitochondrial genome of
Amborella
Mitochondrial genome evolution in Silene
Dan Sloan Doug Taylor
University of Virginia
Mitochondrial mutation rate variation in Silene
Mutation rate and mitochondrial genome size
? ?? ?
16 kb
Mutation rate and mitochondrial genome size
? ?
426 kb253 kb 16 kb
Mutation rate and mitochondrial genome size
426 kb253 kb 16 kb 11,318 kb6,728 kb
Silene noctiflora (6.7 Mb)
•59 chromosomes
•66–192 kb in length
Large multi-chromosomal mitochondrial genomes
•Unprecedented size and structural variation in plant mitochondrial genomes
Genome size summary and conclusions
•Unprecedented size and structural variation in plant mitochondrial genomes
Genome size summary and conclusions
Larger genome size•
Theory: Low mutation rate
•Unprecedented size and structural variation in plant mitochondrial genomes
•Cucurbitaceae and Silene show the opposite pattern
Genome size summary and conclusions
Larger genome size•
Theory: Low mutation rate
•Unprecedented size and structural variation in plant mitochondrial genomes
•Cucurbitaceae and Silene show the opposite pattern
Genome size summary and conclusions
Larger genome size•
Theory: Low mutation rate
•What drives genome size evolution in plant mitochondria?
–mutation rate? Not likely.
–intramolecular recombination? Maybe.
•Unprecedented size and structural variation in plant mitochondrial genomes
•Cucurbitaceae and Silene show the opposite pattern
Genome size summary and conclusions
Larger genome size•
Theory: Low mutation rate
•Much of the "extra" intergenic DNA may derive from the chloroplast and the nuclear genomes
•What drives genome size evolution in plant mitochondria?
–mutation rate? Not likely.
–intramolecular recombination? Maybe.
Outline
1. Mitochondrial genome size evolution
• Cucurbitaceae
• Silene
2. Horizontal gene transfer (HGT) in the mitochondrial genome of
Amborella
The Amborella mitochondrial genome: another monster!
total size = 3.9 Mb
AmborellaArabidopsis
Features in the Amborella mitochondrial
genome
Native mito
Features in the Amborella mitochondrial
genome
chloroplast-derived
Native mito
Features in the Amborella mitochondrial
genome
chloroplast-derived
Native mito
Foreign angiosperm mito
Features in the Amborella mitochondrial
genome
Foreign moss mito
chloroplast-derived
Native mito
Foreign angiosperm mito
Features in the Amborella mitochondrial
genome
Foreign green algal mito
Foreign moss mito
chloroplast-derived
Native mito
Foreign angiosperm mito
Features in the Amborella mitochondrial
genome
Native mito
Features in the Amborella mitochondrial
genome
Foreign green algal mito
Foreign moss mito
Native chloroplast
Native mito
Foreign angiosperm mito
cob
N
Amborella
other angiosperms
mosses
green algae
Other genes show the same pattern as cob
Amborella
other angiosperms
mosses
green algae
N
N
N
N = native
What's going on here?
What the Amborella mitochondrial genome lacks:
Insights into the mechanism of horizontal transfer
What the Amborella mitochondrial genome has:
Insights into the mechanism of horizontal transfer
What the Amborella mitochondrial genome has:
• entire foreign mitochondrial genomes
• donors are all "green plants"
What the Amborella mitochondrial genome lacks:
• foreign nuclear DNA• bacterial DNA • fungal DNA• mitochondrial DNA from non-"green plants"
What the Amborella mitochondrial genome lacks:
Insights into the mechanism of horizontal transfer
What the Amborella mitochondrial genome has:
• entire foreign mitochondrial genomes
• donors are all "green plants"
Mitochondrial fission/fusion arose twice during eukaryotic evolution
The machines that divide and fuse mitochondria. 2007. Ann. Rev. Biochem. 76:751-780.
How do foreign mitochondria get into Amborella?
Amborella is endemic to New Caledonia
How does Amborella acquire foreign mitochondria?
−direct, plant-to-plant contact?
−parasitic angiosperms
−epiphytic plants & algae
How does Amborella acquire foreign mitochondria?
−direct, plant-to-plant contact?
−parasitic angiosperms
−epiphytic plants & algae
Donors are probably lichen-forming
green algae
cob
How does Amborella acquire foreign mitochondria?
−direct, plant-to-plant contact
−parasitic angiosperms
−epiphytes plants & algae
−biological vectoring agents
−viruses
−bacteria
−fungi (pathogenic or mycorrhizal)
−insects
•Growth of the Amborella genome reflects large-scale acquisitions of foreign DNA from other "green" plants
− angiosperms, mosses, and green algae
− mitochondrial DNA
Amborella summary and conclusions
•Growth of the Amborella genome reflects large-scale acquisitions of foreign DNA from other "green" plants
− angiosperms, mosses, and green algae
− mitochondrial DNA
•acquisitions include entire mitochondrial genomes
Amborella summary and conclusions
•Growth of the Amborella genome reflects large-scale acquisitions of foreign DNA from other "green" plants
− angiosperms, mosses, and green algae
− mitochondrial DNA
•acquisitions include entire mitochondrial genomes
Amborella summary and conclusions
•the mechanism of HGT
1. introduction of foreign (but "green") mitochondria
2. fusion between native and foreign mitochondria
•Growth of the Amborella genome reflects large-scale acquisitions of foreign DNA from other "green" plants
− angiosperms, mosses, and green algae
− mitochondrial DNA
•acquisitions include entire mitochondrial genomes
Amborella summary and conclusions
•Are there more Amborella's out there? Almost certainly.
•the mechanism of HGT
1. introduction of foreign (but "green") mitochondria
2. fusion between native and foreign mitochondria
Funding
•NIH Ruth L. Kirschstein postdoctoral fellowship (Alverson)
•NIH Research grant (Palmer)
Acknowledgements
Jeff Palmer
(Indiana)
Dan Sloan
(Virginia/Yale)
Doug Taylor
(Virginia)Danny Rice
(Indiana)