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)