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

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 Science) 1kb = 1000 base pairs

Ward et al Estimated mitochondrial genome sizes in Cucurbitaceae

Ward et al Estimated mitochondrial genome sizes in Cucurbitaceae Prediction: Larger genomes have lower mutation rates

Actual mitochondrial genome sizes in Cucurbitaceae Alverson et al 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

Chloroplast sequences in the mitochondrial genome

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 Plant Cell.

The cucumber mitochondrial and nuclear genomes share a lot of DNA 33% of the mitochondrial genome Alverson et al 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 SloanDoug 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 kb16 kb

Mutation rate and mitochondrial genome size 426 kb253 kb16 kb11,318 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 sizeTheory: 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 sizeTheory: 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 sizeTheory: 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 sizeTheory: 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 Amborella Arabidopsis

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 Ann. Rev. Biochem. 76:

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)