Genomic gigantism in plant mitochondria
This presentation is the property of its rightful owner.
Sponsored Links
1 / 67

Genomic gigantism in plant mitochondria PowerPoint PPT Presentation


  • 139 Views
  • Uploaded on
  • Presentation posted in: General

Genomic gigantism in plant mitochondria. Andy Alverson. Outline. Mitochondrial genome size evolution Cucurbitaceae Silene. Horizontal gene transfer (HGT) in the mitochondrial genome of Amborella. The three plant genomes. The disparate trajectories of organelle genomes.

Download Presentation

Genomic gigantism in plant mitochondria

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


Genomic gigantism in plant mitochondria

Genomic gigantism in plant mitochondria

Andy Alverson


Genomic gigantism in plant mitochondria

Outline

  • Mitochondrial genome size evolution

    • Cucurbitaceae

    • Silene

Horizontal gene transfer (HGT) in the mitochondrial genome of Amborella


Genomic gigantism in plant mitochondria

The three plant genomes


Genomic gigantism in plant mitochondria

The disparate trajectories of organelle genomes


Genomic gigantism in plant mitochondria

The disparate trajectories of organelle genomes

1kb = 1000 base pairs


Genomic gigantism in plant mitochondria

The disparate trajectories of organelle genomes

1kb = 1000 base pairs


Genomic gigantism in plant mitochondria

The disparate trajectories of organelle genomes

Mutation pressure hypothesis (Lynch et al. 2006. Science)

1kb = 1000 base pairs


Genomic gigantism in plant mitochondria

Estimatedmitochondrial genome sizes in Cucurbitaceae

Ward et al. 1981


Genomic gigantism in plant mitochondria

Estimatedmitochondrial genome sizes in Cucurbitaceae

Prediction: Larger genomes have lower mutation rates

Ward et al. 1981


Genomic gigantism in plant mitochondria

Actualmitochondrial genome sizes in Cucurbitaceae

Alverson et al. 2010. Mol. Biol. Evol.


Genomic gigantism in plant mitochondria

CUA

CUC

CUG

CUU

CCA

CCC

CCG

CCU

GGA

GGC

GGG

GGU

Leu

Pro

Gly

Estimating the mutation rate of a genome

  • 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


Genomic gigantism in plant mitochondria

Do large genomes have lower mutation rates?


Genomic gigantism in plant mitochondria

Do large genomes have lower mutation rates?

(dS)


Genomic gigantism in plant mitochondria

Coding sequences in cucurbit mitochondrial genomes

17%

7%

19%

5%

4%

Total coding:


Genomic gigantism in plant mitochondria

Large genomes integrate massive amounts of new sequence


Genomic gigantism in plant mitochondria

Traffic patterns of plant DNA


Genomic gigantism in plant mitochondria

Traffic patterns of plant DNA


Genomic gigantism in plant mitochondria

Chloroplast sequences in the mitochondrial genome


Genomic gigantism in plant mitochondria

Chloroplast-derived sequences turn over rapidly


Genomic gigantism in plant mitochondria

Chloroplast-derived sequences turn over rapidly


Genomic gigantism in plant mitochondria

Chloroplast-derived sequences turn over rapidly


Genomic gigantism in plant mitochondria

Traffic patterns of plant DNA


Genomic gigantism in plant mitochondria

Nuclear–mitochondrial sequence exchange

Huang et al. 2009


Genomic gigantism in plant mitochondria

The cucumber mitochondrial and nuclear genomes

share a lot of DNA

33% of the mitochondrial genome

Alverson et al. 2011. Plant Cell.


Genomic gigantism in plant mitochondria

The cucumber mitochondrial and nuclear genomes

share a lot of DNA

33% of the mitochondrial genome

Alverson et al. 2011. Plant Cell.


Genomic gigantism in plant mitochondria

Outline

  • Mitochondrial genome size evolution

    • Cucurbitaceae

    • Silene

Horizontal gene transfer (HGT) in the mitochondrial genome of Amborella


Genomic gigantism in plant mitochondria

Dan Sloan

Doug Taylor

University of Virginia

Mitochondrial genome evolution in Silene


Genomic gigantism in plant mitochondria

Mitochondrial mutation rate variation in Silene


Genomic gigantism in plant mitochondria

Mutation rate and mitochondrial genome size

?

?

?

?

16 kb


Genomic gigantism in plant mitochondria

Mutation rate and mitochondrial genome size

?

?

253 kb

426 kb

16 kb


Genomic gigantism in plant mitochondria

Mutation rate and mitochondrial genome size

253 kb

426 kb

16 kb

6,728 kb

11,318 kb


Genomic gigantism in plant mitochondria

Large multi-chromosomal mitochondrial genomes

Silene noctiflora (6.7 Mb)

  • 59 chromosomes

  • 66–192 kb in length


Genomic gigantism in plant mitochondria

Genome size summary and conclusions

  • Unprecedented size and structural variation in plant mitochondrial genomes


Genomic gigantism in plant mitochondria

Genome size summary and conclusions

  • Unprecedented size and structural variation in plant mitochondrial genomes

  • Theory: Low mutation rate

Larger genome size


Genomic gigantism in plant mitochondria

Genome size summary and conclusions

  • Unprecedented size and structural variation in plant mitochondrial genomes

  • Theory: Low mutation rate

Larger genome size

  • Cucurbitaceae and Silene show the opposite pattern


Genomic gigantism in plant mitochondria

Genome size summary and conclusions

  • Unprecedented size and structural variation in plant mitochondrial genomes

  • Theory: Low mutation rate

Larger genome size

  • Cucurbitaceae and Silene show the opposite pattern

  • What drives genome size evolution in plant mitochondria?

    • mutation rate? Not likely.

    • intramolecular recombination? Maybe.


Genomic gigantism in plant mitochondria

Genome size summary and conclusions

  • Unprecedented size and structural variation in plant mitochondrial genomes

  • Theory: Low mutation rate

Larger genome size

  • Cucurbitaceae and Silene show the opposite pattern

  • What drives genome size evolution in plant mitochondria?

    • mutation rate? Not likely.

    • intramolecular recombination? Maybe.

  • Much of the "extra" intergenic DNA may derive from the chloroplast and the nuclear genomes


Genomic gigantism in plant mitochondria

Outline

  • Mitochondrial genome size evolution

    • Cucurbitaceae

    • Silene

Horizontal gene transfer (HGT) in the mitochondrial genome of Amborella


Genomic gigantism in plant mitochondria

The Amborella mitochondrial genome: another monster!

Arabidopsis

Amborella

total size = 3.9 Mb


Genomic gigantism in plant mitochondria

Features in the Amborella mitochondrial genome

Native mito


Genomic gigantism in plant mitochondria

Features in the Amborella mitochondrial genome

Native mito

chloroplast-derived


Genomic gigantism in plant mitochondria

Features in the Amborella mitochondrial genome

Native mito

chloroplast-derived

Foreign angiosperm mito


Genomic gigantism in plant mitochondria

Features in the Amborella mitochondrial genome

Native mito

chloroplast-derived

Foreign angiosperm mito

Foreign moss mito


Genomic gigantism in plant mitochondria

Features in the Amborella mitochondrial genome

Native mito

chloroplast-derived

Foreign angiosperm mito

Foreign moss mito

Foreign green algal mito


Genomic gigantism in plant mitochondria

Features in the Amborella mitochondrial genome

Native mito


Genomic gigantism in plant mitochondria

Features in the Amborella mitochondrial genome

Native mito

Native chloroplast

Foreign angiosperm mito

Foreign moss mito

Foreign green algal mito


Genomic gigantism in plant mitochondria

cob

Amborella

other angiosperms

mosses

green algae

N


Genomic gigantism in plant mitochondria

Other genes show the same pattern as cob

Amborella

other angiosperms

mosses

N

green algae

N

N

N = native


Genomic gigantism in plant mitochondria

What's going on here?


Genomic gigantism in plant mitochondria

Insights into the mechanism of horizontal transfer

What the Amborella mitochondrial genome has:

What the Amborella mitochondrial genome lacks:


Genomic gigantism in plant mitochondria

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:


Genomic gigantism in plant mitochondria

Insights into the mechanism of horizontal transfer

What the Amborella mitochondrial genome has:

  • foreign nuclear DNA

  • bacterial DNA

  • fungal DNA

  • mitochondrial DNA from non-"green plants"

  • entire foreign mitochondrial genomes

  • donors are all "green plants"

What the Amborella mitochondrial genome lacks:


Genomic gigantism in plant mitochondria

Mitochondrial fission/fusion arose twice during eukaryotic evolution

The machines that divide and fuse mitochondria. 2007. Ann. Rev. Biochem. 76:751-780.


Genomic gigantism in plant mitochondria

How do foreign mitochondria get into Amborella?


Genomic gigantism in plant mitochondria

Amborella is endemic to New Caledonia


Genomic gigantism in plant mitochondria

How does Amborella acquire foreign mitochondria?

  • direct, plant-to-plant contact?

    • parasitic angiosperms

    • epiphytic plants & algae


Genomic gigantism in plant mitochondria

How does Amborella acquire foreign mitochondria?

  • direct, plant-to-plant contact?

    • parasitic angiosperms

    • epiphytic plants & algae


Genomic gigantism in plant mitochondria

cob

Donors are probably lichen-forming

green algae


Genomic gigantism in plant mitochondria

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


Genomic gigantism in plant mitochondria

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


Genomic gigantism in plant mitochondria

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


Genomic gigantism in plant mitochondria

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

  • the mechanism of HGT

    • introduction of foreign (but "green") mitochondria

    • fusion between native and foreign mitochondria


Genomic gigantism in plant mitochondria

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

  • the mechanism of HGT

    • introduction of foreign (but "green") mitochondria

    • fusion between native and foreign mitochondria

  • Are there more Amborella's out there? Almost certainly.


Genomic gigantism in plant mitochondria

Dan Sloan

(Virginia/Yale)

Doug Taylor

(Virginia)

Jeff Palmer

(Indiana)

Danny Rice

(Indiana)

Acknowledgements

  • Funding

  • NIH Ruth L. Kirschstein postdoctoral fellowship (Alverson)

  • NIH Research grant (Palmer)


  • Login