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Genomic gigantism in plant mitochondria

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.

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Genomic gigantism in plant mitochondria

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  1. Genomic gigantism in plant mitochondria Andy Alverson

  2. Outline • Mitochondrial genome size evolution • Cucurbitaceae • Silene Horizontal gene transfer (HGT) in the mitochondrial genome of Amborella

  3. The three plant genomes

  4. The disparate trajectories of organelle genomes

  5. The disparate trajectories of organelle genomes 1kb = 1000 base pairs

  6. The disparate trajectories of organelle genomes 1kb = 1000 base pairs

  7. The disparate trajectories of organelle genomes Mutation pressure hypothesis (Lynch et al. 2006. Science) 1kb = 1000 base pairs

  8. Estimatedmitochondrial genome sizes in Cucurbitaceae Ward et al. 1981

  9. Estimatedmitochondrial genome sizes in Cucurbitaceae Prediction: Larger genomes have lower mutation rates Ward et al. 1981

  10. Actualmitochondrial genome sizes in Cucurbitaceae Alverson et al. 2010. Mol. Biol. Evol.

  11. 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

  12. Do large genomes have lower mutation rates?

  13. Do large genomes have lower mutation rates? (dS)

  14. Coding sequences in cucurbit mitochondrial genomes 17% 7% 19% 5% 4% Total coding:

  15. Large genomes integrate massive amounts of new sequence

  16. Traffic patterns of plant DNA

  17. Traffic patterns of plant DNA

  18. Chloroplast sequences in the mitochondrial genome

  19. Chloroplast-derived sequences turn over rapidly

  20. Chloroplast-derived sequences turn over rapidly

  21. Chloroplast-derived sequences turn over rapidly

  22. Traffic patterns of plant DNA

  23. Nuclear–mitochondrial sequence exchange Huang et al. 2009

  24. The cucumber mitochondrial and nuclear genomes share a lot of DNA 33% of the mitochondrial genome Alverson et al. 2011. Plant Cell.

  25. The cucumber mitochondrial and nuclear genomes share a lot of DNA 33% of the mitochondrial genome Alverson et al. 2011. Plant Cell.

  26. Outline • Mitochondrial genome size evolution • Cucurbitaceae • Silene Horizontal gene transfer (HGT) in the mitochondrial genome of Amborella

  27. Dan Sloan Doug Taylor University of Virginia Mitochondrial genome evolution in Silene

  28. Mitochondrial mutation rate variation in Silene

  29. Mutation rate and mitochondrial genome size ? ? ? ? 16 kb

  30. Mutation rate and mitochondrial genome size ? ? 253 kb 426 kb 16 kb

  31. Mutation rate and mitochondrial genome size 253 kb 426 kb 16 kb 6,728 kb 11,318 kb

  32. Large multi-chromosomal mitochondrial genomes Silene noctiflora (6.7 Mb) • 59 chromosomes • 66–192 kb in length

  33. Genome size summary and conclusions • Unprecedented size and structural variation in plant mitochondrial genomes

  34. Genome size summary and conclusions • Unprecedented size and structural variation in plant mitochondrial genomes • Theory: Low mutation rate Larger genome size

  35. 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

  36. 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.

  37. 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

  38. Outline • Mitochondrial genome size evolution • Cucurbitaceae • Silene Horizontal gene transfer (HGT) in the mitochondrial genome of Amborella

  39. The Amborella mitochondrial genome: another monster! Arabidopsis Amborella total size = 3.9 Mb

  40. Features in the Amborella mitochondrial genome Native mito

  41. Features in the Amborella mitochondrial genome Native mito chloroplast-derived

  42. Features in the Amborella mitochondrial genome Native mito chloroplast-derived Foreign angiosperm mito

  43. Features in the Amborella mitochondrial genome Native mito chloroplast-derived Foreign angiosperm mito Foreign moss mito

  44. Features in the Amborella mitochondrial genome Native mito chloroplast-derived Foreign angiosperm mito Foreign moss mito Foreign green algal mito

  45. Features in the Amborella mitochondrial genome Native mito

  46. Features in the Amborella mitochondrial genome Native mito Native chloroplast Foreign angiosperm mito Foreign moss mito Foreign green algal mito

  47. cob Amborella other angiosperms mosses green algae N

  48. Other genes show the same pattern as cob Amborella other angiosperms mosses N green algae N N N = native

  49. What's going on here?

  50. Insights into the mechanism of horizontal transfer What the Amborella mitochondrial genome has: What the Amborella mitochondrial genome lacks:

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