1. Genomic gigantism in plant mitochondria Andy Alverson

2. Outline 1.Mitochondrial genome size evolution Cucurbitaceae Silene 2.Horizontal gene transfer (HGT) in the mitochondrial genome of Amborella

3. The three plant genomes

4. The disparate trajectories of organelle genomes

5. 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. Ward et al. 1981 Estimated mitochondrial genome sizes in Cucurbitaceae

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

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

11. 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

12. Do large genomes have lower mutation rates?

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

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

15. Large genomes integrate massive amounts of new sequence

16. Traffic patterns of plant DNA

18. Chloroplast sequences in the mitochondrial genome

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

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

28. Mitochondrial mutation rate variation in Silene

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

30. Mutation rate and mitochondrial genome size ?? 426 kb253 kb16 kb

31. Mutation rate and mitochondrial genome size 426 kb253 kb16 kb11,318 kb6,728 kb

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

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

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

35. 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

36. 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.

37. 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.

38. Outline 1.Mitochondrial genome size evolution Cucurbitaceae Silene 2.Horizontal gene transfer (HGT) in the mitochondrial genome of Amborella

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

40. Features in the Amborella mitochondrial genome Native mito

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

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

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

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

45. Features in the Amborella mitochondrial genome Native mito

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

47. cob N Amborella other angiosperms mosses green algae

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

49. What's going on here?

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

51. 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:

52. 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"

54. Mitochondrial fission/fusion arose twice during eukaryotic evolution The machines that divide and fuse mitochondria. 2007. Ann. Rev. Biochem. 76:751-780.

55. How do foreign mitochondria get into Amborella?

56. Amborella is endemic to New Caledonia

59. How does Amborella acquire foreign mitochondria? −direct, plant-to-plant contact? −parasitic angiosperms −epiphytic plants & algae

60. How does Amborella acquire foreign mitochondria? −direct, plant-to-plant contact? −parasitic angiosperms −epiphytic plants & algae

61. Donors are probably lichen-forming green algae cob

62. 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

63. 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

64. 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

65. 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

66. 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

67. 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)