Retrotransposons in Diatoms: Assessing the Tempo of Evolution

1. Retrotransposons in Diatoms: Assessing the Tempo of Evolution Matthew Oliver1,2, Oscar Schofield1,2, Colomban de Vargas1, Paul Falkowski1,3, Zoe Finkel4, Dmitri Petrov5 1Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Sciences 2Coastal Ocean Observation Laboratory, Institute for Marine and Coastal Sciences, Rutgers University 3Department of Geological Sciences, Wright Geological Laboratory, Rutgers University 4Department of Biological Sciences, Mt. Allison University 5Department of Biological Sciences, Stanford University

2. Eukaryotic Genome Landscape Components of genome correlate with genome size. Adapted from Lynch and Conery (2000) Genome Size Log(Base Pairs) Genome Size Log(Base Pairs) Genome Size Log(Base Pairs)

3. Domain of Impossibility Prokaryotes Eukaryotes ? Known Landscape Left Wall of Complexity Unexplored Landscape ? Eukaryotic Genome Landscape

4. Mobile Elements Discovered by Barbara McClintock in Maize (1950) Challenged the idea that genomes were a static entity Major drivers of genome evolution Transposon Retrotransposon Eukaryotes only “RT” Domain “Cut and Paste” Kazazian Jr., 2004 Kazazian Jr., 2004

5. Diversity of Retrotransposons “RT” Domain Eickbush 1994

6. Evolution of Retrotransposons Boeke 2003 “RT” Appears to be ancient – probably in most lineages

7. Retrotransposition On Long Time Scales Petrov 2002 Walbot and Petrov 2001 Genome Size Control Punctuated Event on Long Time Scales

8. Retrotransposition On Short Time Scales Hirochika et al (1996) Stress induced events in Rice (Tos-17)

9. Domain of Impossibility Prokaryotes Eukaryotes ? Known Landscape Left Wall of Complexity Unexplored Landscape ? Eukaryotic Genome Landscape Genome size is a proxy for Intron and Mobile Element abundance

10. Hypothesis Larger genomes have more retrotransposons Retrotransposon activity contributes to genome size. Hypothesis: The tempo of genome size evolution is positively correlated with genome size. How do we tackle this problem?

11. Realized Rate of Evolution 18s sequence 1000 bootstrap ML tree

12. Genome size Genome size Genetic Distance Time Felsenstien 1985: Proposed method of overcoming non-independence of phenotypic characters Independent Contrasts: Garland 1992: Absolute value of contrast represents minimum amount of phenotypic evolution that has occurred. ~

13. Rate of Genome Size Evolution

14. Hypothesis Tested - Rate of genome size evolution is positively related to genome size. - Large genomes are unstable - Dinoflagellate genomes are the most unstable of these eukaryotes. - Combined effect of insertions and deletions - This rate incorporates effects of retrotransposon copy number as well as specific activity of retrotransposons.

15. Specific Rate of Genome Size Evolution Remove copy number effect by normalizing to genome size Diatoms have most active genomes per DNA quantity

16. Morphological ‘species’ diversity of major phytoplankton over geological time 100 300 500 50 100 150 50 100 150 200 0 20 Cenozoic 40 60 80 100 Mesozoic 120 140 160 180 200 220 My dinos coccos diatoms Bown et al. in press

17. Retrotransposons in Diatoms? Retrotransposons and Genome Size studied in narrow taxanomic ranges Baldauf (2003)

18. Domain of Impossibility Prokaryotes Eukaryotes ? Known Landscape Left Wall of Complexity Unexplored Landscape ? Diatom Genome Sequence ~3% Science, 2004 Mobile elements comprise approx 2% from sequence project Gypsy and Copia elements are very young and/or active (Kapitonov, 2003) Clues from the LTR regions which are “neutral”

19. Search for Retrotransposons in T. weissflogii Used PCR under different stringency to look for similar elements Gypsy 1 from T. pseudonana amplified in T. weissflogii ~600 bp Cloned Gypsy 1 from T. pseudonana and T. weissflogii to compare sequences from species that diverged 10’s of Ma Increasing TM Temperature Sequences were all within 90% similarity Sinninghe Damsté, Science (2004)

20. T. pseudonana (Gypsy 2) ** T. pseudonana (Gypsy 3) ** T. pseudonana 254 683 721 831 276 T. weissflogii 267 389 854 641 646 T. pseudonana (Gypsy 1)** 525 T. weissflogii 973 T. pseudonana 385 T. weissflogii 278 T. pseudonana 166 242 625 900 T. weissflogii 738 714 334 Nucleotide sequences do not group together 278 976 T. pseudonana 756 517

21. Deletion event

22. Conclusions - Large genomes are evolving rapidly - Dinoflagellate genome size evolves fastest - Diatom genome have the highest specific rate of genome size evolution suggesting retrotransposons are highly active - Retrotransposons appear to be active in at least two Diatom species.

23. Possible Directions C-value appears to be a predictor of retrotransposon content …..Correlations to cell size?? Log Cell Volume (mm3)

24. Acknowledgements David Ackerly (Cal Berkeley) Diana Nemergut (U. Colorado) Uwe Ligges (R-project.org) Josh Kohut (Rutgers) Charley Knight (Cal Poly) Mark Moline (Cal Poly)

25. T. pseudonana T. pseudonana T. weissflogii T. weissflogii T. weissflogii T. weissflogii T. weissflogii T. weissflogii T. weissflogii T. pseudonana (Gypsy 1)** T. weissflogii T. pseudonana T. pseudonana T. weissflogii T. pseudonana T. pseudonana T. weissflogii T. weissflogii T. weissflogii T. weissflogii T. weissflogii T. weissflogii T. pseudonana T. pseudonana T. pseudonana T. pseudonana 0.01