Phylogenomic Revisit for Green Contribution to Diatoms
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The Molecular Life of Diatoms June 28, 2013 Collège de France Paris, France http://events.embo.org/13-diatom/
![Eukaryotic Tree of Life [eTOL] “Supergroups”
[e.g., diatoms and dinoflagellates]
Reyes-Prieto et al., Annu. Rev. Genet. 2007. 41:147–68](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)
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Phylogenomic Revisit for Green Contribution to Diatoms
- 1. Phylogenomic Revisit for Green Contribution to Diatoms Ahmed Moustafa1, Klaus Valentin2, Debashish Bhaacharya3 June 28, 2013 The Molecular Life of Diatoms image credit: Atsuko Tanaka, Christian Sardet, Sebastien Colin, and Diana Sarno! 1American University in Cairo, Egypt 2Alfred Wegener Institute, Germany 3Rutgers University, USA
- 2. Eukaryotic Tree of Life [eTOL] “Supergroups” [e.g., diatoms and dinoflagellates] Reyes-Prieto et al., Annu. Rev. Genet. 2007. 41:147–68
- 3. Prochlorococcus Origin of Photosynthesis & Endosymbiosis ArabidopsisChlamydomonas Cyanidioschyzon Emiliania Karenia Cyanophora “Chromalveolate hypothesis” Cavalier-Smith 1999 images: micro*scope (http://microscope.mbl.edu)!
- 4. chimeric carotenoid pathway in diatoms 70% red and 30% green! Frommolt et al. Mol Biol Evol. 2008 Dec;25(12):2653-67.
- 5. Why do we see green genes in diatoms? Horizontal Gene Transfer (HGT) Endosymbiotic Gene Transfer (EGT) “Chromalveolate hypothesis” ??? Phaeodactylum http://genome.jgi-‐psf.org Thalassiosira http://www.awi.de Non-vertical gene transfer
- 6. Reyes-Prieto et al. Annu. Rev. Genet. 2007. 41:147–68 Detection of Non-vertical (H/EGT) Gene Transfer Ho: Gene tree = Species (host) tree HA: Gene tree ≠ Species (host) tree
- 7. Moustafa, Bhattacharya, Allen. CIBEC 103,107, Dec. 2010. Organisms Genes Nuclear + bacterial 3,744 5,544,637 Mitochondrial 1,611 23,228 Plastid 142 14,179 (Database: RefSeq + JGI + dbEST) iTree – Phylogenomic Pipeline http://itree.sourceforge.net
- 8. ¡ Search by topology and bootstrap! ¡ Search for mandatory and optional clades, all possible scenarios:! Moustafa and Bhattacharya. BMC Evol Biol. 2008 Jan 15;8:6. PhyloSort – Sorting Phylogenetic Trees € n n C + n−1 n C + ...+ 1 n C = r n Cr=1 n ∑ • Migration! • New features!
- 9. Phaeodactylum nuclear-encoded proteome (~ 10.5k) Thalassiosira nuclear-encoded proteome (~ 11.5k) Step 1: phylogenomic screening Topological (red + green + diatoms + chromalveolates) BLAST (e-value < 1E-5) à MAFFT à RAxML à PhyloSort 3,468 candidates 3,696 candidates Step 2: phylogenomic screening Topological (as in Step 1) + Statistical (score ≥ 75%) Alignments (from Step 1) à PhyML à PhyloSort 2,423 genes of potential red or green algal origin 2,533 genes of potential red or green algal origin
- 10. 22% of the diatom nuclear gnome of red or green algal origin
- 11. 0 500 1000 1500 2000 2500 3000 Phaeodactylum Thalassiosira Gene families Viridiplantae Rhodophyta Unresolved Contribution of Red and Green to Diatoms Moustafa et al., Science. 2009 450 red : 1800 green à 17% of the diatom genome is green
- 12. Diatom Green Genes in the Green Lineages Ostreococcus Hervé Moreau ~7,000 genes Chlamydomonas Linda Amaral-Zettler ~15,000 genes Prasinophytes Core Chlorophytes ¡ 75%: shared with prasinophytes ¡ 40%: prasinophytes are the closest green neighbor ¡ 25%: exclusively shared with prasinophytes
- 13. Plastids in Chromalveolates Classic Hypothesis
- 14. Plastids in Chromalveolates Proposed model
- 16. Lineage! Organism! Proteins!Dataset source! Bangiophyceae! Cyanidioschyzon merolae! 5,085! Genomic! Bangiophyceae! Galdieria sulphuraria! 6,796! Genomic! Bangiophyceae! Porphyra purpurea! 223,550!Transcriptomic! Bangiophyceae! Porphyra umbilicalis! 123,661!Transcriptomic! Bangiophyceae! Porphyridium purpureum! 23,277!Transcriptomic! Compsopogonophyceae!Boldia erythrosiphon! 80,535!Transcriptomic! Compsopogonophyceae!Rhodochaete parvula! 58,506!Transcriptomic! Florideophyceae! Calliarthron tuberculosum! 23,365!Transcriptomic! Florideophyceae! Chondrus crispus! 9,671! Genomic! Lineage! Organism! Proteins! Dataset type! Chlorophyceae! Chlamydomonas reinhardtii! 14,332! Genomic! Chlorophyceae! Volvox carteri! 14,328! Genomic! Embryophyta! Arabidopsis thaliana! 32,779! Genomic! Embryophyta! Brachypodium distachyon! 24,100! Genomic! Embryophyta! Medicago truncatula! 44,823! Genomic! Embryophyta! Oryza sativa! 28,418! Genomic! Embryophyta! Physcomitrella patens! 35,544! Genomic! Embryophyta! Ricinus communis! 31,214! Genomic! Embryophyta! Selaginella moellendorffii! 33,146! Genomic! Embryophyta! Vitis vinifera! 23,349! Genomic! Embryophyta! Zea mays! 22,230! Genomic! Mamiellophyceae! Micromonas pusilla! 10,244! Genomic! Mamiellophyceae! Micromonas sp! 10,113! Genomic! Mamiellophyceae! Ostreococcus lucimarinus! 7,403! Genomic! Mamiellophyceae! Ostreococcus sp! 7,492! Genomic! Mamiellophyceae! Ostreococcus tauri! 7,965! Genomic! Trebouxiophyceae! Chlorella variabilis! 9,829! Genomic! Trebouxiophyceae! Coccomyxa subellipsoidea! 19,425! Genomic! Lineage! Organism! Proteins! Dataset type! Bangiophyceae! Cyanidioschyzon merolae! 5,085! Genomic!2009! 2013! +8 red data! sets!
- 17. Phylogenomics of diatoms versus ToL vertical transfer within the SAR clade? !
- 18. Red and green affiliations in diatoms
- 19. Red and green affiliations in chromalveolates ¡ In the different chromalveolate lineages, the ratio ≈ 2 reds : 3 greens! ¡ The major green neighbor lineage is the prasinophytes! ¡ Distribution of red and green genes is similar across chromalveolates with red or green plastids.! > 10 genomes à ≈ 100k proteins à phylogenomics à ≈ 100k ML trees -‐ve +ve
- 20. S A H C SA SH SC AH AC HC SAH SAC SHC AHC SAHC 0 250 500 750 1000 Clades Phylogenetic Affiliation Rhodophyta Viridiplantae Lineages S: Stramenopiles A: Alveolates H: Haptophytes C: Cryptophytes Shared protein families Shared and lineage-specific red and green genes 297 70 249 434 218 232 24 50 954 289 170 326 97 142 344 S A H C 94 20 129 242 175 111 6 19 595 147 65 145 27 74 222 S A H C S: Stramenopiles A: Alveolates H: Haptophytes C: Cryptophytes p-value << 0.001
- 21. Phylogenetic placement on a reference tree Phytoene dehydrogenase! The four diatoms!
- 22. Plastids in Chromalveolates Proposed model Loss of red plastid! Geoff McFadden! Chlorarachniophytes! (e.g., Bigelowiella)!
- 23. ¡ If the shared red genes transferred through endosymbiosis then why not the more abundant green genes? ! ¡ There is no compelling reason to reject the hypothesis of cryptic green plastid in the ancestor of the chromalveolates.! ¡ These two endosymbioses (red and green) supplied the chromalveolates with the genetic potential to become the most successful marine primary producers and protist supergroup on our planet.! ¡ Next: are there outstanding metabolic trends in terms of the red and green composition? Exclusively red or green pathways? Chimeric pathways?! Summary 94 20 129 242 175 111 6 19 595 147 65 145 27 74 222 S A H C 297 70 249 434 218 232 24 50 954 289 170 326 97 142 344 S A H C background image: http://deepbluehome.blogspot.com/2011/01/psychedelic-diatoms.html!