Phylogenomic Revisit for Green
Contribution to Diatoms
Ahmed Moustafa1, Klaus Valentin2, Debashish Bhaacharya3
June 28, 2...
Eukaryotic Tree of Life [eTOL] “Supergroups”
[e.g., diatoms and dinoflagellates]
Reyes-Prieto et al., Annu. Rev. Genet. 20...
Prochlorococcus
Origin of Photosynthesis & Endosymbiosis
ArabidopsisChlamydomonas
Cyanidioschyzon	
  
Emiliania Karenia
Cy...
chimeric carotenoid pathway in diatoms
70% red and 30% green!
Frommolt et al. Mol Biol Evol. 2008 Dec;25(12):2653-67.
Why do we see green genes in diatoms?
Horizontal
Gene Transfer
(HGT)
Endosymbiotic
Gene Transfer
(EGT)
“Chromalveolate hyp...
Reyes-Prieto et al.
Annu. Rev. Genet.
2007. 41:147–68
Detection of Non-vertical (H/EGT) Gene Transfer
Ho: Gene tree = Spec...
Moustafa, Bhattacharya, Allen. CIBEC 103,107, Dec. 2010.
Organisms Genes
Nuclear + bacterial 3,744 5,544,637
Mitochondrial...
¡  Search by topology and bootstrap!
¡  Search for mandatory and optional clades,
all possible scenarios:!
Moustafa and ...
Phaeodactylum
nuclear-encoded
proteome (~ 10.5k)
Thalassiosira
nuclear-encoded
proteome (~ 11.5k)
Step 1: phylogenomic scr...
22% of the diatom
nuclear gnome of
red or green algal
origin
0
500
1000
1500
2000
2500
3000
Phaeodactylum Thalassiosira Gene families
Viridiplantae
Rhodophyta
Unresolved
Contribution ...
Diatom Green Genes in the Green Lineages
Ostreococcus
Hervé Moreau
~7,000 genes
Chlamydomonas
Linda Amaral-Zettler
~15,000...
Plastids in Chromalveolates
Classic Hypothesis
Plastids in Chromalveolates
Proposed model
Lineage! Organism! Proteins!Dataset source!
Bangiophyceae! Cyanidioschyzon merolae! 5,085! Genomic!
Bangiophyceae! Galdier...
Phylogenomics
of diatoms
versus ToL
vertical transfer within the SAR clade? !
Red and green
affiliations in
diatoms
Red and green affiliations in chromalveolates
¡ In the different
chromalveolate
lineages, the ratio ≈
2 reds : 3 greens!
...
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...
Phylogenetic placement
on a reference tree
Phytoene dehydrogenase!
The four diatoms!
Plastids in Chromalveolates
Proposed model
Loss of red plastid!
Geoff McFadden!
Chlorarachniophytes!
(e.g., Bigelowiella)!
¡ If the shared red genes transferred through
endosymbiosis then why not the more abundant
green genes? !
¡ There is no ...
Phylogenomic Revisit for Green Contribution to Diatoms
Phylogenomic Revisit for Green Contribution to Diatoms
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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/

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Phylogenomic Revisit for Green Contribution to Diatoms

  1. 1. Phylogenomic Revisit for Green Contribution to Diatoms Ahmed Moustafa1, Klaus Valentin2, Debashish Bhaacharya3 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. 2. Eukaryotic Tree of Life [eTOL] “Supergroups” [e.g., diatoms and dinoflagellates] Reyes-Prieto et al., Annu. Rev. Genet. 2007. 41:147–68
  3. 3. Prochlorococcus Origin of Photosynthesis & Endosymbiosis ArabidopsisChlamydomonas Cyanidioschyzon   Emiliania Karenia Cyanophora “Chromalveolate hypothesis” Cavalier-Smith 1999 images: micro*scope (http://microscope.mbl.edu)!
  4. 4. chimeric carotenoid pathway in diatoms 70% red and 30% green! Frommolt et al. Mol Biol Evol. 2008 Dec;25(12):2653-67.
  5. 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. 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. 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. 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. 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. 10. 22% of the diatom nuclear gnome of red or green algal origin
  11. 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. 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. 13. Plastids in Chromalveolates Classic Hypothesis
  14. 14. Plastids in Chromalveolates Proposed model
  15. 15. 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!
  16. 16. Phylogenomics of diatoms versus ToL vertical transfer within the SAR clade? !
  17. 17. Red and green affiliations in diatoms
  18. 18. 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  
  19. 19. 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
  20. 20. Phylogenetic placement on a reference tree Phytoene dehydrogenase! The four diatoms!
  21. 21. Plastids in Chromalveolates Proposed model Loss of red plastid! Geoff McFadden! Chlorarachniophytes! (e.g., Bigelowiella)!
  22. 22. ¡ 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!

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