The Molecular Life of Diatoms June 28, 2013 Collège de France Paris, France http://events.embo.org/13-diatom/

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. 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!