phylogenomic revisit for green contribution to diatoms

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

Eukaryotic Tree of Life [eTOL] “Supergroups”

[e.g., diatoms and dinoflagellates]

Reyes-Prieto et al., Annu. Rev. Genet. 2007. 41:147–68

Prochlorococcus

Origin of Photosynthesis & Endosymbiosis

Arabidopsis Chlamydomonas

Cyanidioschyzon  

Emiliania Karenia

Cyanophora

“Chromalveolate hypothesis” Cavalier-Smith 1999

images: micro*scope (http://microscope.mbl.edu)!

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 hypothesis” ???

Phaeodactylum http://genome.jgi-­‐psf.org  

Thalassiosira http://www.awi.de  

Non-vertical gene transfer

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

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

¡  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 – Mining Phylogenetic Trees

€

nnC + n−1

nC + ...+ 1nC = r

nCr=1

n∑

•  Migration!•  Bug fixes!•  New features!

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

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 of Red and Green to Diatoms

Moustafa et al., Science. 2009

450 red : 1800 green à 17% of the diatom genome is green

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

Plastids in Chromalveolates

Classic Hypothesis

Plastids in Chromalveolates

Proposed model

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!

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!Baniophyceae! 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!

2013!

+8 red data!sets!

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!

¡  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  

S

A

H

C

SA

SH

SC

AH

AC

HC

SAH

SAC

SHC

AHC

SAHC

0

25

0

50

0

75

0

10

00

Cla

de

s

Phylogenetic AffiliationRhodophyta

Viridiplantae

LineagesS: 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

289170 326

97

142

344

S A

H C

94

20

129

242

175

111

6

19

595

14765 145

27

74

222

S A

H C

S: Stramenopiles A: Alveolates H: Haptophytes C: Cryptophytes

p-value << 0.001

Phylogenetic placement on a reference tree Phytoene dehydrogenase!

The four diatoms!

Plastids in Chromalveolates

Proposed model

Loss of red plastid!

¡ 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

14765 145

27

74

222

S A

H C

297

70

249

434

218

232

24

50

954

289170 326

97

142

344

S A

H C

background image: http://deepbluehome.blogspot.com/2011/01/psychedelic-diatoms.html!