Genome duplications (polyploidy) / ancient genome duplications (paleopolyploidy)

How to detect paleoploidy?

For example: a diploid cell undergoes failed meiosis, producing diploid gametes, which self-fertilize to produce a tetraploid zygote. Timing of duplication by trees (phylogenetic timing) Phylogenetic timing of duplicates

b Paramecium genome duplications Comparison of two scaffolds originating from a common ancestor at the recent WGD Saccharomyces cerevisiae Just before genome duplication Just after genome duplication More time after genome duplication Unaligned view (removing gaps just like in cerev has occurred)

Saccharomyces cerevisiae Problem reciprocal gene loss (extreme case); how to solve? Problem reciprocal gene loss (extreme case); how to solve? Just before genome duplication

Outgroup! Just after genome duplication

Outgroup Just after genome duplication

Outgroup More time after genome duplication

Outgroup Problem (extreme case); how to solve?

Outgroup Outgroup Outgroup Outgroup Outgroup Using other genomes

Wong et al. 2002 PNAS Centromeres Vertebrate genome duplication Nature. 2011 Apr 10. [Epub ahead of print] Ancestral polyploidy in seed plants and angiosperms. Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, Leebens-Mack J, Depamphilis CW. Flowering plants

MOSS Vertebrates Teleosts

S. serevisiae and close relatives

Paramecium Reconstructed map of genome duplications allows unprecedented mapping of evolutionary history of genes in genomes Reconstructed map of genome duplications allows unprecedented mapping of evolutionary history of genes in genomes Major fate is gene loss In paramecium 3 or 4 genome duplications! Massive gene loss Correlation to (adaptive) radiation? Correlation to (adaptive) radiation? Explanations for adaptive radiation? Incompatibility at essential loci Plants Explanations for adaptive radiation? Regulatory innovations Berend, kun je dit paper toevoegen aan de literatuur voor morgen? Het is bedoeld voor de "attackers". Ik zou graag zien dat ze dit eerst bespreken, met name de sequentie analyse resultaten, en dat dan de mensen die aangewezen zijn als "defenders" het andere manuscript bespreken en dan daaruit het eerste artikel "attacken" kan dat nog?

(anders is er zo weinig discussie)

Human-specific gain of function in a developmental enhancer. Prabhakar S, Visel A, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Morrison H, Fitzpatrick DR, Afzal V, Pennacchio LA, Rubin EM, Noonan JP. Science. 2008 Sep 5;321(5894):1346-50. Participants Monday Tuesday Wednesday Thursday Friday

Critique/Defen Critique/Defen Critique/Def Critique/Defend Critique/Defend d d end Sepideh Babaei C D D C D Joachim Bargsten C C D D D Punto Bawono C D C C D Bastiaan Berg, van den C C C D D

Erik Bergh, van den C D D C D Corina Ceapa C C D D D Pieter Coussement C D C D D

Hanneke Deutekom, van C C C D D Aline Dousse C D D C D Koen Illeghems C C D C D

Arun Kommadath D D C C C

Aleksandra Kos D C C D C

Wouter Meuleman D D D C C Umesh Nandal D C D D C Ingrid Paffen D D C C C Raquel Quintilla Mateo D C C D C Elke Schaper D D D C C Wim Spee D C D D C Priscilla Zwartjens D D C C C Saulo Aflitos D C C D C

ToL

Proc Natl Acad Sci U S A. 2008 Dec here 23;105(51):20356-61. Epub 2008 Dec 10. The archaebacterial origin of eukaryotes. Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. here here Mol Biol Evol. 2005 Nov;22(11):2142- 6. The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic. Huang J, Xu Y, Gogarten JP. Mitochondria diseases functions Calcium signaling Coenzyme synthesis Parkinson Citric acid cycle Leigh syndrome

Heme synthesis Urea cycle

Friederich’s ataxia Myopathies

FeS clusters Apoptosis Electrical signaling

Alzheimer ATP production Leber’s syndrome Fatty acids oxidation Heat generation What does a mitochondrion look like? “double membrane”

Cartoon of membrane topology

http://en.wikipedia.org/wiki/Mitochondrion Present day eukaryotes often “eat” bacteria by phagocytosis

schematic

picture

http://en.wikipedia.org/wiki/Phagocytosis http://academic.brooklyn.cuny.edu/biology/bio4fv/page/phago.htm Similarity in membrane “topology” between a mitochondria and a eukaryotic cell that eats a bacterium: the double membrane topology

http://en.wikipedia.org/wiki/Phagocytosis DNA

Mitchondria have their own chromosome … but this chromosome is circular and not enveloped in a “nucleus”

prokaryotes eukaryotes Circular chromosomes, Linear chromosomes no organelles organelles

http://home.nc.rr.com/ambiient/site/mtdna.htm Phylogenetic tree of mito rRNA + bact rRNA

•Mitochondrial chromosome, genes, rRNA

•Tree: eukaryotic mitochondria cluster within bacteria, within alpha -proteobacteria, next to rickettsia Rickettsia obligate intracellular parasites of eukaryotic cells

Picture of alife richetssia

http://www.textbookofbacteriology.net/Rickettsia.html Endosymbiotic origin of mitochondria

•Double Membrane •ciricular, non organaller enveloped chromosome •mitochondrial rRNA descendant from alpha proteo bacteria

Free-living, alpha-proteobacterial ancestor

? Rickettsia

Mitochondria Endosymbiotic origin of mitochondria

• What was the lifestyle of this mitochondrial ancestor? • How many genes did it import into the eukaryote?(present day animal mitochondrial genomes contain only 13 protein coding genes) • What was the original reason for this symbiosis? • What happened to the influx of all these genes? Free-living, alpha-proteobacterial ancestor

Gene transfer of genes from mitochondrial genome to nuclear Rickettsia genome

Mitochondria Detecting eukaryotic genes of alpha-proteobacterial ancestry GENOME alpha-proteobacteria ( alpha-proteobacteria GENOMES Eukaryotes Bacteria+Archaea SELECTION OF HOMOLOGS LIST

ALIGNMENTS AND TREE TREE “phylome” SCANNING

PHYLOME Identifying eukaryotic proteins with an alpha- proteobacterial origin based on their phylogeny

Eukaryotic + alpha-proteobacteria Alpha-proteobacterial proteins with in the same branch the rest of the bacteria and archaea Benchmarking?

1. “a control” 2. ML works! Reconstruction of the Proto-mitochondrial Cell The majority of the proto-mitochondrial proteome is not mitochondrial (anymore) 566 Gabaldon & Huynen Yeast mitochondrial proteome: Science 2003 alpha-prot. Eric Schon, Methods Cell Biol 2001 (manually curated) 35 303 59 293 10

Huh et al., Nature 2003 (green fluorescent genomics) 527

Human mitochondrial proteome: 755

Eric Schon, 113 508 Methods Cell Biol 2001 From endosymbiont to organell, not only loss and gain of proteins but also “retargeting”:

proteins loss re-targeting ~65% of the alpha- proteobacteria derived set is not mitochondrial. Ancestor Modern mitochondria

~16% of the mitochondrial yeast proteins are of alpha- gain proteobacterial origin.

t

Gabaldon and Huynen, Science 2004 ToL

Proc Natl Acad Sci U S A. 2008 Dec here 23;105(51):20356-61. Epub 2008 Dec 10. The archaebacterial origin of eukaryotes. Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. here here Mol Biol Evol. 2005 Nov;22(11):2142- 6. The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic. Huang J, Xu Y, Gogarten JP. Interpreting the tree: Horizontal Gene Transfer ( HGT )

Bacteria

Eukarya Archaea