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The Origin of Chloroplasts
Comparative Analysis of the
Genomes of Cyanobacteria
and Plants
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1883 – Schimper – Independent binary fission of chloroplasts,
and a resemblance of chloroplasts to cyanobacteria
Naoki Sato
Presented by Ken Ober
Akin to Kin?
The Origin of Chloroplasts
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1883 – Schimper – Independent binary fission of chloroplasts,
and a resemblance of chloroplasts to cyanobacteria
1905 - Mereschkowsky – Endosymbiosis
http://www.bio.mtu.edu/~jkoyadom/algae_webpage/charophyceans/Spirogyra_jason4_chassel2_20125.jpg
http://tolweb.org/tree/eubacteria/cyanobacteria/prochloron.200.jpeg
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The Proposed Story
The Origin of Chloroplasts
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www.lifesci.utexas.edu/faculty/sjasper/images/john4.16.jpg
http://www.biol.tsukuba.ac.jp/~inouye/ino/gl/Cyanophora.GIF
The Origin of Chloroplasts
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1883 – Schimper – Independent binary fission of chloroplasts,
and a resemblance of chloroplasts to cyanobacteria
1905 - Mereschkowsky – Endosymbiosis
1924 - Korshikov - Cyanophora paradoxa fossil described –
transition organism
1959 - Stocking and Gifford - Independent DNA in chloroplasts
1883 – Schimper – Independent binary fission of chloroplasts,
and a resemblance of chloroplasts to cyanobacteria
1905 - Mereschkowsky – Endosymbiosis
1924 - Korshikov - Cyanophora paradoxa fossil described –
transition organism
The Origin of Chloroplasts
n
n
n
n
n
1883 – Schimper – Independent binary fission of chloroplasts,
and a resemblance of chloroplasts to cyanobacteria
1905 - Mereschkowsky – Endosymbiosis
1924 - Korshikov - Cyanophora paradoxa fossil described –
transition organism
1959 - Stocking and Gifford - Independent DNA in chloroplasts
1970 – Margulis – Endosymbiosis PR
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The Origin of Chloroplasts
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1883 – Schimper – Independent binary fission of chloroplasts,
and a resemblance of chloroplasts to cyanobacteria
1905 - Mereschkowsky – Endosymbiosis
1924 - Korshikov - Cyanophora paradoxa fossil described –
transition organism
1959 - Stocking and Gifford - Independent DNA in chloroplasts
1970 – Margulis – Endosymbiosis PR
1972 - Pigott and Carr - Quantitative relatedness study of
Euglena chloroplast DNA and cyanobacterial DNA.
The Origin of Chloroplasts
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The Origin of Chloroplasts
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1883 – Schimper – Independent binary fission of chloroplasts,
and a resemblance of chloroplasts to cyanobacteria
1905 - Mereschkowsky – Endosymbiosis
1924 - Korshikov - Cyanophora paradoxa fossil described –
transition organism
1959 - Stocking and Gifford - Independent DNA in chloroplasts
1970 – Margulis – Endosymbiosis PR
1972 - Pigott and Carr - Quantitative relatedness study of
Euglena chloroplast DNA and cyanobacterial DNA.
1978 - Schwartz and Dayhoff – Protein and RNA or DNA
sequencing suggests chloroplasts are reduced forms of
cyanobacteria
1993 - Hallick et al., Reith and Munholland - Entire chloroplast
sequences for Euglena and Porphyra; similarity in organization of
genes in operons
1883 – Schimper – Independent binary fission of chloroplasts,
and a resemblance of chloroplasts to cyanobacteria
1905 - Mereschkowsky – Endosymbiosis
1924 - Korshikov - Cyanophora paradoxa fossil described –
transition organism
1959 - Stocking and Gifford - Independent DNA in chloroplasts
1970 – Margulis – Endosymbiosis PR
1972 - Pigott and Carr - Quantitative relatedness study of
Euglena chloroplast DNA and cyanobacterial DNA.
1978 - Schwartz and Dayhoff – Protein and RNA or DNA
sequencing suggests chloroplasts are reduced forms of
cyanobacteria
The Origin of Chloroplasts
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1883 – Schimper – Independent binary fission of chloroplasts,
and a resemblance of chloroplasts to cyanobacteria
1905 - Mereschkowsky – Endosymbiosis
1924 - Korshikov - Cyanophora paradoxa fossil described –
transition organism
1959 - Stocking and Gifford - Independent DNA in chloroplasts
1970 – Margulis – Endosymbiosis PR
1972 - Pigott and Carr - Quantitative relatedness study of
Euglena chloroplast DNA and cyanobacterial DNA.
1978 - Schwartz and Dayhoff – Protein and RNA or DNA
sequencing suggests chloroplasts are reduced forms of
cyanobacteria
1993 - Hallick et al., Reith and Munholland - Entire chloroplast
sequences for Euglena And Porphyra; similarity in organization of
genes in operons
2002 – Sato – Elucidation of homology in cyanobacteria and
plants, using complete genome/proteome sequences
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Doing It The “Sato” Way!
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The question: What novel information is
provided by a whole-genome/proteome
comparison of cyanobacteria and plants?
Experimental Design:
– Look for homology in three species of
cyanobacteria
– See how the homologies change by adding in
three more
– Then perform this analysis including a plant
species and negative control species
The Analysis
n Genome
Sequences
For Your Reference (and Mine)
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Cyanobacteria
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Sy = Synechocystis
An = Anabaena
Np = Nostoc
Pm1 = Prochlorococcus marinus MED4
Pm2 = P. marinus MIT9313
S81 = Synechococcus
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Plant
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Negative Controls
– Ath = Arabidopsis
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–
–
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Ec = Escherichia
Bs = Bacillus
Hp = Helicobacter
Sc = Saccharomyces
Draft Sequences
– Rp = Rhodopseudomonas
– Rs = Rhodobacter
The Results – Short Sequence
Features
– GC Skew (siseq)
– Palindromes (siseq)
– Rare Restriction Endonuclease Sites
– Dinucleotide Relative Abundance (dinucf)
§ Phylogenetic tree construction by taking the
mean of the differences of DRA’s (phylip)
n Proteome
sequences
– Homology Groups (blast)
§ Phylogenetic tree construction by the
Parsimony method (phylip)
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The Analysis
n Genome
Sequences
The Results – Dinucleotide
Relative Abundances
– GC Skew (siseq)
– Palindromes (siseq)
– Rare Restriction Endonuclease Sites
– Dinucleotide Relative Abundance (dinucf)
§ Phylogenetic tree construction by taking the
mean of the differences of DRA’s (phylip)
n Proteome
sequences
– Homology Groups (blast)
§ Phylogenetic tree construction by the
Parsimony method (phylip)
The Analysis
n Genome
The Results – Homology
Sequences
– GC Skew (siseq)
– Palindromes (siseq)
– Rare Restriction Endonuclease Sites
– Dinucleotide Relative Abundance (dinucf)
§ Phylogenetic tree construction by taking the
mean of the differences of DRA’s (phylip)
n Proteome
sequences
– Homology Groups (blast)
§ Phylogenetic tree construction by the
Parsimony method (phylip)
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The Results - Homology
The Analysis
n Genome
Sequences
– GC Skew (siseq)
– Palindromes (siseq)
– Rare Restriction Endonuclease Sites
– Dinucleotide Relative Abundance (dinucf)
§ Phylogenetic tree construction by taking the
mean of the differences of DRA’s (phylip)
n Proteome
sequences
– Homology Groups (blast)
§ Phylogenetic tree construction by the
Parsimony method (phylip)
How do these data answer
the original question?
The Results - Homology
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What novel information is provided by a
whole-genome/proteome comparison of
cyanobacteria and plants?
Higher confidence
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More detail
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– Bigger data sets
– Whole-sequence patterns vs. single
gene/protein patterns
– Life “core” (238 groups)
– Endosymbiosis “core” (80 groups)
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Acknowledgements
n Judith
Klein-Seetharaman
n Natalie & Scottie
¿Preguntas?
Biological Language Modeling
Cyanobacteria
Photosynthetic
Organism 1
Photosynthetic
Organism 2
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