Predicting ancestral syntenies
Eric Tannier, INRIA, University of Lyon
joint work with
Cedric Chauve, Simon Fraser University, VancouverFrédéric Boyer, CEA Grenoble, France
MarieFrance Sagot, INRIA, University of Lyon
Paleogenomics in vertebrates, or the recovery of lost genomes from the mist of times.M. Muffato and H. R. Crollius. BioEssays, 30:122–134, 2008.
Ancestral Animal Genome ReconstructionsV. L. Rascol, P. Pontarotti, and A. Levasseur.Current Opinions in Immunology, 19:542–546, 2008.
Addressing chromosome evolution in the wholegenome sequence era. T. Faraut. Chromosome Research, 16:5–16, 2008.
Paleogenomics
Paleogenomics in vertebrates, or the recovery of lost genomes from the mist of times.M. Muffato and H. R. Crollius. BioEssays, 2008
Local and global methods
10a
10b
10a
10b
10a10b3c
2a
5b
6c
6c 5b
3c
2a
6c
5b
3c
2a
Explain the difference between extantspecies using a minimum number of
evolutionary events
Dog Chimp Mouse
10a
10b
10a
10b
10a10b3c
2a
5b
6c
6c 5b
3c
2a
6c
5b
2a
Dog Chimp Mouse
If some chromosome segments are cont-iguous in several extant species, then
they are probably contiguous intheir common ancestor
3c
Local and global methods
10a
10b
10a
10b
10a10b3c
2a
5b
6c
6c 5b
3c
2a
6c
5b
3c
2a
10a
10b
6c
5b
3c
2a
10a
10b
6c
5b
3c
2a
Explain the difference between extantspecies using a minimum number of
evolutionary events
Dog Chimp Mouse
10a
10b
10a
10b
10a10b3c
2a
5b
6c
6c 5b
3c
2a
6c
5b
2a
Dog Chimp Mouse
If some chromosome segments are cont-iguous in several extant species, then
they are probably contiguous intheir common ancestor
10b
10a 5b
2a
6c
3c
3c
Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?Froenicke, Garcia Caldes, Graphodatsky, Muller, Lyons, Robinson, Volleth, Yang, WienbergGenome Research, mars 2006.
The convergence of cytogenetics and rearrangementbased models for ancestral genome reconstructionBourque, Pevzner, TeslerGenome Research, mars 2006.
Ancestral genomes reconstruction: An integrated, multidisciplinary approachis neededRocchi, Archidiacono, StanyonGenome Research, décembre 2006.
Two different reconstructions ofthe same ancestral genome (boreoeutherian)
Bourque et al, Genome Research, 2006.
A general framework for local methods
Physical mapping technique
Probes
DNA segment
probes
segments
1 0
Physical mapping technique
probes
segments
Physical mapping technique
A B C D E F G H I
1 1 1 0 0 0 1 1 0
1 1 1 1 0 0 0 0 0
0 0 0 1 0 1 0 0 0
0 1 1 0 0 0 0 0 0
0 0 0 0 1 0 0 0 1
probes
segments
Physical mapping technique
G H A B C D E F I
1 1 1 1 1 0 0 0 0
0 0 1 1 1 1 0 0 0
0 0 0 0 0 1 0 1 0
0 0 0 1 1 0 0 0 0
0 0 0 0 0 0 1 0 1
probes
segments
Physical mapping technique
G H A B C D F E I
1 1 1 1 1 0 0 0 0
0 0 1 1 1 1 0 0 0
0 0 0 0 0 1 1 0 0
0 0 0 1 1 0 0 0 0
0 0 0 0 0 0 0 1 1
Linear time Method: McConnell, SODA, 2005
All solutions can be represented in a compact way
G H D F
E I
A B C
G H A B C D F E I
1 1 1 1 1 0 0 0 0
0 0 1 1 1 1 0 0 0
0 0 0 0 0 1 1 0 0
0 0 0 1 1 0 0 0 0
0 0 0 0 0 0 0 1 1
How to obtain ancestral segmentsM. Muffato and H. R. Crollius. BioEssays, 2008
How to obtain ancestral segments
computation of syntenies
M. Muffato and H. R. Crollius. BioEssays, 2008
How to obtain ancestral segments
computation of double syntenies
M. Muffato and H. R. Crollius. BioEssays, 2008
26 segments of the boreoeutherian ancestor
Muffato et al, Bioessays, 2008
Segments of the amniote ancestor
Segments of the amniote ancestor
Kohn et al, Trends in Genetics, 2006
Nakatani et al, Genome Research, 2007
present method
syntenic associations between chicken chromosome segments
Future works
✗ In case of absence of solution to the consecutive one's
(C1) problem, an optimisation phase is needed (we
discard a minimum number of putative ancestral
segments).
✗ A better understanding of the combinatorics of non C1
matrices would improve this framework.
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