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Insights into the structural evolution of amniote...
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Insights into the structural evolution of amniote genomes A. Ouangraoua 1,2 , A. McPherson 1 , C. Chauve 1 and E. Tannier 3 1 Simon Fraser University, Burnaby (BC), Canada [email protected], [email protected], [email protected] 2 Université du Québec à Montréal, Montréal (QC), Canada. 3 INRIA Rhône-Alpes, LBBE, University of Lyon, France I [email protected] Abstract We investigate the problem of inferring contiguous ancestral regions (CARs) of the genome of the last common ancestor of all extant amniotes. We use the complete genome sequences and assemblies of 14 vertebrate species: 11 amniote genomes as ingroups and 3 teleost fish genomes as outgroups. We infer large regions or syntenies of three ancestral genomes: the amniote, therian and boreoeutherian ones. We then infer patterns of genome structural evolution in amniotes: types of rearrangements, long and short branches of the underlying phylogenetic tree, convergent and divergent karyotypic evolution. We encounter and explore several methodological issues: the construction of good conserved orthology blocks among all amniotes; the detection of conserved synteny signals between amniotes and teleost fishes based on the principle of Doubly Conserved Syntenies (DCS) used in (Jaillon et al. 2004) and taking into account the whole genome duplication in the teleost lineage; the detection of conserved contiguity and synteny signals between amniotes and the construction of large Contiguous Ancestral Regions (CARs) of ancestral genomes (as in Chauve and Tannier, PLoS Comput Biol 2008) and the linkage of CARs according to the DCS signal; the detection of reliable ancestral genome rearrangements (as in Zaho and Bourque, Genome Res 2009). The ancestral boreoeutherian genome we infer is in almost complete agreement with previous cytogenetics and computational studies. Therian and amniote ancestral genomes still miss good references, as two previous studies (Nakatani et al. Genome Res 2007, Kohn et al. Trends in Genetics 2004) gave divergent results. Still the amniote ancestral genome is found relatively close to the chicken genome in all studies, including this one. We analyse every karyotypic change in the chicken and therian branches. Acknowledgement Eric Tannier is funded by the ANR (ANR-08-GENO-003-01 and NT05- 3 45205) and by the CNRS. Cedric Chauve is funded by NSERC and SFU. Aïda Ouangraoua is funded by SFU and UQAM. References 1. M. J. Benton and P. C. J. Donoghue. Paleontological Evidence to Date the Tree of Life. Molecular Biology and Evolution 24(1):26-53,2007. 2. C. Chauve and E. Tannier. A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genome. PLoS Comput. Biol. 4:e1000234, 2008. 3. M. Kohn etal. Reconstruction of a 450-my-old ancestral vertebrate protokaryotype. Trends Genet., 22:203–210, 2006. 4. J. Ma et al. D. Haussler, and W. Miller. Reconstructing contiguous regions of an ancestral genome. Genome Research, 16:1557–1565, 2006. 5. Y. Nakatani, H. Takeda, and S. Morishita. Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res., 17:1254–1265, 2007. 6. H. Zhao et G. Bourque. Recovering Genome Rearrangements in the Mammalian Phylogeny. Genome Research 19(5):934-42, 2009. Detecting signals of ancestral rearrangement events Detecting contiguity and synteny signals between amniotes ... a b c d e ... ... u v ... ... -v -u ... -Contiguity signals: conserved adjacencies between extant amniotes species. -Synteny signals: maximum common intervals between extant amniote species. -Recovering adjacencies and telomeres in two ancestral genomes. -Rearrangement signals: Double-Cut-and-Join operations that correspond to reversals, translocation, fusion, fission or transpositions. Input data (species tree and gene trees) -Pecan 12-amniotes-vertebrates multiple alignments from Ensembl-Compara 54, -Gene trees from Ensembl-Compara 54. Orthology blocks and orthologous genes ... x -y ... ... y -x ... ... -b a -e d c ... Computing Contiguous Ancestral Regions -Weighting adjacencies and ancestral syntenies according to their conservation in species. -Removing false positive contiguity and synteny signals and ordering orthology blocks. Chauve and Tannier, 2008. Zhao and Bourque, 2009. Linking CARs according to the DCS signal -Linking couples of orthology blocks that belong to two different CARs but to the same DCS. Detecting synteny signals (DCS) between amniotes and fishes -Double Conserved Syntenies (DCS): sets of orthology blocks contained in an amniote genome segments whose genes have orthologs in two segments of a fish genome. Orthology blocks on chicken genome: 48%. Orthology blocks on human genome: 43%. Orthologous genes on human genome Orthologous genes on chicken genome Contiguity signals of amniote ancestor on chicken genome Synteny signals of amniote ancestor on chicken genome Amniote ancestor - 159 CARs - 87 CARs containing more than 1 block. - 58% of colinearity with chicken genome - 59% of colinearity with human genome Chicken Human-Teleost DCS Medaka Stickleback Tetraodon Chicken Oppossum Cow Dog Horse Rat Mouse Macaca Orangutan Chimpanzee Human Amniote ancestor Therian ancestor Boreoeutherian ancestor 7.64 2.35 2.49 7.50 4.51 2.99 0.70 2.29 1.49 0.79 0.81 1.23 0.24 0.92 0.55 0.19 0.35 0.15 0.19 Benton and Donoghue, 2007. Therian ancestor - 61 CARs - 47 CARs containing more than 1 block. Boreoeutherian ancestor - 28 CARs - 27 CARs containing more than 1 block. Human A B C D A B C D A B C D A A B C D C - A - B D Therian CAR 5 Therian CAR 11 Boreo. CAR 7 Boreo. CAR 8 Boreo. CAR 26 Boreo. CAR 22 Boreo. CAR 2 Fission Translocation Fission Fission A B C D A - B - C D A - C - D B Reversal Fission Therian CAR 21 Boreo. CAR 12 Boreo. CAR 19 A B C D - D - A C B Therian CAR 23 Therian CAR 24 Boreo. CAR 14 Boreo. CAR 16 Translocation From therians ancestor to boreoeutherian ancestor B -690 non-overlapping orthology blocks on amniotes spanning 48% of human genome and 43% or chicken genome. - 572356 gene orthologies between amniotes and teleost fishes. Amniote CAR 70 Amniote CAR 71 DCS on human chromosome 5 Chicken Kohn et al [3] Nakatani et al. [5] Poster method 2-9-16, 1-24, 5-10, 17-Z 21-26-23-32, 3-14, 8-18 2-9, 13-17-Z 1-7, 1-14-18 3-7-22, 18-27 17-Z, 21-26 Syntenic associations between chicken chromosomes
Transcript of Insights into the structural evolution of amniote...
Insights into the structural evolution of amniote genomesA. Ouangraoua1,2, A. McPherson1, C. Chauve1 and E. Tannier3
1 Simon Fraser University, Burnaby (BC), [email protected], [email protected], [email protected]
2 Université du Québec à Montréal, Montréal (QC), Canada.3 INRIA Rhône-Alpes, LBBE, University of Lyon, France I
AbstractWe investigate the problem of inferring contiguous ancestral regions (CARs) of the genome of the last common ancestor of all extant amniotes. We use the complete genome sequences and assemblies of 14 vertebrate species: 11 amniote genomes as ingroups and 3 teleost fish genomes as outgroups. We infer large regions or syntenies of three ancestral genomes: the amniote, therian and boreoeutherian ones. We then infer patterns of genome structural evolution in amniotes: types of rearrangements, long and short branches of the underlying phylogenetic tree, convergent and divergent karyotypic evolution. We encounter and explore several methodological issues:
the construction of good conserved orthology blocks among all amniotes; the detection of conserved synteny signals between amniotes and teleost fishes based on the principle of Doubly Conserved Syntenies (DCS) used in (Jaillon et al. 2004) and taking into account the whole genome duplication in the teleost lineage; the detection of conserved contiguity and synteny signals between amniotes and the construction of large Contiguous Ancestral Regions (CARs) of ancestral genomes (as in Chauve and Tannier, PLoS Comput Biol 2008) and the linkage of CARs
according to the DCS signal; the detection of reliable ancestral genome rearrangements (as in Zaho and Bourque, Genome Res 2009).
The ancestral boreoeutherian genome we infer is in almost complete agreement with previous cytogenetics and computational studies. Therian and amniote ancestral genomes still miss good references, as two previous studies (Nakatani et al. Genome Res 2007, Kohn et al. Trends in Genetics 2004) gave divergent results. Still the amniote ancestral genome is found relatively close to the chicken genome in all studies, including this one. We analyse every karyotypic change in the chicken and therian branches.
AcknowledgementEric Tannier is funded by the ANR (ANR-08-GENO-003-01 and NT05- 3 45205) and by the CNRS. Cedric Chauve is funded by NSERC and SFU. Aïda Ouangraoua is funded by SFU and UQAM.
References1. M. J. Benton and P. C. J. Donoghue. Paleontological Evidence to Date the Tree of Life. Molecular Biology and Evolution 24(1):26-53,2007.2. C. Chauve and E. Tannier. A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genome. PLoS Comput. Biol. 4:e1000234, 2008.3. M. Kohn etal. Reconstruction of a 450-my-old ancestral vertebrate protokaryotype. Trends Genet., 22:203–210, 2006.4. J. Ma et al. D. Haussler, and W. Miller. Reconstructing contiguous regions of an ancestral genome. Genome Research, 16:1557–1565, 2006.5. Y. Nakatani, H. Takeda, and S. Morishita. Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res., 17:1254–1265, 2007.6. H. Zhao et G. Bourque. Recovering Genome Rearrangements in the Mammalian Phylogeny. Genome Research 19(5):934-42, 2009.
Detecting signals of ancestral rearrangement events
Detecting contiguity and synteny signals between amniotes
... a b c d e ...
... u v ...
... -v -u ...
-Contiguity signals: conserved adjacencies between extant amniotes species.
-Synteny signals: maximum common intervals between extant amniote species.
-Recovering adjacencies and telomeres in two ancestral genomes.
-Rearrangement signals: Double-Cut-and-Join operations that correspond to reversals, translocation, fusion, fission or transpositions.
Input data (species tree and gene trees)
-Pecan 12-amniotes-vertebrates multiple alignments from Ensembl-Compara 54,
-Gene trees from Ensembl-Compara 54.
Orthology blocks and orthologous genes
... x -y ...
... y -x ...
... -b a -e d c ...
Computing Contiguous Ancestral Regions
-Weighting adjacencies and ancestral syntenies according to their conservation in species.
-Removing false positive contiguity and synteny signals and ordering orthology blocks.
Chauve and Tannier, 2008.Zhao and Bourque, 2009.
Linking CARs according to the DCS signal
-Linking couples of orthology blocks that belong to two different CARs but to the same DCS.
Detecting synteny signals (DCS) between amniotes and fishes
-Double Conserved Syntenies (DCS): sets of orthology blocks contained in an amniote genome segments whose genes have orthologs in two segments of a fish genome.
Orthology blocks on chicken genome: 48%. Orthology blocks on
human genome: 43%.
Orthologous genes on human genome
Orthologous genes on chicken genome
Contiguity signals of amniote ancestor on chicken genome
Synteny signals of amniote ancestor on chicken genome
Amniote ancestor- 159 CARs- 87 CARs containing more than 1 block.- 58% of colinearity with chicken genome - 59% of colinearity with human genome
Chicken
Human-Teleost DCSMedaka
Stickleback
Tetraodon
Chicken
Oppossum
Cow
Dog
Horse
Rat
Mouse
Macaca
Orangutan
Chimpanzee
Human
Amniote ancestor Therian
ancestor
Boreoeutherian ancestor
7.642.35
2.49
7.50
4.51
2.99
0.70
2.29
1.490.79
0.81
1.230.24
0.92
0.55
0.19
0.35
0.150.19
Benton and Donoghue, 2007.
Therian ancestor- 61 CARs- 47 CARs containing more than 1 block.
Boreoeutherian ancestor- 28 CARs- 27 CARs containing more than 1 block.
Human
A B C D A B C D
A B C D
A
A B C D
C - A - B D
Therian CAR 5 Therian CAR 11
Boreo. CAR 7
Boreo. CAR 8Boreo. CAR 26Boreo. CAR 22 Boreo. CAR 2
Fission
Translocation
Fission
Fission
A B C D
A - B- C D
A - C - D B
Reversal
Fission
Therian CAR 21
Boreo. CAR 12 Boreo. CAR 19
A B C D
- D - A C B
Therian CAR 23 Therian CAR 24
Boreo. CAR 14 Boreo. CAR 16
Translocation
From therians ancestor to boreoeutherian ancestor
B
-690 non-overlapping orthology blocks on amniotes spanning 48% of human genome and 43% or chicken genome.
- 572356 gene orthologies between amniotes and teleost fishes.
Amniote CAR 70 Amniote CAR 71
DCS on human chromosome 5
Chicken
Kohn et al [3] Nakatani et al. [5] Poster method
2-9-16, 1-24, 5-10, 17-Z21-26-23-32, 3-14, 8-18
2-9, 13-17-Z1-7, 1-14-18
3-7-22, 18-2717-Z, 21-26
Syntenic associations between chicken chromosomes
