Structural and Evolutionary Genomics NATURAL SELECTION IN GENOME EVOLUTION Giorgio Bernardi
Evolutionary Comparative Genomics: Understanding the Origins of Genome Architecture
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S Evolutionary Comparative Genomics: Understanding the origins of genome architecture Steve Moss Evolutionary Biology Group Department of Biological Sciences Dr Dave Lunt Dr Domino Joyce
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My presentation to the members of the biological sciences department at the post-graduate day in April 2011.
Transcript of Evolutionary Comparative Genomics: Understanding the Origins of Genome Architecture
S
Evolutionary Comparative Genomics: Understanding the origins of genome
architecture
Steve MossEvolutionary Biology Group
Department of Biological Sciences
Dr Dave LuntDr Domino Joyce
Comparative Genomics
Genome evolution
Fundamental questions
Comparative Genomics
Automated analysis
Pipeline development
Teleost fishDanio rerioGasterosteus aculeatusOryzias latipesTakifugu rubripesTetraodon nigroviridis
Summary
Reliable and robust pipeline
Study and compare whole genomes
Focus on particular features
Partition into areas of interest
Visualize and summarize the data
Key evolutionary questions
Intron test case has been very insightful
Future directions
Introns
Homology, Ontology, Synteny, Gene families
Evolutionary questions
Expansion of studies
52 genomes
Phylogenetic comparisons
Thank you!
Any questions?
Steve Moss
Email: [email protected]
Twitter: @gawbul
Web: http://stevemoss.ath.cx/
Intron Description
Danio rerioGasterosteus
aculeatusOryzias latipes
Takifugu rubripes
Tetraodon nigroviridis
U2 Type (Major) Number
207,336 170,137 156,282 161,778 155,012
U2 Type Percentage
93.57% 85.23% 84.25% 86.07% 82.51%
U12 Type (Minor) Number
184 139 161 105 103
U12 Type Percentage
0.08% 0.07% 0.09% 0.06% 0.05%
Other Number 14,069 29,348 29,051 26,079 32,760
Other Percentage
6.35% 14.70% 15.16% 13.87% 17.44%
Total Number 221,589 199,624 185,494 187,692 187,875
Intron Position Danio rerioGasterosteus
aculeatusOryzias latipes
Takifugu rubripes
Tetraodon nigroviridis
5’ UTR Number 4,611 3,572 2,830 831 1,000
5’ UTR Percentage
2.08% 1.79% 1.53% 0.44% 0.53%
3’ UTR Number 1,271 682 355 46 313
3’ UTR Percentage
0.57% 0.34% 0.19% 0.02% 0.17%
CDS Number 215,707 195,370 182,309 187,085 186,562
CDS Percentage
97.35% 97.87% 98.28% 99.54% 99.30%
Total Number 221,589 199,624 185,494 187,692 187,875
Repeat Description
Danio rerioGasterosteus
aculeatusOryzias latipes
Takifugu rubripes
Tetraodon nigroviridis
Repeat Number
2,927,753 622,107 446,619 297,226 268,530
Repeat Length 13,406,652 1,266,916 1,449,300 1,045,873 942,285
Low complexity
- 43,349 41,853 24,540 9,685
Simple repeat - 260,849 76,562 189,034 132,712
Dust 994,329 207,519 314,952 122,924 137,745
Trf 11,023,152 539,295 1,007,398 686,489 655,888
Other 1,389,171 215,904 8,535 22,886 6,255
