SLIDE 1
1 AGENDA 1. Summary 2. Genome comparison 3. Rearrangement - - PowerPoint PPT Presentation
1 AGENDA 1. Summary 2. Genome comparison 3. Rearrangement - - PowerPoint PPT Presentation
Genome Rearrangements Joao Meidanis Campinas, Brazil 2015 1 AGENDA 1. Summary 2. Genome comparison 3. Rearrangement events 4. Example: mouse vs. human (X-chromosome) 5. Rearrangement distance 6. Known results 7. Current research
SLIDE 2
SLIDE 3
3
- One of the big challenges of contemporary Biology is to measure evolution
- Besides point mutations, evolution is known to occur by means of movements
- f large chunks of DNA (genome rearrangements)
- The advent of entire genomes brings a whole new facet to this issue
- As a first estimate of the amount of evolution between two species, one can use
the formula number of events unit of time
- Our research focus on efficient ways of computing the number of
rearrangement events between two or more genomes
SUMMARY
SLIDE 4
4
AGENDA
1. Summary 2. Genome comparison 3. Rearrangement events 4. Example: mouse vs. human (X-chromosome) 5. Rearrangement distance 6. Known results 7. Current research lines
SLIDE 5
5
GENOME COMPARISON Point mutations
...TATCGATAGACCACTG... ...TATC--TAGACGACTA...
SLIDE 6
6
GENOME COMPARISON Genome rearragements
A B C D E F G H A B C D E F G H Movement of large segments within the genome. Above, segment E – F – G flips over
SLIDE 7
7
AGENDA
1. Summary 2. Genome comparison 3. Rearrangement events 4. Example: mouse vs. human (X-chromosome) 5. Rearrangement distance 6. Known results 7. Current research lines
SLIDE 8
8
REARRANGEMENT EVENTS
- Insertion / Deletion
- Reversal
- Transposition
- Fission / Fusion
- Block Interchange
- Others: duplication, genome doubling
SLIDE 9
9
INSERTION / DELETION Gene gain / loss between genomes
A B C D E F G H I J A B C D E G H I J
SLIDE 10
10
REVERSAL A segment is reversed between genomes
A B C D E F G H I J A B C D E F G H I J
SLIDE 11
11
TRANSPOSITION A segment moves to a new position (or: exchange of two adjacent segments)
A B C D E F G H I J A B E F G C D H I J
SLIDE 12
12
FISSION / FUSION Genome breaks in two / Two genomes join
A B C D E F G H I J A B C D E F G H I J
SLIDE 13
13
BLOCK INTERCHANGE Exchange of two nonadjacent segments
A B C D E F G H I J A B G H E F C D I J
SLIDE 14
14
AGENDA
1. Summary 2. Genome comparison 3. Rearrangement events 4. Example: mouse vs. human (X-chromosome) 5. Rearrangement distance 6. Known results 7. Current research lines
SLIDE 15
15
Figure 2. X-chromosome: from local similarities, to synteny blocks, to breakpoint graph, to rearrangement scenario EXAMPLE: HUMAN AND MOUSE X-CHROMOSOME Pavel Pevzner et al. Genome Res. 2003; 13: 37-45
Thanks to:
SLIDE 16
16
AGENDA
1. Summary 2. Genome comparison 3. Rearrangement events 4. Example: mouse vs. human (X-chromosome) 5. Rearrangement distance 6. Known results 7. Current research lines
SLIDE 17
17
REARRANGEMENT DISTANCE Maximum parsimony approach
Given two genomes, and a set of events, the rearrangement distance between the genomes is the length of the shortest series
- f events that transforms one genome into
the other. In the previous example: Genome 1: mouse X-chromosome Genome 2: human X-chromosome Set of events: reversals only Distance: 7 events
SLIDE 18
18
AGENDA
1. Summary 2. Genome comparison 3. Rearrangement events 4. Example: mouse vs. human (X-chromosome) 5. Rearrangement distance 6. Known results 7. Current research lines
SLIDE 19
19
KNOWN RESULTS
- Insertion / Deletion distance : efficient algorithm known
- Reversal distance : efficient algorithm known
- Transposition distance : NP-hard; approximative algorithms
- Fission / Fusion distance : efficient algorithm known
- Block Interchange distance : efficient algorithm known
SLIDE 20
20
AGENDA
1. Summary 2. Genome comparison 3. Rearrangement events 4. Example: mouse vs. human (X-chromosome) 5. Rearrangement distance 6. Known results 7. Current research lines
SLIDE 21
21
CURRENT RESEARCH LINES
- Comparions of three or more genomes
- More realistic models with several operations, or basic operations that can