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 lines 2
SUMMARY • One of the big challenges of contemporary Biology is to measure evolution • Besides point mutations, evolution is known to occur by means of movements of 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 3
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 4
GENOME COMPARISON Point mutations ...TATCGATAGACCACTG... ...TATC--TAGACGACTA... 5
GENOME COMPARISON Genome rearragements D D E C C G F B B F G A H A H E Movement of large segments within the genome. Above, segment E – F – G flips over 6
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 7
REARRANGEMENT EVENTS • Insertion / Deletion • Reversal • Transposition • Fission / Fusion • Block Interchange • Others: duplication, genome doubling 8
INSERTION / DELETION Gene gain / loss between genomes A B A B C C J J D I I D H E H E G G F 9
REVERSAL A segment is reversed between genomes A B A B C C J J D F I I E H E H D G F G 10
TRANSPOSITION A segment moves to a new position (or: exchange of two adjacent segments) A B A B C E J J D F I I H E H G G F D C 11
FISSION / FUSION Genome breaks in two / Two genomes join A A B B C E J C D D I F H E G J G F I H 12
BLOCK INTERCHANGE Exchange of two nonadjacent segments A B A B C G J J D H I I H E D E G F C F 13
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 14
EXAMPLE: HUMAN AND MOUSE X-CHROMOSOME Pavel Pevzner et al. Genome Res. 2003; 13: 37-45 Figure 2. X-chromosome: from local similarities, to synteny blocks, to breakpoint graph, to rearrangement scenario Thanks to: 15
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 16
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 of 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 17
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 18
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 19
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 20
CURRENT RESEARCH LINES • Comparions of three or more genomes • More realistic models with several operations, or basic operations that can form several others, e.g., DCJ or SCJ 21
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