Quality and genome duplication .


51 views
Uploaded on:
Description
Quality a d genome duplication. Nadia El-Mabrouk Universit
Transcripts
Slide 1

Quality a d genome duplication Nadia El-Mabrouk Université de Montréal Canada

Slide 2

Plan Genome reworking and multigene families Genome Duplication of chromosomal sections Conclusion

Slide 3

Genome modification Chromosomes developed by inclusion, cancellation, development of qualities Genomic approach: Compare quality requests Hypothesis : Homologous qualities are known Chromosome grouping of marked qualities (or pieces) b - a d - e - c f

Slide 4

Multigene families In the human genome ~15% protein qualities copied ( Li, Wang, Nekrutenko, 2001 ) ~16% yeast, ~25% Arabidopsis ( Wolfe, 2001 ) Compare successions of marked qualities permitting many duplicates of every quality b –a d a –e –c e f d a

Slide 5

Multigene families because of: Single quality duplication ; Segment duplication : Tandem duplication or duplication transposition a b c d e f g a b c d e f b c d g Horizontal quality exchange ; all inclusive multiplying occasion

Slide 6

Algorithms and models Genome adjustment with multigene families Exemplar approach, Sankoff 1999 Insertion, erasure, quality duplication, Marron,Swensen, Moret 2003 Reconciliation investigation , anticipating quality tree on phylogenetic tree Hallett, Lagergren 2000, Page, Cotton 2000; Chen, Durand, Farach 2000, Sankoff, El-Mabrouk 2000 Probabilistic models for the era of multigene families

Slide 7

Find the progenitor of a genome with numerous quality duplicates Genome duplication N. El-Mabrouk and D. Sankoff, SIAM, J. Comp., 2003 Duplication of chromosomal sections N. El-Mabrouk, J. Comp. Sys. Sci., 2002 Genome duplication for unordered chromosomes N. El-Mabrouk and D. Sankoff 1998

Slide 8

Plan Genome reworking and multigene families Genome Duplication of chromosomal sections Conclusion

Slide 9

Genome multiplying Tetraploid = 4n chromosomes Evidence over the eukaryote range; Two duplications in early vertebrate development ( McLysaght et al. 2002) Particularly common in plants (rice, oats, corn, wheat, soybeans, Arabidopsis… )

Slide 10

Wolfe, Shields 1997 : Traces of duplication in Saccharomyces cerevisiae . 55 copied areas speaking to half of the genome From 8 to 16 chromosomes

Slide 11

Originally, copied genome = 2 indistinguishable duplicates of every chromosome After adjustments, copied portions scattered among the genome Present–day genome : Signed quality successions, 2 duplicates of every quality Reconstruct unique quality request at time of duplication Minimum number of inversion as well as translocation

Slide 12

Inversion

Slide 13

Translocation Reciprocal translocation: Fusion: Fission:

Slide 14

Problem: Rearranged copied genome G : 1: +a +b –c +b - d 3: - e +g - f - d 2: - c - a +f 4: +h +e - g +h Unknown copied genome H: 1: +a +b - d 3: +h +c +f - g +e 2: +a +b - d 4: +h +c +f - g +e Min. num. of reversal or potentially translocation trans-framing G into H Multi-chromosomal case : H has a significantly number of chromosomes. Not really the situation for G

Slide 15

The round case

Slide 16

Method Genome revision : Minimum number of adjustments to change one genome into another First polynomial calculation by Hannenhalli and Pevzner for Reversals just Translocations just Reversals and translocations Ancestral copied genome of G limiting the HP equation

Slide 17

The breakpoint chart G 1 = +1 +4 - 6 +9 - 7 +5 - 8 +10 +3 +2 +11 +12 G 2 = +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 t h t +a - a

Slide 18

Multichromosomal case G 1 : I : 1 3 9 II : 7 8 4 5 6 III : 10 2 11 12 13 G 2 : I : 1 2 3 4 5 6 II : 7 8 9 III : 10 11 12 13

Slide 19

When G 1 =G 2 , greatest number of cycles Perform inversions expanding nb of cycles Good segment : Can be unraveled by great inversions Bad segment : Requires terrible inversions HP: RD ( G 1 , G 2 ) = b – c + m + f b : red edges; c : cycles; m : awful segments; f : Correction of 0, 1 or 2

Slide 20

Genome splitting Partial diagram for G: Set of substantial dark edges speaking to a copied genome Find an arrangement of legitimate dark edges limiting HP

Slide 21

Decomposition into characteristic subgraphs Natural subgraphs of even size are completable Amalgamate common charts into completable powerful charts Example: Amalgamate S 2 and S 5 S 1 , S 25 , S 3 , S 4

Slide 22

Upper bound on the quantity of cycles S e an otherworldly diagram of n edges, S e ( G e ) a finished diagram with c e cycles If S e not amalgamated, c e ≤ n/2 +1 Otherwise, c e ≤ n/2

Slide 23

Maximizing cycles – Multichromosomal case Complete each subgraph independently Avoid to make roundabout sections Bad diagram: a 1 d 1 a 2 d 2 c 1 b 1 c 2 b 2

Slide 24

Maximizing cycles 2 Avoid dark edges making round pieces: A couple of edges that does not make a round piece nor an awful diagram is called conceivable

Slide 25

Algorithm dedouble 2-edges chart: n-edges chart:

Slide 26

Algorithm dedouble 2 Linear time calculation developing a maximal finished chart with c cycles: c = n/2 + g n : number of red edges g : number of normal charts (not amalgamated)

Slide 27

Bad segments Related to subpermutations or preserved interims minSP : SP not contained in any SP a - b c - d e - g h - f i Rearrangement by translocations : Bad segments = minSPs Rearrangement by invertions or potentially translocations : Bad segments subset of minSPs

Slide 28

Bad segments 2 Local SPs of G : Lemma : In a maximum finished chart, if there is minSP not a nearby SP , then remedy to wipe out the minSP Corollary : If G does not contain neighborhood SPs, then copied genome H created by the calculation is to such an extent that: RO(G,H) negligible

Slide 29

Bad segments 3 General case: RO(G) = n/2 – (G) + m(G) + f (G) n : nb of red edges; g ( G ) : nb of regular charts ; m (G) : nb of awful neighborhood SPs ; f ( G ) : rectification relying upon nearby SPs Multichromosomal case : Exact calculation Circular case : Uncertainty of up to 2 inversions

Slide 30

Application: Yeast genome Degenerate tetraploid, duplication 10 8 years back ( Wolfe and Shield, 1997 ). 55 copied districts Sorting by translocations : 45 translocations Sorting by reversals as well as translocations : No neighborhood SPs, subsequently no inversion. Still 45 translocations

Slide 31

A round genome Mitochondrial genome of Marchantia polymorpha : numerous qualities in 2 or 3 duplicates ( Oda et al. 1992 ) Unlikely to be a tetraploid A guide with 25 sets of qualities was separated from the Genbank section Sorting by inversions : least of 25 inversions Similar to an arbitrary dissemination No hint of duplication

Slide 32

Plan Genome revamp and multigene families Genome Duplication of chromosomal portions Conclusion

Slide 33

Duplication of chromosomal sections Duplication of whole locales starting with one area then onto the next in the genome a b c d e f g a b c d e f b c d g Very late portion duplication in the human genome ( Eichler et al., 1999 )

Slide 34

Data : A genome containing many duplicates of every quality Problem : A genealogical genome containing one duplicate of every quality, limiting inversions + fragment duplication D(G) : Number of rehashes of G +a - b +c +x +d - e +e - d +a - b +c +y

Slide 35

At most two duplicates of every quality An inversion can diminish by at most two number of rehashes of G Find I limiting RD(G,I) = D(I) + R(G,I) Ignoring awful segments limit D (G) = D(I) +n(G)- c(G,I)

Slide 36

Genome: a 1 b 1 x h 1 f 1 e 1 g 1 - c 1 - a 2 - b 2 - z d 2 e 2 - g 2 - c 2 –f 2 y Natural charts: E : Graphs of even size with just copied qualities D (G) ≥ D(G) - | E |

Slide 37

Algorithm For diagrams not in E , red edges = dark edges; For diagrams in E , like genome duplication BUT: Possibly more than one round part. A redress is required Approximation calculation with tight limits in O(| E | n )

Slide 38

1, 2, 3, 4, 5, 6, 7, 8 Paralog pairings 1, { 2, 3 } , 4, 5, 6, { 7, 8 } Remove one duplicate of each copy 1, 2, 4, 5, 6, 7 Paralog pairings { 1, 2 } , 4, 6, { 5, 7 } Remove one duplicate of each copy 1, 4, 6, 5 { 1, 4 } , { 6, 5 } 1, 6 1

Slide 40

Conclusion First bioinformatics devices to remake the transformative history of a solitary Genome duplication : A straight time correct calculation for inversions as well as translocations Segment duplication : A polynomial guess calculation with limits for inversions Extension : Consider the centromere . A few translocations not permitted

Recommended
View more...