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Comparative genomics Joachim Bargsten February 2012

Comparative genomics Joachim Bargsten February 2012. Comparative genomics The study of the relationship of genome structure and function across different biological species or strains . Why should we do this? How are we going to do this?. Study evolution. Resolve Differences

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Comparative genomics Joachim Bargsten February 2012

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  1. Comparative genomics Joachim Bargsten February 2012

  2. Comparative genomics The study of the relationship of genome structure and function across different biological species or strains. • Why should we do this? • How are we going to do this?

  3. Study evolution • Resolve • Differences • Mechanism Tree of life http://www.tolweb.org/tree/

  4. Motivation • Transfer knowledge from and to simpler model organisms C. elegans Human

  5. Motivation

  6. Overview • Molecular phylogenetics • Multiple sequence alignment • Phylogenetic tree estimation • Ortholog prediction • Genome rearrangements • Large scale inversions, deletions and translocations • Synteny & Collinearity • Structural variations • Presented by Lin Ke

  7. Molecular phylogenetics • The use of molecular data to establish the relationship between species, organisms or gene families Homology sequences that share common ancestry. This is a all or nothing relation.Sequences are never “a bit” homologous. • Orthologs:homologs in different species derived by a speciation event • Paralogs: homologs in the same or different species derived by a duplication event

  8. Homology last common ancestor (co-)orthologs

  9. Homology last common ancestor inparalogs

  10. Homology last common ancestor outparalogs

  11. Phylogenetic tree estimation • How do we estimate a phylogenetic tree? • Identify evolutionary conserved region • Multiple sequence alignment • MAFFT • Estimate the phylogenetic tree • PhyML

  12. Phylogenetic tree estimation • Multiple sequence alignment

  13. Phylogenetic tree estimation

  14. Phylogenetic tree estimation • Infer evolutionary relationshipsbetween species and genes/proteins • Rooted tree • Order of evolutionaryevents • Unrooted tree • Evolutionary relationshipsbetween descendants

  15. Non-coding regions • Phylogenetic footprinting • Distantly related species • Phylogenetic shadowing • Closely related species • Use sequence comparison andmultiple alignment to find exonsand non-coding functional regions • E.g. Transcription factorbinding sites

  16. What can we do with it? • Gene annotation • Gene or protein function prediction • Identify non-coding elements in the genome • Species phylogeny • Genome evolution

  17. Genome alignment • Pairwise alignment • Match chromosome sequence from species A to species B

  18. Genome alignment – dot plot

  19. Dot-plot chromosome 2L tomato - potato

  20. Synteny & collinearity • Syntenygene loci are on the same chromosome • Conserved syntenygene loci are on the same chromosome in different species • CollinearityThe order of the gene loci is preserved across species

  21. inverted

  22. Resources • Comparative genomics plants • Plant Genome Duplication Database • http://chibba.agtec.uga.edu/duplication/ • Plaza • http://bioinformatics.psb.ugent.be/plaza/

  23. Exercise ssh–X USERNAME@137.224.100.212 cd /mnt/geninf15/work/bif_course_2012/comparative_genomics_jwb less assignment.txt kwriteassignment.txt

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