Comparative genomics Joachim Bargsten February 2012.
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Transcript of Comparative genomics Joachim Bargsten February 2012.
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Comparative genomicsJoachim Bargsten
February 2012
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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?
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Study evolution
• Resolve
• Differences
• Mechanism
Tree of lifehttp://www.tolweb.org/tree/
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Motivation
• Transfer knowledge from and to simpler model organisms
Human
C. elegans
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Motivation
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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
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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
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Homology
(co-)orthologs
lastcommonancestor
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Homology
inparalogs
lastcommonancestor
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Homology
outparalogs
lastcommonancestor
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Phylogenetic tree estimation
• How do we estimate a phylogenetic tree?
• Identify evolutionary conserved region
• Multiple sequence alignment• MAFFT
• Estimate the phylogenetic tree• PhyML
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Phylogenetic tree estimation
• Multiple sequence alignment
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Phylogenetic tree estimation
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Phylogenetic tree estimation
• Infer evolutionary relationshipsbetween species and genes/proteins
• Rooted tree• Order of evolutionary
events
• Unrooted tree• Evolutionary relationships
between descendants
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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
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What can we do with it?
• Gene annotation
• Gene or protein function prediction
• Identify non-coding elements in the genome
• Species phylogeny
• Genome evolution
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Genome alignment
• Pairwise alignment• Match chromosome sequence from species A to species B
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Genome alignment – dot plot
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Dot-plot chromosome 2L tomato - potato
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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
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inverted
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Resources
• Comparative genomics plants• Plant Genome Duplication Database
• http://chibba.agtec.uga.edu/duplication/
• Plaza• http://bioinformatics.psb.ugent.be/plaza/
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Exercise
ssh –X [email protected]
cd /mnt/geninf15/work/bif_course_2012/comparative_genomics_jwb
less assignment.txt
kwrite assignment.txt