Comparative Genomics

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Comparative Genomics
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Overview of the Talk

• Comparing Genomes
• Homologies Families
• Sequence Alignments

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Evolution at the DNA Level
Deletion
Mutation
ACTGACATGTACCA
Sequence edits
AC----CATGCACCA
Rearrangements
Inversion
Translocation
Duplication
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Why Compare Genomes?

• We can better understand evolution/ speciation
• We can find important, functional regions of the
  sequence (codons, promoters, regulatory regions)
• It can help us locate genes in other species that
  are missing or not well-defined (also through
  comparison and alignments).

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Comparing Genomes

• Mammals have roughly 3 billion base pairs in
  their genomes
• Over 98 human genes are shared with primates,
  wth more than 95-98 similarity between genes.
• Even the fruit fly shares 60 of its genes with
  humans! (March 2000)
• Differences gene structure, sequence
• Remember one nucleotide change can cause
  disease such as sickle cell anemia and cancer.

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How Does Ensembl Predict Homology?

• Uses all the species
• Uses a representative protein (the longest) for
  every gene
• Builds a gene tree
• EnsemblCompara GeneTrees Analysis of complete,
  duplication aware phylogenetic trees in
  vertebrates. Vilella AJ, Severin J, Ureta-Vidal
  A, Durbin R, Heng L, Birney E. Genome Res. 2008
  Nov 24.

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Steps in Homology Prediction
WU Blastp SmithWaterman longest translation of
every gene against every other (Blast
Reciprocal Hit/ Blast Score Ratio)
Load Genes and Longest Translation from all
species
Protein Clustering
For each cluster, build a multiple alignment
(MUSCLE) based on the protein sequences
From each alignment, build a gene tree
Reconcile each gene tree with the species tree to
call duplication event on internal nodes (njTree)
Inference of homologues
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Viewing Trees in Ensembl
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Types of Homologues

• Orthologues any gene pairwise relation where
  the ancestor node is a speciation event
• Paralogues any gene pairwise relation where the
  ancestor node is a duplication event

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The Gene Tree for INS (insulin precursor)
A blue square is a speciation event (Orthologues)
A red square is a duplication event (Paralogues)
Nodes (squares) are ancestors. INS (insulin
precursor) is compared across species.
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Reconciliation
M
R
H
species tree
M
H
R
unrooted gene tree
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Orthologue Types
What is 1 to 1?
What is 1 to many?
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• Find the cow MYL6 gene go to its gene summary.
• How many paralogues does it have? Find them in
  the gene tree.
• Is there an orthologue predicted for this gene in
  zebrafish? Jump to its gene summary.

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• From the fish page you are in, click on protein
  families at the left.
• How were these families determined? (Click the
  Help button).

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Protein Families

• How Cluster proteins for every isoform in every
  species UniProt proteins.
• BLASTP comparison of
• all Ensembl ENSP
• all metazoan (animal) proteins in UniProt

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Families
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Ensembl Proteins in the Family
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Overview of the Talk

• Comparing Genomes
• Homologies and Families
• Sequence Alignments

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Non-Coding Regions

• Large stretches of non-coding regions in
  vertebrates
• Regulatory regions of
• Developmental genes
• Transcription factors
• miRNA

Kikuta et. al, Genome Research, May 2007
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Comparative Genomics today
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Aligning Whole Genomes- Why?

• To identify homologous regions
• To spot trouble gene predictions
• Conserved regions could be functional
• To define syntenic regions (long regions of DNA
  sequences where order and orientation is highly
  conserved)

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Aligning large genomic sequences

• Difficulties
• Requires a significant computer resource
• Scalability, as more and more genomes are
• sequenced
• Time constraint
• As the true alignment is not known, then
  difficult to measure the alignment accuracy and
  apply the right method

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Methods of Alignment- Ensembl

• BLASTZ-net (comparison on nucleotide level) is
  used for species that are evolutionary close,
  e.g. human mouse
• Translated BLAT (comparison on amino acid level)
  is used for evolutionary more distant species,
  e.g. human zebrafish
• EPO/PECAN global alignment used for multispecies
  alignments

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Conserved Regions Exercise

• Find the Ensembl MYH2 gene for cow and go to
  Region in Detail.
• Turn on a pairwise alignment (H.sap-B.tau)
• Would you expect an orthologous gene in human?

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Conserved Regions Exercise

• Jump to the human region.
• What is the constrained elements track?

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Acknowledgements

• Javier Herrero
• Benoît Ballester
• Kathryn Beal
• Stephen Fitzgerald
• Albert Vilella
• Ensembl team